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Acta Crystallographica Section E: Crystallographic Communications logoLink to Acta Crystallographica Section E: Crystallographic Communications
. 2019 Apr 2;75(Pt 5):537–539. doi: 10.1107/S2056989019004079

Crystal structure of 4-[(1R,2S,5R)-2-isopropyl-5-methyl­cyclo­hex­yl] 2-methyl (2S,4S,5R)-1-[(2S,3R,5R)-5-meth­oxy­carbonyl-2-(2-methyl­phen­yl)pyrrolidine-3-carbon­yl]-5-(2-methyl­phen­yl)pyrrolidine-2,4-di­carboxyl­ate

Polina M Ivantcova a, Mikhail N Sokolov a, Konstantin V Kudryavtsev a,*, Andrei V Churakov b
PMCID: PMC6505609  PMID: 31110780

The title compound represents a chiral β-proline dipeptide. Corresponding stereogenic centres of constituting pyrrolidine units have opposite absolute configurations. The central amide fragment is planar within 0.1 Å and adopts a Z configuration along the N—CO bond.

Keywords: β-proline oligomers, β-peptides, peptide bond configuration, crystal structure

Abstract

The title compound, C38H50N2O7, represents a chiral β-proline dipeptide. Corresponding stereogenic centres of constituting pyrrolidine units have opposite absolute configurations. The central amide fragment is planar within 0.1 Å and adopts a Z configuration along the N—CO bond. In the crystal, the hydrogen atoms of the methyl­ene groups form several short inter­molecular C—H⋯O contacts with the carbonyl oxygen atoms of an adjacent mol­ecule. The only active amino hydrogen atom is not involved in hydrogen bonding.

Chemical context  

We have developed an asymmetric protecting-group-free method for the efficient synthesis of alternating β-proline oligopeptides utilizing the stereospecific cyclo­addition of non-racemic homochiral acryl­amides to azomethine ylides (Kudryavtsev et al., 2013, 2015b ). Several members of this novel β-peptide class display cell-cycle-directed anti­proliferative activity in hormone-refractory prostate cancer cells (Kudryavtsev et al., 2015a ,b ; 2016). The preference for the Z configuration of β-amide bonds in alternating β-proline oligopeptides was explained by inter­action between a lone pair of the carbonyl oxygen atom of the β-amide group and a vacant π* orbital of C of the meth­oxy­carbonyl groups (Kudryavtsev et al., 2015b ).graphic file with name e-75-00537-scheme1.jpg

Structural commentary  

The title compound (Fig. 1) is a chiral dimeric β-proline derivative. The central amide fragment C4,C1,N1,C18,O5,C20 is planar within 0.1 Å and adopts a Z configuration along the N—CO bond. The Z/E or trans/cis configuration of a peptide bond is assigned by IUPAC rules due to its partial double-bond character (IUPAC–IUB, 1970). The amino N2 atom is clearly trigonal–pyramidal with C—N—C and C—N—H bond angles varying from 104.4 (4) to 112 (4)°. Both pyrrolidine rings possess envelope conformations with flap atoms C3 and C19. These atoms deviate from the basal planes of the envelopes by 0.582 (7) and 0.524 Å, respectively. In contrast to the previously reported structures of β-proline oligomers, the flap atoms C3 and C19 are not connected to the amide or carboxyl­ate substituents (see below). Both tolyl groups are almost perpendicular to the pyrrolidine fragments, subtending dihedral angles equal to 84.0 (1) and 75.8 (2)°.

Figure 1.

Figure 1

Labelling scheme for the title compound. Displacement ellipsoids are shown at 50% probability level. Hydrogen atoms (except amino H11) were omitted for clarity.

Supra­molecular features  

The title mol­ecule contains seven oxygen atoms suitable for hydrogen bonding. Surprisingly, the only active amino hydrogen atom H11 is not involved in hydrogen bonding. This is the result of steric hindrance by the two bulky β-substituents on pyrrolidine ring atom N1. In the crystal, the hydrogen atoms of the methyl­ene groups C3 and C49 form several short inter­molecular C—H⋯O contacts (Table 1, Fig. 2) with the carbonyl oxygen atoms O4, O5 and O7 of an adjacent mol­ecule (Inline graphic + x, Inline graphic − y, 1 − z) with H⋯O separations of 2.52, 2.58 and 2.63 Å, respectively. A similar absence of hydrogen bonding has been observed in the structures of closely related β-proline trimers and tetra­mers (Kudryavtsev et al., 2013, 2015a ).

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A D—H H⋯A DA D—H⋯A
C3—H3B⋯O4i 0.99 2.52 3.254 (6) 131
C3—H3B⋯O5i 0.99 2.58 3.462 (6) 149
C49—H49A⋯O7i 0.99 2.63 3.511 (7) 149

Symmetry code: (i) Inline graphic.

Figure 2.

Figure 2

Fragment of the crystal packing showing the shortest inter­molecular C—H⋯O contacts (Table 1) as dashed lines.

Database survey  

The Cambridge database (version 5.39, Aug 2018; Groom et al., 2016) contains 11 structures of β-proline oligomers. Among these, three are dimeric (CIKHOV, ILOZOY, and ZUYBUS), three are trimeric [CIKHEL and CIKHIP (Kudryavtsev et al., 2013) and OWALEF (Kudryavtsev et al., 2016)] and five are tetra­meric (XOQDOY and XOQDUE (Kudryavtsev et al., 2015a ), ZUYGUX, ZUYHAE, and ZUYHEI (Kudryavtsev et al., 2015b )]. In total, these structures comprises 25 pyrrolidine fragments. Inter­estingly, all 25 pyrrolidine rings adopt envelope conformations with the flap carbon atom bearing linking amide –C(=O)N=or terminal –CO2 R groups. Endocyclic carbon atoms with aryl substituents and nitro­gen atoms always lie in the basal planes of the proline moieties.

Synthesis and crystallization  

The synthesis and spectroscopic data for the title compound have been reported by Kudryavtsev et al. (2016). The crystal studied was grown by slow evaporation of a methanol solution of the title compound.

Refinement  

Crystal data, data collection and structure refinement details are summarized in Table 2. Aromatic H atoms were placed in calculated positions with C—H = 0.95 Å and refined as riding atoms with U iso(H) = 1.2U eq(C). Methyl H atoms were also placed in calculated positions with C—H = 0.98 Å and refined as riding atoms with U iso(H) = 1.5U eq(C) and free rotation about the C—Me bonds. The amino H atom was found from the difference-Fourier synthesis and refined with both positional and thermal parameters. As the oxygen atoms are the heaviest in the structure, the absolute configuration could not be determined reliably from the diffraction data. The absolute configuration of the pyrrolidine stereogenic centres was assigned on the base of known chirality of the l-menthol precursor (Kudryavtsev et al., 2016).

Table 2. Experimental details.

Crystal data
Chemical formula C38H50N2O7
M r 646.80
Crystal system, space group Orthorhombic, P212121
Temperature (K) 150
a, b, c (Å) 10.993 (8), 13.198 (10), 23.799 (19)
V3) 3453 (5)
Z 4
Radiation type Mo Kα
μ (mm−1) 0.09
Crystal size (mm) 0.50 × 0.10 × 0.04
 
Data collection
Diffractometer Bruker SMART APEXII
Absorption correction Multi-scan (SADABS; Bruker, 2008)
T min, T max 0.959, 0.997
No. of measured, independent and observed [I > 2σ(I)] reflections 19713, 3438, 1990
R int 0.169
(sin θ/λ)max−1) 0.596
 
Refinement
R[F 2 > 2σ(F 2)], wR(F 2), S 0.060, 0.113, 1.03
No. of reflections 3438
No. of parameters 436
H-atom treatment H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.19, −0.21

Computer programs: APEX2 and SAINT (Bruker, 2008) and SHELXTL (Sheldrick, 2008).

Supplementary Material

Crystal structure: contains datablock(s) I. DOI: 10.1107/S2056989019004079/eb2015sup1.cif

e-75-00537-sup1.cif (42.6KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989019004079/eb2015Isup2.hkl

e-75-00537-Isup2.hkl (168.6KB, hkl)

Supporting information file. DOI: 10.1107/S2056989019004079/eb2015Isup3.cml

CCDC reference: 1905705

Additional supporting information: crystallographic information; 3D view; checkCIF report

supplementary crystallographic information

Crystal data

C38H50N2O7 F(000) = 1392
Mr = 646.80 Dx = 1.244 Mg m3
Orthorhombic, P212121 Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab Cell parameters from 2257 reflections
a = 10.993 (8) Å θ = 2.4–20.4°
b = 13.198 (10) Å µ = 0.09 mm1
c = 23.799 (19) Å T = 150 K
V = 3453 (5) Å3 Needle, colourless
Z = 4 0.50 × 0.10 × 0.04 mm

Data collection

Bruker SMART APEXII diffractometer 3438 independent reflections
Radiation source: fine-focus sealed tube 1990 reflections with I > 2σ(I)
Graphite monochromator Rint = 0.169
ω scans θmax = 25.1°, θmin = 2.3°
Absorption correction: multi-scan (SADABS; Bruker, 2008) h = −13→13
Tmin = 0.959, Tmax = 0.997 k = −15→15
19713 measured reflections l = −27→28

Refinement

Refinement on F2 Secondary atom site location: difference Fourier map
Least-squares matrix: full Hydrogen site location: mixed
R[F2 > 2σ(F2)] = 0.060 H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.113 w = 1/[σ2(Fo2) + (0.0294P)2] where P = (Fo2 + 2Fc2)/3
S = 1.03 (Δ/σ)max < 0.001
3438 reflections Δρmax = 0.19 e Å3
436 parameters Δρmin = −0.21 e Å3
0 restraints Extinction correction: SHELXTL (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methods Extinction coefficient: 0.0035 (7)

Special details

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.
Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > 2sigma(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

x y z Uiso*/Ueq
N1 0.3110 (4) 0.8167 (3) 0.43708 (16) 0.0312 (10)
N2 0.4319 (4) 1.1224 (3) 0.4206 (2) 0.0436 (12)
H11 0.407 (6) 1.116 (5) 0.457 (3) 0.10 (3)*
O1 0.1121 (3) 0.5592 (3) 0.37321 (14) 0.0422 (9)
O2 0.0621 (4) 0.6760 (3) 0.30922 (16) 0.0501 (11)
O3 0.2308 (3) 0.7761 (3) 0.58012 (14) 0.0464 (10)
O4 0.3899 (3) 0.7031 (3) 0.53704 (15) 0.0442 (9)
O5 0.4036 (3) 0.9273 (2) 0.49501 (14) 0.0403 (9)
O6 0.7399 (3) 1.1224 (3) 0.47147 (16) 0.0510 (10)
O7 0.5675 (3) 1.1762 (3) 0.51165 (17) 0.0573 (12)
C1 0.2786 (4) 0.7736 (4) 0.3819 (2) 0.0334 (12)
H1 0.2707 0.8293 0.3537 0.040*
C2 0.1512 (4) 0.7294 (4) 0.3953 (2) 0.0349 (13)
H2 0.0931 0.7877 0.3943 0.042*
C3 0.1600 (4) 0.6968 (4) 0.4560 (2) 0.0358 (13)
H3A 0.2042 0.6318 0.4596 0.043*
H3B 0.0784 0.6897 0.4731 0.043*
C4 0.2309 (4) 0.7833 (4) 0.48281 (19) 0.0341 (13)
H4 0.1733 0.8393 0.4923 0.041*
C5 0.3734 (4) 0.6966 (4) 0.3617 (2) 0.0325 (12)
C6 0.3970 (5) 0.6843 (4) 0.3047 (2) 0.0378 (13)
C7 0.4838 (5) 0.6134 (4) 0.2886 (2) 0.0454 (15)
H7 0.5010 0.6046 0.2498 0.054*
C8 0.5454 (5) 0.5555 (5) 0.3274 (2) 0.0482 (15)
H8 0.6047 0.5078 0.3154 0.058*
C9 0.5203 (5) 0.5676 (4) 0.3839 (2) 0.0469 (15)
H9 0.5608 0.5272 0.4111 0.056*
C10 0.4355 (4) 0.6392 (4) 0.4004 (2) 0.0393 (13)
H10 0.4199 0.6488 0.4393 0.047*
C11 0.1050 (5) 0.6535 (4) 0.3537 (2) 0.0347 (13)
C12 0.2549 (5) 0.4131 (4) 0.3088 (2) 0.0519 (16)
H12 0.2946 0.4681 0.3312 0.062*
C13 0.3418 (6) 0.3231 (5) 0.3088 (3) 0.074 (2)
H13A 0.3423 0.2917 0.3461 0.111*
H13B 0.4240 0.3464 0.2995 0.111*
H13C 0.3150 0.2734 0.2809 0.111*
C14 0.2384 (6) 0.4538 (5) 0.2488 (2) 0.0645 (18)
H14A 0.3182 0.4697 0.2327 0.097*
H14B 0.1886 0.5154 0.2498 0.097*
H14C 0.1981 0.4024 0.2257 0.097*
C15 −0.2423 (5) 0.3419 (4) 0.3906 (3) 0.0611 (18)
H15A −0.2895 0.2858 0.3748 0.092*
H15B −0.2943 0.4019 0.3940 0.092*
H15C −0.2118 0.3227 0.4278 0.092*
C16 0.2962 (5) 0.7515 (4) 0.5349 (2) 0.0357 (13)
C17 0.2759 (5) 0.7423 (5) 0.6340 (2) 0.0579 (17)
H17A 0.2106 0.7463 0.6619 0.087*
H17B 0.3437 0.7857 0.6457 0.087*
H17C 0.3041 0.6721 0.6310 0.087*
C18 0.3889 (5) 0.8945 (4) 0.4471 (2) 0.0334 (12)
C19 0.3782 (4) 1.0456 (4) 0.3845 (2) 0.0376 (13)
H19 0.3982 1.0647 0.3449 0.045*
C20 0.4485 (4) 0.9445 (4) 0.3976 (2) 0.0378 (13)
H20 0.4506 0.8986 0.3642 0.045*
C21 0.5763 (4) 0.9835 (4) 0.4127 (2) 0.0437 (15)
H21A 0.6346 0.9690 0.3820 0.052*
H21B 0.6060 0.9513 0.4476 0.052*
C22 0.5611 (5) 1.0986 (4) 0.4208 (2) 0.0412 (14)
H22 0.5995 1.1335 0.3880 0.049*
C23 0.6197 (5) 1.1381 (4) 0.4736 (3) 0.0430 (14)
C24 0.8099 (5) 1.1593 (5) 0.5196 (3) 0.0618 (18)
H24A 0.8920 1.1779 0.5073 0.093*
H24B 0.8152 1.1059 0.5481 0.093*
H24C 0.7695 1.2188 0.5356 0.093*
C25 0.2412 (4) 1.0401 (3) 0.3886 (2) 0.0349 (13)
C26 0.1694 (5) 1.0283 (4) 0.3403 (2) 0.0381 (13)
C27 0.0444 (5) 1.0164 (4) 0.3473 (3) 0.0551 (17)
H27 −0.0051 1.0071 0.3150 0.066*
C28 −0.0096 (6) 1.0178 (4) 0.3992 (4) 0.066 (2)
H28 −0.0951 1.0091 0.4025 0.080*
C29 0.0595 (6) 1.0314 (5) 0.4460 (3) 0.0619 (19)
H29 0.0223 1.0322 0.4821 0.074*
C30 0.1839 (5) 1.0443 (4) 0.4410 (2) 0.0478 (15)
H30 0.2313 1.0562 0.4738 0.057*
C31 0.2218 (5) 1.0293 (4) 0.2826 (2) 0.0540 (17)
H31A 0.1569 1.0182 0.2551 0.081*
H31B 0.2827 0.9754 0.2792 0.081*
H31C 0.2604 1.0951 0.2755 0.081*
C32 0.3347 (5) 0.7466 (4) 0.2601 (2) 0.0518 (16)
H32A 0.2468 0.7472 0.2671 0.078*
H32B 0.3509 0.7170 0.2231 0.078*
H32C 0.3659 0.8161 0.2612 0.078*
C44 0.0484 (5) 0.4778 (4) 0.3427 (2) 0.0407 (14)
H44A 0.0258 0.5020 0.3043 0.049*
C45 0.1339 (5) 0.3885 (4) 0.3380 (2) 0.0451 (14)
H45 0.1538 0.3664 0.3771 0.054*
C46 0.0616 (5) 0.3019 (4) 0.3104 (2) 0.0557 (17)
H46A 0.0371 0.3220 0.2720 0.067*
H46B 0.1137 0.2409 0.3075 0.067*
C47 −0.0515 (5) 0.2770 (4) 0.3450 (3) 0.0550 (16)
H47A −0.0964 0.2213 0.3264 0.066*
H47B −0.0260 0.2528 0.3825 0.066*
C48 −0.1351 (5) 0.3657 (4) 0.3520 (2) 0.0468 (15)
H48 −0.1676 0.3849 0.3142 0.056*
C49 −0.0645 (5) 0.4561 (4) 0.3758 (2) 0.0426 (14)
H49C −0.1175 0.5168 0.3755 0.051*
H49A −0.0421 0.4418 0.4153 0.051*

Atomic displacement parameters (Å2)

U11 U22 U33 U12 U13 U23
N1 0.032 (2) 0.026 (3) 0.035 (2) −0.003 (2) 0.002 (2) 0.0005 (19)
N2 0.036 (3) 0.038 (3) 0.056 (3) −0.003 (2) −0.008 (3) −0.002 (3)
O1 0.050 (2) 0.028 (2) 0.048 (2) −0.0019 (18) −0.012 (2) −0.0016 (17)
O2 0.064 (3) 0.035 (2) 0.051 (2) −0.006 (2) −0.018 (2) 0.0069 (19)
O3 0.044 (2) 0.060 (3) 0.036 (2) 0.0077 (19) 0.006 (2) 0.0026 (18)
O4 0.042 (2) 0.040 (2) 0.050 (2) 0.0087 (19) −0.005 (2) 0.0033 (17)
O5 0.047 (2) 0.033 (2) 0.041 (2) −0.0036 (17) 0.002 (2) −0.0061 (17)
O6 0.044 (2) 0.051 (3) 0.058 (3) −0.0057 (19) −0.005 (2) −0.011 (2)
O7 0.045 (3) 0.068 (3) 0.059 (3) −0.001 (2) 0.002 (2) −0.018 (2)
C1 0.032 (3) 0.033 (3) 0.036 (3) −0.006 (2) 0.001 (3) −0.002 (2)
C2 0.031 (3) 0.035 (3) 0.039 (3) 0.004 (2) −0.001 (3) 0.000 (3)
C3 0.029 (3) 0.036 (3) 0.043 (3) −0.005 (2) 0.002 (3) 0.001 (3)
C4 0.026 (3) 0.036 (3) 0.040 (3) 0.002 (2) 0.001 (3) −0.002 (2)
C5 0.031 (3) 0.030 (3) 0.036 (3) −0.005 (2) 0.001 (3) 0.000 (2)
C6 0.034 (3) 0.041 (4) 0.039 (3) −0.007 (3) 0.000 (3) 0.001 (3)
C7 0.040 (3) 0.054 (4) 0.042 (3) 0.004 (3) 0.009 (3) −0.004 (3)
C8 0.037 (3) 0.053 (4) 0.055 (4) 0.009 (3) 0.001 (3) −0.010 (3)
C9 0.039 (3) 0.047 (4) 0.055 (4) 0.007 (3) −0.003 (3) −0.001 (3)
C10 0.028 (3) 0.044 (4) 0.045 (3) 0.002 (3) −0.004 (3) −0.006 (3)
C11 0.024 (3) 0.031 (4) 0.049 (3) 0.003 (2) 0.003 (3) 0.006 (3)
C12 0.055 (4) 0.049 (4) 0.052 (4) 0.004 (3) 0.005 (3) −0.014 (3)
C13 0.069 (5) 0.056 (5) 0.097 (5) 0.013 (4) 0.018 (4) −0.013 (4)
C14 0.063 (4) 0.079 (5) 0.052 (4) −0.006 (4) 0.009 (4) −0.013 (3)
C15 0.062 (4) 0.045 (4) 0.076 (4) −0.012 (3) −0.008 (4) 0.008 (3)
C16 0.033 (3) 0.034 (3) 0.041 (3) −0.004 (3) 0.003 (3) 0.006 (3)
C17 0.061 (4) 0.079 (5) 0.034 (3) 0.007 (3) 0.000 (3) 0.005 (3)
C18 0.031 (3) 0.029 (3) 0.040 (3) 0.004 (3) 0.001 (3) −0.001 (3)
C19 0.038 (3) 0.036 (4) 0.039 (3) 0.001 (3) −0.001 (3) 0.002 (3)
C20 0.034 (3) 0.033 (3) 0.047 (3) −0.002 (2) 0.009 (3) −0.010 (3)
C21 0.035 (3) 0.040 (4) 0.056 (4) −0.010 (2) 0.006 (3) −0.008 (3)
C22 0.045 (3) 0.031 (4) 0.047 (3) −0.014 (3) 0.001 (3) 0.001 (3)
C23 0.036 (3) 0.036 (4) 0.057 (4) −0.004 (3) 0.002 (3) −0.002 (3)
C24 0.043 (4) 0.076 (5) 0.066 (4) 0.000 (3) −0.007 (4) −0.019 (3)
C25 0.035 (3) 0.022 (3) 0.048 (3) 0.002 (2) 0.004 (3) 0.003 (2)
C26 0.031 (3) 0.028 (3) 0.055 (4) −0.001 (2) −0.001 (3) 0.001 (3)
C27 0.040 (4) 0.042 (4) 0.084 (5) 0.001 (3) −0.002 (4) −0.002 (3)
C28 0.033 (4) 0.042 (4) 0.124 (7) 0.007 (3) 0.015 (5) 0.019 (4)
C29 0.048 (4) 0.055 (5) 0.083 (5) 0.021 (3) 0.018 (4) 0.019 (4)
C30 0.047 (4) 0.040 (4) 0.056 (4) 0.012 (3) 0.007 (3) 0.010 (3)
C31 0.050 (4) 0.052 (4) 0.060 (4) 0.005 (3) −0.011 (3) −0.016 (3)
C32 0.054 (4) 0.053 (4) 0.048 (3) 0.009 (3) 0.009 (3) 0.002 (3)
C44 0.049 (4) 0.028 (3) 0.044 (3) −0.004 (3) −0.011 (3) −0.005 (3)
C45 0.044 (3) 0.040 (4) 0.051 (3) 0.003 (3) −0.004 (3) −0.007 (3)
C46 0.063 (4) 0.038 (4) 0.066 (4) −0.002 (3) 0.000 (4) −0.013 (3)
C47 0.066 (4) 0.034 (4) 0.065 (4) −0.011 (3) −0.015 (4) −0.004 (3)
C48 0.044 (4) 0.038 (4) 0.058 (4) −0.003 (3) −0.010 (3) 0.010 (3)
C49 0.048 (3) 0.030 (3) 0.050 (3) 0.002 (3) −0.006 (3) 0.005 (3)

Geometric parameters (Å, º)

N1—C18 1.357 (6) C15—H15C 0.9800
N1—C4 1.468 (6) C17—H17A 0.9800
N1—C1 1.475 (6) C17—H17B 0.9800
N2—C19 1.453 (6) C17—H17C 0.9800
N2—C22 1.455 (7) C18—C20 1.501 (7)
N2—H11 0.91 (6) C19—C25 1.511 (7)
O1—C11 1.331 (6) C19—C20 1.573 (7)
O1—C44 1.473 (6) C19—H19 1.0000
O2—C11 1.196 (6) C20—C21 1.538 (7)
O3—C16 1.333 (6) C20—H20 1.0000
O3—C17 1.446 (6) C21—C22 1.540 (7)
O4—C16 1.213 (6) C21—H21A 0.9900
O5—C18 1.231 (5) C21—H21B 0.9900
O6—C23 1.339 (6) C22—C23 1.505 (7)
O6—C24 1.464 (6) C22—H22 1.0000
O7—C23 1.185 (6) C24—H24A 0.9800
C1—C5 1.533 (7) C24—H24B 0.9800
C1—C2 1.550 (6) C24—H24C 0.9800
C1—H1 1.0000 C25—C30 1.399 (7)
C2—C11 1.497 (7) C25—C26 1.403 (7)
C2—C3 1.511 (7) C26—C27 1.393 (7)
C2—H2 1.0000 C26—C31 1.489 (8)
C3—C4 1.523 (7) C27—C28 1.370 (9)
C3—H3A 0.9900 C27—H27 0.9500
C3—H3B 0.9900 C28—C29 1.360 (9)
C4—C16 1.493 (7) C28—H28 0.9500
C4—H4 1.0000 C29—C30 1.384 (8)
C5—C10 1.376 (7) C29—H29 0.9500
C5—C6 1.389 (6) C30—H30 0.9500
C6—C7 1.391 (7) C31—H31A 0.9800
C6—C32 1.507 (7) C31—H31B 0.9800
C7—C8 1.376 (7) C31—H31C 0.9800
C7—H7 0.9500 C32—H32A 0.9800
C8—C9 1.382 (7) C32—H32B 0.9800
C8—H8 0.9500 C32—H32C 0.9800
C9—C10 1.384 (7) C44—C49 1.498 (7)
C9—H9 0.9500 C44—C45 1.512 (7)
C10—H10 0.9500 C44—H44A 1.0000
C12—C13 1.524 (8) C45—C46 1.539 (7)
C12—C45 1.536 (7) C45—H45 1.0000
C12—C14 1.537 (7) C46—C47 1.525 (7)
C12—H12 1.0000 C46—H46A 0.9900
C13—H13A 0.9800 C46—H46B 0.9900
C13—H13B 0.9800 C47—C48 1.498 (8)
C13—H13C 0.9800 C47—H47A 0.9900
C14—H14A 0.9800 C47—H47B 0.9900
C14—H14B 0.9800 C48—C49 1.532 (7)
C14—H14C 0.9800 C48—H48 1.0000
C15—C48 1.527 (7) C49—H49C 0.9900
C15—H15A 0.9800 C49—H49A 0.9900
C15—H15B 0.9800
C18—N1—C4 118.4 (4) C20—C19—H19 107.0
C18—N1—C1 126.9 (4) C18—C20—C21 111.3 (5)
C4—N1—C1 113.5 (4) C18—C20—C19 108.3 (4)
C19—N2—C22 104.4 (4) C21—C20—C19 102.2 (4)
C19—N2—H11 112 (4) C18—C20—H20 111.6
C22—N2—H11 106 (4) C21—C20—H20 111.6
C11—O1—C44 118.8 (4) C19—C20—H20 111.6
C16—O3—C17 117.1 (4) C20—C21—C22 105.1 (4)
C23—O6—C24 116.0 (5) C20—C21—H21A 110.7
N1—C1—C5 111.8 (4) C22—C21—H21A 110.7
N1—C1—C2 100.4 (4) C20—C21—H21B 110.7
C5—C1—C2 115.4 (4) C22—C21—H21B 110.7
N1—C1—H1 109.6 H21A—C21—H21B 108.8
C5—C1—H1 109.6 N2—C22—C23 110.2 (5)
C2—C1—H1 109.6 N2—C22—C21 108.5 (4)
C11—C2—C3 117.6 (4) C23—C22—C21 113.6 (5)
C11—C2—C1 115.0 (4) N2—C22—H22 108.1
C3—C2—C1 104.2 (4) C23—C22—H22 108.1
C11—C2—H2 106.4 C21—C22—H22 108.1
C3—C2—H2 106.4 O7—C23—O6 124.9 (5)
C1—C2—H2 106.4 O7—C23—C22 125.3 (5)
C2—C3—C4 102.7 (4) O6—C23—C22 109.7 (5)
C2—C3—H3A 111.2 O6—C24—H24A 109.5
C4—C3—H3A 111.2 O6—C24—H24B 109.5
C2—C3—H3B 111.2 H24A—C24—H24B 109.5
C4—C3—H3B 111.2 O6—C24—H24C 109.5
H3A—C3—H3B 109.1 H24A—C24—H24C 109.5
N1—C4—C16 114.4 (4) H24B—C24—H24C 109.5
N1—C4—C3 102.8 (4) C30—C25—C26 118.8 (5)
C16—C4—C3 112.6 (4) C30—C25—C19 120.3 (5)
N1—C4—H4 109.0 C26—C25—C19 120.9 (5)
C16—C4—H4 109.0 C27—C26—C25 118.0 (6)
C3—C4—H4 109.0 C27—C26—C31 119.6 (6)
C10—C5—C6 119.8 (5) C25—C26—C31 122.5 (5)
C10—C5—C1 119.4 (4) C28—C27—C26 122.3 (6)
C6—C5—C1 120.7 (5) C28—C27—H27 118.9
C5—C6—C7 118.4 (5) C26—C27—H27 118.9
C5—C6—C32 122.6 (5) C29—C28—C27 119.9 (6)
C7—C6—C32 119.0 (5) C29—C28—H28 120.0
C8—C7—C6 121.8 (5) C27—C28—H28 120.0
C8—C7—H7 119.1 C28—C29—C30 119.8 (7)
C6—C7—H7 119.1 C28—C29—H29 120.1
C7—C8—C9 119.4 (5) C30—C29—H29 120.1
C7—C8—H8 120.3 C29—C30—C25 121.1 (6)
C9—C8—H8 120.3 C29—C30—H30 119.4
C8—C9—C10 119.3 (5) C25—C30—H30 119.4
C8—C9—H9 120.3 C26—C31—H31A 109.5
C10—C9—H9 120.3 C26—C31—H31B 109.5
C5—C10—C9 121.3 (5) H31A—C31—H31B 109.5
C5—C10—H10 119.4 C26—C31—H31C 109.5
C9—C10—H10 119.4 H31A—C31—H31C 109.5
O2—C11—O1 124.3 (5) H31B—C31—H31C 109.5
O2—C11—C2 123.6 (5) C6—C32—H32A 109.5
O1—C11—C2 112.0 (5) C6—C32—H32B 109.5
C13—C12—C45 112.2 (5) H32A—C32—H32B 109.5
C13—C12—C14 110.3 (5) C6—C32—H32C 109.5
C45—C12—C14 113.1 (5) H32A—C32—H32C 109.5
C13—C12—H12 107.0 H32B—C32—H32C 109.5
C45—C12—H12 107.0 O1—C44—C49 105.9 (4)
C14—C12—H12 107.0 O1—C44—C45 108.1 (4)
C12—C13—H13A 109.5 C49—C44—C45 113.9 (4)
C12—C13—H13B 109.5 O1—C44—H44A 109.6
H13A—C13—H13B 109.5 C49—C44—H44A 109.6
C12—C13—H13C 109.5 C45—C44—H44A 109.6
H13A—C13—H13C 109.5 C44—C45—C12 114.0 (5)
H13B—C13—H13C 109.5 C44—C45—C46 106.9 (4)
C12—C14—H14A 109.5 C12—C45—C46 114.3 (5)
C12—C14—H14B 109.5 C44—C45—H45 107.1
H14A—C14—H14B 109.5 C12—C45—H45 107.1
C12—C14—H14C 109.5 C46—C45—H45 107.1
H14A—C14—H14C 109.5 C47—C46—C45 110.5 (5)
H14B—C14—H14C 109.5 C47—C46—H46A 109.5
C48—C15—H15A 109.5 C45—C46—H46A 109.5
C48—C15—H15B 109.5 C47—C46—H46B 109.5
H15A—C15—H15B 109.5 C45—C46—H46B 109.5
C48—C15—H15C 109.5 H46A—C46—H46B 108.1
H15A—C15—H15C 109.5 C48—C47—C46 113.1 (5)
H15B—C15—H15C 109.5 C48—C47—H47A 109.0
O4—C16—O3 123.5 (5) C46—C47—H47A 109.0
O4—C16—C4 126.2 (5) C48—C47—H47B 109.0
O3—C16—C4 110.1 (4) C46—C47—H47B 109.0
O3—C17—H17A 109.5 H47A—C47—H47B 107.8
O3—C17—H17B 109.5 C47—C48—C15 112.3 (5)
H17A—C17—H17B 109.5 C47—C48—C49 109.8 (4)
O3—C17—H17C 109.5 C15—C48—C49 109.2 (5)
H17A—C17—H17C 109.5 C47—C48—H48 108.5
H17B—C17—H17C 109.5 C15—C48—H48 108.5
O5—C18—N1 120.7 (5) C49—C48—H48 108.5
O5—C18—C20 121.0 (5) C44—C49—C48 112.0 (4)
N1—C18—C20 118.1 (4) C44—C49—H49C 109.2
N2—C19—C25 113.6 (4) C48—C49—H49C 109.2
N2—C19—C20 106.0 (4) C44—C49—H49A 109.2
C25—C19—C20 115.9 (4) C48—C49—H49A 109.2
N2—C19—H19 107.0 H49C—C49—H49A 107.9
C25—C19—H19 107.0
C18—N1—C1—C5 82.6 (6) N1—C18—C20—C19 100.2 (5)
C4—N1—C1—C5 −110.1 (4) N2—C19—C20—C18 85.9 (5)
C18—N1—C1—C2 −154.5 (4) C25—C19—C20—C18 −41.1 (6)
C4—N1—C1—C2 12.8 (5) N2—C19—C20—C21 −31.7 (5)
N1—C1—C2—C11 −163.0 (4) C25—C19—C20—C21 −158.6 (5)
C5—C1—C2—C11 −42.6 (6) C18—C20—C21—C22 −102.5 (5)
N1—C1—C2—C3 −32.9 (5) C19—C20—C21—C22 12.9 (5)
C5—C1—C2—C3 87.5 (5) C19—N2—C22—C23 −154.8 (4)
C11—C2—C3—C4 169.7 (4) C19—N2—C22—C21 −29.9 (6)
C1—C2—C3—C4 41.1 (5) C20—C21—C22—N2 9.5 (6)
C18—N1—C4—C16 −57.3 (6) C20—C21—C22—C23 132.5 (5)
C1—N1—C4—C16 134.2 (4) C24—O6—C23—O7 −2.5 (8)
C18—N1—C4—C3 −179.7 (4) C24—O6—C23—C22 178.5 (4)
C1—N1—C4—C3 11.9 (5) N2—C22—C23—O7 5.4 (8)
C2—C3—C4—N1 −32.2 (5) C21—C22—C23—O7 −116.6 (6)
C2—C3—C4—C16 −155.7 (4) N2—C22—C23—O6 −175.6 (4)
N1—C1—C5—C10 31.8 (6) C21—C22—C23—O6 62.4 (6)
C2—C1—C5—C10 −82.1 (6) N2—C19—C25—C30 −43.5 (6)
N1—C1—C5—C6 −148.2 (4) C20—C19—C25—C30 79.5 (6)
C2—C1—C5—C6 97.8 (6) N2—C19—C25—C26 138.0 (5)
C10—C5—C6—C7 0.0 (8) C20—C19—C25—C26 −99.0 (6)
C1—C5—C6—C7 −179.9 (5) C30—C25—C26—C27 −3.1 (7)
C10—C5—C6—C32 −178.4 (5) C19—C25—C26—C27 175.4 (5)
C1—C5—C6—C32 1.7 (8) C30—C25—C26—C31 176.2 (5)
C5—C6—C7—C8 0.4 (8) C19—C25—C26—C31 −5.3 (7)
C32—C6—C7—C8 178.8 (5) C25—C26—C27—C28 1.2 (8)
C6—C7—C8—C9 0.3 (9) C31—C26—C27—C28 −178.1 (5)
C7—C8—C9—C10 −1.4 (9) C26—C27—C28—C29 0.3 (9)
C6—C5—C10—C9 −1.1 (8) C27—C28—C29—C30 0.2 (9)
C1—C5—C10—C9 178.9 (4) C28—C29—C30—C25 −2.2 (9)
C8—C9—C10—C5 1.8 (8) C26—C25—C30—C29 3.6 (7)
C44—O1—C11—O2 −9.1 (7) C19—C25—C30—C29 −174.9 (5)
C44—O1—C11—C2 167.9 (4) C11—O1—C44—C49 −102.4 (5)
C3—C2—C11—O2 158.3 (5) C11—O1—C44—C45 135.1 (5)
C1—C2—C11—O2 −78.4 (6) O1—C44—C45—C12 −57.3 (6)
C3—C2—C11—O1 −18.7 (6) C49—C44—C45—C12 −174.7 (4)
C1—C2—C11—O1 104.6 (5) O1—C44—C45—C46 175.4 (4)
C17—O3—C16—O4 −0.1 (7) C49—C44—C45—C46 58.0 (6)
C17—O3—C16—C4 174.5 (4) C13—C12—C45—C44 175.8 (5)
N1—C4—C16—O4 −39.9 (7) C14—C12—C45—C44 −58.7 (6)
C3—C4—C16—O4 76.9 (6) C13—C12—C45—C46 −60.9 (6)
N1—C4—C16—O3 145.6 (4) C14—C12—C45—C46 64.6 (6)
C3—C4—C16—O3 −97.5 (5) C44—C45—C46—C47 −57.6 (6)
C4—N1—C18—O5 9.4 (7) C12—C45—C46—C47 175.3 (5)
C1—N1—C18—O5 176.1 (5) C45—C46—C47—C48 58.6 (6)
C4—N1—C18—C20 −165.7 (4) C46—C47—C48—C15 −175.3 (4)
C1—N1—C18—C20 1.0 (7) C46—C47—C48—C49 −53.6 (6)
C22—N2—C19—C25 166.6 (4) O1—C44—C49—C48 −174.8 (4)
C22—N2—C19—C20 38.2 (5) C45—C44—C49—C48 −56.2 (6)
O5—C18—C20—C21 36.7 (7) C47—C48—C49—C44 51.4 (6)
N1—C18—C20—C21 −148.3 (4) C15—C48—C49—C44 174.9 (4)
O5—C18—C20—C19 −74.8 (6)

Hydrogen-bond geometry (Å, º)

D—H···A D—H H···A D···A D—H···A
C3—H3B···O4i 0.99 2.52 3.254 (6) 131
C3—H3B···O5i 0.99 2.58 3.462 (6) 149
C49—H49A···O7i 0.99 2.63 3.511 (7) 149

Symmetry code: (i) x−1/2, −y+3/2, −z+1.

Funding Statement

This work was funded by Russian Foundation for Basic Research grant 18-33-01260 to M. N. Sokolov. Scholarship of the President of the Russian Federation grant SP-1278.2018.4 to P. M. Ivantcova.

References

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  2. Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171–179. [DOI] [PMC free article] [PubMed]
  3. IUPAC–IUB (1970). Biochemistry, 9, 3471–3479. [DOI] [PubMed]
  4. Kudryavtsev, K. V., Ivantcova, P. M., Churakov, A. V., Wiedmann, S., Luy, B., Muhle-Goll, C., Zefirov, N. S. & Bräse, S. (2013). Angew. Chem. Int. Ed. 52, 12736–12740. [DOI] [PubMed]
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  8. Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [DOI] [PubMed]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Crystal structure: contains datablock(s) I. DOI: 10.1107/S2056989019004079/eb2015sup1.cif

e-75-00537-sup1.cif (42.6KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989019004079/eb2015Isup2.hkl

e-75-00537-Isup2.hkl (168.6KB, hkl)

Supporting information file. DOI: 10.1107/S2056989019004079/eb2015Isup3.cml

CCDC reference: 1905705

Additional supporting information: crystallographic information; 3D view; checkCIF report


Articles from Acta Crystallographica Section E: Crystallographic Communications are provided here courtesy of International Union of Crystallography

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