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Acta Crystallographica Section E: Structure Reports Online logoLink to Acta Crystallographica Section E: Structure Reports Online
. 2010 Jan 13;66(Pt 2):o351. doi: 10.1107/S1600536810000863

5α-Pregna-1,20-dien-3-one

Guang-ying Chen a,*, Mei-Yan Wei b, Ni Tan c, Zhen Liu d, Rui-Yun Yang e
PMCID: PMC2979690  PMID: 21579778

Abstract

The title compound, C21H30O, was isolated from the soft coral Sinularia sp. The mol­ecule contains four alicyclic rings, all trans-fused, among which three six-membered rings are in different distorted chair conformations while a five-membered ring assumes an envelope form.

Related literature

For general background to marine pregnanes isolated from marine organisms, see: Higgs & Faulkner (1977 ▶); Blackman et al. (1985 ▶); Hooper & Davies-Coleman (1995 ▶); Kittakoop et al. (1999 ▶); Li et al. (2009 ▶); Yan et al. (2004 ▶, 2007 ▶); Zhang et al. (2005 ▶); Seo et al. (1995 ▶).graphic file with name e-66-0o351-scheme1.jpg

Experimental

Crystal data

  • C21H30O

  • M r = 298.45

  • Orthorhombic, Inline graphic

  • a = 7.2619 (13) Å

  • b = 10.998 (2) Å

  • c = 21.964 (4) Å

  • V = 1754.2 (6) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.07 mm−1

  • T = 293 K

  • 0.25 × 0.22 × 0.20 mm

Data collection

  • Bruker APEXII CCD diffractometer

  • Absorption correction: multi-scan (SADABS; Sheldrick, 1996 ▶) T min = 0.984, T max = 0.987

  • 7653 measured reflections

  • 1995 independent reflections

  • 1563 reflections with I > 2σ(I)

  • R int = 0.053

Refinement

  • R[F 2 > 2σ(F 2)] = 0.051

  • wR(F 2) = 0.114

  • S = 1.10

  • 1995 reflections

  • 201 parameters

  • H-atom parameters constrained

  • Δρmax = 0.13 e Å−3

  • Δρmin = −0.18 e Å−3

Data collection: APEX2 (Bruker, 2004 ▶); cell refinement: SAINT (Bruker, 2004 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: SHELXTL (Sheldrick, 2008 ▶) and DIAMOND (Brandenburg, 2006 ▶); software used to prepare material for publication: SHELXTL.

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810000863/gk2251sup1.cif

e-66-0o351-sup1.cif (19.5KB, cif)

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810000863/gk2251Isup2.hkl

e-66-0o351-Isup2.hkl (98.2KB, hkl)

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

The authors acknowledge financial support from the National Natural Science Foundation of China (grant No. 20862005), the Program for New Century Excellent Talents in Universities (grant No. NCET-08-0656), the Youthful Fund of Guangdong Medical College (grant No. XQ0511) and the Open Research Fund Program of the Key Laboratory of Marine Drugs (Ocean University of China), the Ministry of Education [grant No. KLMD (OUC) 200801].

supplementary crystallographic information

Comment

Soft corals have been well recognized as marine organisms containing large quantities of secondary metabolites that exhibit various biological activities. In this regard, 5α-pregna-1,20-dien-3-one was firstly isolated as a marine natural product from an unknown coral (Higgs et al., 1977), subsequently from a soft coral of the genus Capnella (Blackman et al., 1985; Hooper et al., 1995), Scleronephthya pallida (Kittakoop et al., 1999), Scleronephthya sp. (Yan et al., 2004), Spongodes sp. (Yan et al., 2004; Yan et al., 2007), all of those belong to the family Nephtheidae. Furthermore, the title compound was also reported to be isolated from the family Alcyoniidae from two soft corals Sinularia papillosa (Zhang et al., 2005) and Alcyonium gracillimun(Seo et al., 1995). In course of our investigations of bioactive substances from marine organisms (Li et al., 2009), a soft coral Sinularia sp. which was collected from Sanya, was studied. In this paper, we describe the isolation, structure elucidation and crystal structure of the title compound.

The molecular structure of the title compound is shown in Fig. 1. The four fused rings are in different distorted conformations. Due to the C1=C2 double bond, ring A is highly distorted with a half-chair conformation. Rings B and C have slightly flattened chair conformations. Ring D assumes an unusual envelope conformation, probably induced by the vinyl substituent. Sstablization of the crystal structure is due only to weak van der Waals interactions.

Experimental

The soft coral Sinularia sp. was collected by SCUBA diving off coral reef at a depth of 15–20 m at Sanya in Hainan Island, PR China, in June 2005. The sample was frozen immediately after collection. The species was identified by Professor Renlin Zou (South China Sea Institute of Oceanology, Chinese Academy of Sciences). The soft coral (800 g, wet weight) was homogenized and extracted with MeOH for three times at room temperature, and the MeOH extracts were combined and then concentrated under vacuo to give a dark brown residue (25.6 g). The residue was partitioned between H2O and EtOAc. The ethyl acetate fraction was subjected to column chromatography over silica gel and Sephadex LH-20 to give the pure title compound (54.9 mg). The crystalline compound was obtained through the slow evaporation of the ethyl acetate solution of the title compound.

Refinement

All H atoms were positioned geometrically and treated as riding, with C—H bond lengths constrained to 0.93 Å (CH), 0.97 Å (CH2) 0.96 Å (methyl CH3), and with Uiso(H) = 1.2Ueq(C) or 1.5Ueq(methyl).

Figures

Fig. 1.

Fig. 1.

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View of the title molecular structure with atom numbering scheme and 30% probability displacement ellipsoids for non-hydrogen atoms.

Crystal data

C21H30O F(000) = 656
Mr = 298.45 Dx = 1.130 Mg m−3
Orthorhombic, P212121 Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab Cell parameters from 7653 reflections
a = 7.2619 (13) Å θ = 2.1–26.0°
b = 10.998 (2) Å µ = 0.07 mm−1
c = 21.964 (4) Å T = 293 K
V = 1754.2 (6) Å3 Block, colorless
Z = 4 0.25 × 0.22 × 0.20 mm
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Data collection

Bruker APEXII CCD diffractometer 1995 independent reflections
Radiation source: fine-focus sealed tube 1563 reflections with I > 2σ(I)
graphite Rint = 0.053
Detector resolution: 0 pixels mm-1 θmax = 26.0°, θmin = 2.1°
φ and ω scans h = −8→6
Absorption correction: multi-scan (SADABS; Sheldrick, 1996) k = −13→13
Tmin = 0.984, Tmax = 0.987 l = −27→25
7653 measured reflections
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Refinement

Refinement on F2 Primary atom site location: structure-invariant direct methods
Least-squares matrix: full Secondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.051 Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.114 H-atom parameters constrained
S = 1.10 w = 1/[σ2(Fo2) + (0.0531P)2] where P = (Fo2 + 2Fc2)/3
1995 reflections (Δ/σ)max < 0.001
201 parameters Δρmax = 0.13 e Å−3
0 restraints Δρmin = −0.17 e Å−3
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Special details

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s 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 > σ(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.
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Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

x y z Uiso*/Ueq
C1 0.4468 (4) 0.1678 (3) 0.18505 (11) 0.0607 (8)
H1 0.5613 0.1344 0.1760 0.073*
C2 0.4398 (5) 0.2554 (3) 0.22674 (13) 0.0709 (10)
H2 0.5495 0.2815 0.2442 0.085*
C3 0.2683 (5) 0.3124 (3) 0.24637 (12) 0.0684 (9)
C4 0.0964 (4) 0.2700 (3) 0.21577 (12) 0.0602 (8)
H4A 0.0108 0.3375 0.2127 0.072*
H4B 0.0391 0.2075 0.2405 0.072*
C5 0.1328 (4) 0.2193 (2) 0.15234 (11) 0.0470 (7)
H5 0.1822 0.2870 0.1284 0.056*
C6 −0.0413 (4) 0.1780 (3) 0.11961 (11) 0.0507 (7)
H6A −0.1328 0.2422 0.1210 0.061*
H6B −0.0918 0.1071 0.1399 0.061*
C7 0.0026 (4) 0.1469 (2) 0.05360 (11) 0.0500 (7)
H7A −0.1075 0.1149 0.0344 0.060*
H7B 0.0363 0.2210 0.0324 0.060*
C8 0.1565 (3) 0.0555 (2) 0.04637 (11) 0.0417 (6)
H8 0.1119 −0.0234 0.0610 0.050*
C9 0.3289 (3) 0.0902 (2) 0.08406 (11) 0.0414 (6)
H9 0.3736 0.1667 0.0666 0.050*
C10 0.2826 (4) 0.1193 (2) 0.15166 (11) 0.0446 (6)
C11 0.4847 (4) −0.0019 (2) 0.07458 (11) 0.0500 (7)
H11A 0.4480 −0.0796 0.0916 0.060*
H11B 0.5932 0.0255 0.0964 0.060*
C12 0.5332 (4) −0.0188 (2) 0.00707 (11) 0.0477 (7)
H12A 0.5836 0.0564 −0.0089 0.057*
H12B 0.6266 −0.0814 0.0032 0.057*
C13 0.3649 (3) −0.0546 (2) −0.02996 (11) 0.0430 (6)
C14 0.2141 (3) 0.0410 (2) −0.01977 (11) 0.0429 (6)
H14 0.2689 0.1190 −0.0315 0.051*
C15 0.0723 (4) 0.0120 (3) −0.06889 (11) 0.0591 (8)
H15A 0.0036 0.0842 −0.0802 0.071*
H15B −0.0133 −0.0498 −0.0551 0.071*
C16 0.1885 (4) −0.0347 (3) −0.12272 (13) 0.0706 (9)
H16A 0.1441 −0.1135 −0.1360 0.085*
H16B 0.1811 0.0215 −0.1567 0.085*
C17 0.3882 (4) −0.0446 (3) −0.09989 (11) 0.0528 (7)
H17 0.4484 0.0334 −0.1083 0.063*
C18 0.3017 (4) −0.1838 (2) −0.01350 (13) 0.0591 (8)
H18A 0.4009 −0.2398 −0.0204 0.089*
H18B 0.1985 −0.2059 −0.0384 0.089*
H18C 0.2664 −0.1863 0.0286 0.089*
C19 0.2221 (5) 0.0030 (3) 0.18588 (12) 0.0617 (9)
H19A 0.3250 −0.0512 0.1895 0.093*
H19B 0.1252 −0.0363 0.1636 0.093*
H19C 0.1785 0.0245 0.2257 0.093*
C20 0.5016 (5) −0.1414 (3) −0.12920 (12) 0.0672 (9)
H20 0.4512 −0.2189 −0.1317 0.081*
C21 0.6668 (5) −0.1253 (4) −0.15167 (14) 0.0843 (12)
H21A 0.7218 −0.0490 −0.1500 0.101*
H21B 0.7292 −0.1903 −0.1693 0.101*
O1 0.2658 (4) 0.3879 (3) 0.28688 (11) 0.1084 (10)
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Atomic displacement parameters (Å2)

U11 U22 U33 U12 U13 U23
C1 0.052 (2) 0.083 (2) 0.0466 (16) −0.0024 (18) −0.0062 (13) −0.0025 (15)
C2 0.061 (2) 0.096 (3) 0.0553 (18) −0.013 (2) −0.0124 (15) −0.0138 (18)
C3 0.079 (2) 0.080 (2) 0.0458 (16) −0.006 (2) −0.0011 (16) −0.0092 (16)
C4 0.064 (2) 0.069 (2) 0.0477 (17) 0.0012 (17) 0.0080 (15) −0.0002 (14)
C5 0.0485 (17) 0.0497 (16) 0.0428 (14) −0.0039 (14) 0.0042 (12) 0.0054 (11)
C6 0.0385 (16) 0.0609 (17) 0.0528 (15) 0.0040 (15) 0.0040 (12) 0.0011 (13)
C7 0.0376 (15) 0.0606 (17) 0.0519 (15) 0.0020 (15) −0.0075 (12) 0.0021 (12)
C8 0.0352 (15) 0.0439 (15) 0.0461 (14) −0.0050 (13) −0.0032 (11) 0.0046 (11)
C9 0.0386 (15) 0.0432 (15) 0.0425 (13) −0.0045 (13) −0.0013 (11) 0.0055 (11)
C10 0.0430 (16) 0.0523 (15) 0.0386 (13) −0.0017 (14) −0.0032 (12) 0.0046 (11)
C11 0.0402 (16) 0.0606 (18) 0.0493 (15) 0.0031 (14) −0.0084 (12) −0.0012 (13)
C12 0.0408 (17) 0.0443 (15) 0.0580 (16) 0.0010 (13) −0.0012 (12) −0.0028 (12)
C13 0.0400 (16) 0.0423 (15) 0.0468 (15) −0.0025 (13) −0.0002 (12) 0.0019 (11)
C14 0.0392 (15) 0.0463 (15) 0.0432 (14) −0.0017 (13) −0.0053 (12) 0.0050 (11)
C15 0.0547 (18) 0.074 (2) 0.0490 (17) 0.0044 (17) −0.0140 (14) −0.0022 (14)
C16 0.072 (2) 0.092 (2) 0.0473 (16) 0.003 (2) −0.0123 (16) −0.0092 (16)
C17 0.0557 (19) 0.0532 (17) 0.0494 (16) −0.0035 (16) 0.0026 (13) −0.0025 (13)
C18 0.061 (2) 0.0501 (17) 0.0664 (17) −0.0050 (16) −0.0004 (15) 0.0007 (14)
C19 0.071 (2) 0.0659 (19) 0.0482 (16) 0.0009 (18) 0.0012 (14) 0.0170 (13)
C20 0.075 (2) 0.077 (2) 0.0502 (17) 0.000 (2) 0.0013 (16) −0.0143 (15)
C21 0.071 (3) 0.108 (3) 0.074 (2) 0.013 (2) 0.009 (2) −0.027 (2)
O1 0.114 (2) 0.125 (2) 0.0864 (17) 0.003 (2) −0.0065 (16) −0.0523 (16)
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Geometric parameters (Å, °)

C1—C2 1.330 (4) C11—H11B 0.9700
C1—C10 1.498 (4) C12—C13 1.520 (3)
C1—H1 0.9300 C12—H12A 0.9700
C2—C3 1.460 (5) C12—H12B 0.9700
C2—H2 0.9300 C13—C18 1.536 (4)
C3—O1 1.217 (3) C13—C14 1.534 (4)
C3—C4 1.493 (4) C13—C17 1.549 (3)
C4—C5 1.524 (4) C14—C15 1.525 (3)
C4—H4A 0.9700 C14—H14 0.9800
C4—H4B 0.9700 C15—C16 1.541 (4)
C5—C6 1.523 (4) C15—H15A 0.9700
C5—C10 1.547 (4) C15—H15B 0.9700
C5—H5 0.9800 C16—C17 1.539 (4)
C6—C7 1.523 (4) C16—H16A 0.9700
C6—H6A 0.9700 C16—H16B 0.9700
C6—H6B 0.9700 C17—C20 1.492 (4)
C7—C8 1.512 (3) C17—H17 0.9800
C7—H7A 0.9700 C18—H18A 0.9600
C7—H7B 0.9700 C18—H18B 0.9600
C8—C14 1.520 (3) C18—H18C 0.9600
C8—C9 1.549 (3) C19—H19A 0.9600
C8—H8 0.9800 C19—H19B 0.9600
C9—C11 1.532 (3) C19—H19C 0.9600
C9—C10 1.556 (3) C20—C21 1.309 (4)
C9—H9 0.9800 C20—H20 0.9300
C10—C19 1.547 (4) C21—H21A 0.9300
C11—C12 1.535 (4) C21—H21B 0.9300
C11—H11A 0.9700
C2—C1—C10 124.4 (3) H11A—C11—H11B 107.9
C2—C1—H1 117.8 C13—C12—C11 111.3 (2)
C10—C1—H1 117.8 C13—C12—H12A 109.4
C1—C2—C3 123.2 (3) C11—C12—H12A 109.4
C1—C2—H2 118.4 C13—C12—H12B 109.4
C3—C2—H2 118.4 C11—C12—H12B 109.4
O1—C3—C2 121.5 (3) H12A—C12—H12B 108.0
O1—C3—C4 122.0 (3) C12—C13—C18 110.7 (2)
C2—C3—C4 116.5 (2) C12—C13—C14 108.6 (2)
C3—C4—C5 112.4 (2) C18—C13—C14 112.7 (2)
C3—C4—H4A 109.1 C12—C13—C17 115.1 (2)
C5—C4—H4A 109.1 C18—C13—C17 109.4 (2)
C3—C4—H4B 109.1 C14—C13—C17 100.0 (2)
C5—C4—H4B 109.1 C8—C14—C15 120.8 (2)
H4A—C4—H4B 107.9 C8—C14—C13 114.1 (2)
C6—C5—C4 113.4 (2) C15—C14—C13 103.6 (2)
C6—C5—C10 111.5 (2) C8—C14—H14 105.7
C4—C5—C10 113.0 (2) C15—C14—H14 105.7
C6—C5—H5 106.1 C13—C14—H14 105.7
C4—C5—H5 106.1 C14—C15—C16 104.1 (2)
C10—C5—H5 106.1 C14—C15—H15A 110.9
C5—C6—C7 110.0 (2) C16—C15—H15A 110.9
C5—C6—H6A 109.7 C14—C15—H15B 110.9
C7—C6—H6A 109.7 C16—C15—H15B 110.9
C5—C6—H6B 109.7 H15A—C15—H15B 109.0
C7—C6—H6B 109.7 C17—C16—C15 106.8 (2)
H6A—C6—H6B 108.2 C17—C16—H16A 110.4
C8—C7—C6 113.8 (2) C15—C16—H16A 110.4
C8—C7—H7A 108.8 C17—C16—H16B 110.4
C6—C7—H7A 108.8 C15—C16—H16B 110.4
C8—C7—H7B 108.8 H16A—C16—H16B 108.6
C6—C7—H7B 108.8 C20—C17—C16 115.5 (3)
H7A—C7—H7B 107.7 C20—C17—C13 116.0 (2)
C7—C8—C14 111.9 (2) C16—C17—C13 103.0 (2)
C7—C8—C9 112.2 (2) C20—C17—H17 107.3
C14—C8—C9 108.3 (2) C16—C17—H17 107.3
C7—C8—H8 108.1 C13—C17—H17 107.3
C14—C8—H8 108.1 C13—C18—H18A 109.5
C9—C8—H8 108.1 C13—C18—H18B 109.5
C11—C9—C8 111.2 (2) H18A—C18—H18B 109.5
C11—C9—C10 115.2 (2) C13—C18—H18C 109.5
C8—C9—C10 112.7 (2) H18A—C18—H18C 109.5
C11—C9—H9 105.6 H18B—C18—H18C 109.5
C8—C9—H9 105.6 C10—C19—H19A 109.5
C10—C9—H9 105.6 C10—C19—H19B 109.5
C1—C10—C19 106.4 (2) H19A—C19—H19B 109.5
C1—C10—C5 107.6 (2) C10—C19—H19C 109.5
C19—C10—C5 112.5 (2) H19A—C19—H19C 109.5
C1—C10—C9 111.6 (2) H19B—C19—H19C 109.5
C19—C10—C9 110.8 (2) C21—C20—C17 124.9 (3)
C5—C10—C9 107.9 (2) C21—C20—H20 117.5
C9—C11—C12 112.4 (2) C17—C20—H20 117.5
C9—C11—H11A 109.1 C20—C21—H21A 120.0
C12—C11—H11A 109.1 C20—C21—H21B 120.0
C9—C11—H11B 109.1 H21A—C21—H21B 120.0
C12—C11—H11B 109.1
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Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: GK2251).

References

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Associated Data

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

Supplementary Materials

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810000863/gk2251sup1.cif

e-66-0o351-sup1.cif (19.5KB, cif)

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810000863/gk2251Isup2.hkl

e-66-0o351-Isup2.hkl (98.2KB, hkl)

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography

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