4-(3,4-Dihydro-β-carbolin-1-yl)pyrimidin-2-amine

Mat Ropi Mukhtar; Anissuhailin Zainal Abidin; Khalijah Awang; A Hamid A Hadi; Seik Weng Ng

doi:10.1107/S160053680900600X

. 2009 Feb 25;65(Pt 3):o594. doi: 10.1107/S160053680900600X

4-(3,4-Dihydro-β-carbolin-1-yl)pyrimidin-2-amine

Mat Ropi Mukhtar ^a, Anissuhailin Zainal Abidin ^a, Khalijah Awang ^a, A Hamid A Hadi ^a, Seik Weng Ng ^a,^*

PMCID: PMC2968656 PMID: 21582249

Abstract

The molecule of accanthomine A, C₁₅H₁₃N₅, is approximately planar, with the indolyl fused-ring and the pyrimidyl ring being twisted by 31.7 (1)° The amino group of the five-membered ring is an intramolecular hydrogen-bond donor to a nitrogen acceptor of the pyrimide ring. The amino group of the pyrimide ring is a hydrogen-bond donor to the N atoms of adjacent molecules. These hydrogen-bonding interactions give rise to a layered network with a 4.8² topology.

Related literature

The β-carboline fragment is found in the crystal structures of two compounds that show selective CDK4-cycli D1 inhibitory activity; see: García et al. (2006 ▶). For related compounds, see: Costa et al. (2006 ▶); Kobayashi et al. (1995 ▶).

Experimental

Crystal data

C₁₅H₁₃N₅
M _r = 263.30
Monoclinic,
a = 11.4758 (2) Å
b = 12.6095 (2) Å
c = 8.9241 (2) Å
β = 102.116 (1)°
V = 1262.59 (4) Å³
Z = 4
Mo Kα radiation
μ = 0.09 mm⁻¹
T = 120 K
0.45 × 0.35 × 0.15 mm

Data collection

Bruker SMART APEX diffractometer
Absorption correction: none
11840 measured reflections
2905 independent reflections
2485 reflections with I > 2σ(I)
R _int = 0.026

Refinement

R[F ² > 2σ(F ²)] = 0.037
wR(F ²) = 0.102
S = 1.02
2905 reflections
193 parameters
3 restraints
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.26 e Å⁻³
Δρ_min = −0.23 e Å⁻³

Data collection: APEX2 (Bruker, 2007 ▶); cell refinement: SAINT (Bruker, 2007 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: OLEX (Dolomanov et al., 2003 ▶) and X-SEED (Barbour, 2001 ▶); software used to prepare material for publication: publCIF (Westrip, 2009 ▶).

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S160053680900600X/hg2480sup1.cif

e-65-0o594-sup1.cif^{(17.2KB, cif)}

Structure factors: contains datablocks I. DOI: 10.1107/S160053680900600X/hg2480Isup2.hkl

e-65-0o594-Isup2.hkl^{(142.6KB, hkl)}

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

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

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H11⋯N2ⁱ	0.89 (2)	2.14 (2)	2.994 (3)	161 (3)
N1—H12⋯N5ⁱⁱ	0.91 (3)	2.25 (3)	3.138 (3)	165 (3)
N4—H4⋯N3	0.88 (2)	2.29 (3)	2.825 (3)	119 (2)

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Symmetry codes: (i) Inline graphic ; (ii) .

Acknowledgments

We thank the University of Malaya for supporting this study (by PPP/PS231/2008B and Science Fund 12–02-03–2063).

supplementary crystallographic information

Comment

The molecule of Accanthomine A (I) is approximately planar; the amino group of the five-membered ring is hydrogen-bond donor to a nitrogen acceptor of the pyrimidyl ring (Fig. 1). The amino group of the pyrimidyl ring is a hydrogen-bond donor to the nitrogen atoms of adjacent molecules. The hydrogen bonding interactions give rise to a layer network with a 4.8 (2) topology (Fig. 2).

Experimental

Litsea machilifolia was collected from the Mukim Telang Reserve, Kuala Lipis, Pahang. Specimens (KL5459) were deposited at the herbarium, Department of Chemistry, University of Malaya.

Dried and grounded leaves of Litsea machilifolia (2.1 kg) were extracted with dichloromethane. The dichloromethane extract was concentrated under reduced pressure to a volume of 500 ml and this was repeatedly extracted with 5% hydrocloric acid. The combined extracts were then basified with 10% ammonium hydroxide to a pH 11, and then re-extracted with dichloromethane. The crude alkaloid fraction was dark brown (4.0 g). A portion (4.0 g) was subjected to column chromatography on silica gel 60 GF₂₅₄ by using a step gradient of dichloromethane and methanol. One of the fractions when further purified by CC with 100% dichloromethane afforded the pure compound, accanthomine A (8 mg), whose formulation was established by NMR spectroscopic analysis.