organic compounds
Abacavir methanol 2.5-solvate
aDepartment of Chemistry, Penn State Worthington Scranton, 120 Ridge View Drive, Dunmore, Pennsylvania 18512, USA
*Correspondence e-mail: ptp2@psu.edu
The structure of abacavir (systematic name: {(1S,4R)-4-[2-amino-6-(cyclopropylamino)-9H-purin-9-yl]cyclopent-2-en-1-yl}methanol), C14H18N6O·2.5CH3OH, consists of hydrogen-bonded ribbons which are further held together by additional hydrogen bonds involving the hydroxyl group and two N atoms on an adjacent purine. The also contains 2.5 molecules of methanol solvate which were grossly disordered and were excluded using SQUEEZE subroutine in PLATON [Spek, (2009). Acta Cryst. D65, 148–155].
Related literature
For a related structure, see: Huang et al. (2007). For the synthesis, see: Vince & Hua (1990). For an X-ray powder of abacavir hemisulfate, see: Monger & Varlashkin (2005).
Experimental
Crystal data
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Refinement
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Data collection: SMART (Bruker, 2003); cell SAINT (Bruker, 2006); 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); software used to prepare material for publication: SHELXTL.
Supporting information
10.1107/S1600536809027743/pv2180sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536809027743/pv2180Isup2.hkl
Abacavir was prepared according to literature procedure (Vince & Hua, 1990). The compound was dissolved in a minimal amount of hot methanol and the solution was then placed in a chamber saturated with dichloromethane at room temperature, covered and allowed to crystallize for two weeks. The resulting clear colorless rod shaped crystals were washed with cold methanol, dried then collected and a suitable crystal was selected for structural determination.
The program PLATON (Spek, 2009) indicated solvent accessible void space of 688.7 Å3, corresponding to 179 electrons in a
equivalent to ten molecules of methanol solvate. Since the solvent molecules were grossly disordered and could not be modeled, their contribution was excluded using the subroutine SQUEEZE. H atoms were placed in idealized positions and treated as riding atoms with distances: O—H = 0.84, N—H 0.88 and C—H in the range 0.95–1.00 Å and Uiso(H) = 1.2Ueq(parent atom). An could not be determined by anoimalous dispersion effects; Friedel pairs (2405) were therefore merged.Data collection: SMART (Bruker, 2003); cell
SAINT (Bruker, 2006); data reduction: SAINT (Bruker, 2006); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).C14H18N6O·2.5CH4O | F(000) = 788 |
Mr = 366.45 | Dx = 1.243 Mg m−3 |
Monoclinic, C2 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: C 2y | Cell parameters from 2936 reflections |
a = 19.857 (4) Å | θ = 2.4–27.4° |
b = 7.2552 (15) Å | µ = 0.09 mm−1 |
c = 13.735 (3) Å | T = 173 K |
β = 98.27 (3)° | Rod, colorless |
V = 1958.2 (7) Å3 | 0.60 × 0.30 × 0.15 mm |
Z = 4 |
Bruker SMART Platform CCD diffractometer | 2405 independent reflections |
Radiation source: normal-focus sealed tube | 2231 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.024 |
area detector, ω scans per ϕ | θmax = 27.5°, θmin = 1.5° |
Absorption correction: multi-scan (SADABS; Bruker, 2003) | h = −25→25 |
Tmin = 0.948, Tmax = 0.987 | k = −9→9 |
10335 measured reflections | l = −17→17 |
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)] = 0.036 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.099 | H-atom parameters constrained |
S = 1.01 | w = 1/[σ2(Fo2) + (0.0623P)2 + 0.4691P] where P = (Fo2 + 2Fc2)/3 |
2405 reflections | (Δ/σ)max < 0.001 |
190 parameters | Δρmax = 0.18 e Å−3 |
1 restraint | Δρmin = −0.19 e Å−3 |
C14H18N6O·2.5CH4O | V = 1958.2 (7) Å3 |
Mr = 366.45 | Z = 4 |
Monoclinic, C2 | Mo Kα radiation |
a = 19.857 (4) Å | µ = 0.09 mm−1 |
b = 7.2552 (15) Å | T = 173 K |
c = 13.735 (3) Å | 0.60 × 0.30 × 0.15 mm |
β = 98.27 (3)° |
Bruker SMART Platform CCD diffractometer | 2405 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2003) | 2231 reflections with I > 2σ(I) |
Tmin = 0.948, Tmax = 0.987 | Rint = 0.024 |
10335 measured reflections |
R[F2 > 2σ(F2)] = 0.036 | 1 restraint |
wR(F2) = 0.099 | H-atom parameters constrained |
S = 1.01 | Δρmax = 0.18 e Å−3 |
2405 reflections | Δρmin = −0.19 e Å−3 |
190 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.78278 (7) | 0.9453 (2) | 0.79352 (11) | 0.0435 (4) | |
H1O | 0.8119 | 1.0020 | 0.7664 | 0.065* | |
N1 | 0.41393 (7) | 0.5553 (3) | 0.92222 (10) | 0.0353 (4) | |
H1A | 0.4354 | 0.5494 | 0.9828 | 0.042* | |
H1B | 0.3694 | 0.5669 | 0.9115 | 0.042* | |
N2 | 0.41135 (7) | 0.5588 (2) | 0.75419 (9) | 0.0265 (3) | |
N3 | 0.40604 (7) | 0.5727 (2) | 0.58458 (9) | 0.0302 (4) | |
H3N | 0.4273 | 0.5824 | 0.5328 | 0.036* | |
N4 | 0.51700 (7) | 0.5290 (2) | 0.86615 (9) | 0.0252 (3) | |
N5 | 0.56198 (7) | 0.5232 (3) | 0.62195 (9) | 0.0307 (3) | |
N6 | 0.61422 (7) | 0.4984 (2) | 0.77840 (9) | 0.0259 (3) | |
C1 | 0.44957 (8) | 0.5466 (3) | 0.84530 (11) | 0.0253 (3) | |
C2 | 0.44332 (8) | 0.5568 (3) | 0.67411 (11) | 0.0253 (3) | |
C3 | 0.33305 (10) | 0.5746 (4) | 0.57052 (13) | 0.0413 (5) | |
H3 | 0.3100 | 0.4545 | 0.5796 | 0.050* | |
C4 | 0.29783 (13) | 0.7005 (5) | 0.49353 (15) | 0.0589 (8) | |
H4A | 0.2545 | 0.6579 | 0.4555 | 0.071* | |
H4B | 0.3265 | 0.7770 | 0.4560 | 0.071* | |
C5 | 0.29839 (14) | 0.7448 (5) | 0.60113 (15) | 0.0671 (9) | |
H5B | 0.3274 | 0.8480 | 0.6294 | 0.080* | |
H5C | 0.2554 | 0.7290 | 0.6289 | 0.080* | |
C6 | 0.51484 (8) | 0.5376 (3) | 0.68753 (11) | 0.0249 (3) | |
C7 | 0.54633 (8) | 0.5233 (2) | 0.78383 (11) | 0.0234 (3) | |
C8 | 0.61989 (8) | 0.5003 (3) | 0.67988 (11) | 0.0295 (4) | |
H8 | 0.6621 | 0.4863 | 0.6558 | 0.035* | |
C9 | 0.66820 (9) | 0.4790 (3) | 0.86407 (11) | 0.0295 (4) | |
H9 | 0.6478 | 0.4289 | 0.9210 | 0.035* | |
C10 | 0.70507 (9) | 0.6626 (3) | 0.89483 (14) | 0.0346 (4) | |
H10A | 0.7068 | 0.6837 | 0.9664 | 0.042* | |
H10B | 0.6811 | 0.7675 | 0.8590 | 0.042* | |
C11 | 0.77807 (9) | 0.6425 (3) | 0.86777 (13) | 0.0314 (4) | |
H11 | 0.8127 | 0.6785 | 0.9248 | 0.038* | |
C12 | 0.78314 (10) | 0.4411 (3) | 0.84697 (14) | 0.0349 (4) | |
H12 | 0.8245 | 0.3822 | 0.8380 | 0.042* | |
C13 | 0.72425 (9) | 0.3522 (3) | 0.84218 (13) | 0.0322 (4) | |
H13 | 0.7182 | 0.2250 | 0.8269 | 0.039* | |
C14 | 0.78838 (11) | 0.7532 (3) | 0.77666 (15) | 0.0398 (5) | |
H14A | 0.8339 | 0.7260 | 0.7589 | 0.048* | |
H14B | 0.7539 | 0.7160 | 0.7208 | 0.048* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0336 (7) | 0.0455 (9) | 0.0523 (9) | −0.0024 (6) | 0.0089 (6) | −0.0002 (7) |
N1 | 0.0258 (7) | 0.0635 (12) | 0.0166 (6) | 0.0035 (8) | 0.0027 (5) | −0.0004 (8) |
N2 | 0.0227 (6) | 0.0382 (9) | 0.0180 (6) | 0.0001 (6) | 0.0008 (5) | −0.0003 (6) |
N3 | 0.0257 (7) | 0.0492 (10) | 0.0152 (6) | 0.0062 (7) | 0.0012 (5) | 0.0002 (6) |
N4 | 0.0262 (7) | 0.0330 (8) | 0.0159 (6) | 0.0000 (6) | 0.0018 (5) | 0.0005 (6) |
N5 | 0.0295 (7) | 0.0447 (10) | 0.0184 (6) | −0.0011 (7) | 0.0048 (5) | 0.0009 (7) |
N6 | 0.0238 (6) | 0.0370 (9) | 0.0172 (6) | −0.0004 (6) | 0.0034 (5) | 0.0005 (6) |
C1 | 0.0253 (7) | 0.0303 (9) | 0.0204 (7) | −0.0002 (7) | 0.0032 (6) | −0.0003 (7) |
C2 | 0.0280 (8) | 0.0281 (9) | 0.0191 (7) | −0.0002 (7) | 0.0012 (6) | −0.0008 (7) |
C3 | 0.0315 (9) | 0.0679 (15) | 0.0232 (8) | 0.0054 (10) | −0.0006 (7) | 0.0001 (9) |
C4 | 0.0509 (13) | 0.096 (2) | 0.0273 (10) | 0.0352 (15) | −0.0019 (9) | 0.0021 (12) |
C5 | 0.0587 (15) | 0.112 (3) | 0.0296 (11) | 0.0447 (17) | 0.0021 (10) | −0.0025 (14) |
C6 | 0.0278 (7) | 0.0304 (9) | 0.0166 (7) | −0.0006 (7) | 0.0036 (6) | 0.0016 (7) |
C7 | 0.0226 (7) | 0.0273 (9) | 0.0200 (7) | −0.0034 (7) | 0.0018 (5) | 0.0012 (7) |
C8 | 0.0260 (8) | 0.0441 (11) | 0.0190 (7) | −0.0011 (8) | 0.0051 (6) | 0.0000 (8) |
C9 | 0.0259 (8) | 0.0459 (11) | 0.0163 (7) | −0.0034 (8) | 0.0017 (6) | −0.0001 (7) |
C10 | 0.0254 (9) | 0.0472 (12) | 0.0316 (9) | −0.0024 (8) | 0.0049 (7) | −0.0144 (8) |
C11 | 0.0186 (8) | 0.0504 (12) | 0.0240 (8) | −0.0018 (7) | −0.0012 (6) | −0.0036 (8) |
C12 | 0.0270 (9) | 0.0460 (12) | 0.0309 (9) | 0.0075 (8) | 0.0011 (7) | 0.0055 (8) |
C13 | 0.0329 (9) | 0.0385 (10) | 0.0245 (8) | 0.0041 (8) | 0.0015 (7) | 0.0035 (8) |
C14 | 0.0417 (11) | 0.0444 (13) | 0.0345 (10) | −0.0079 (9) | 0.0097 (8) | −0.0045 (9) |
O1—C14 | 1.419 (3) | C4—C5 | 1.511 (3) |
O1—H1O | 0.8394 | C4—H4A | 0.9900 |
N1—C1 | 1.355 (2) | C4—H4B | 0.9900 |
N1—H1A | 0.8798 | C5—H5B | 0.9900 |
N1—H1B | 0.8801 | C5—H5C | 0.9900 |
N2—C2 | 1.347 (2) | C6—C7 | 1.383 (2) |
N2—C1 | 1.370 (2) | C8—H8 | 0.9500 |
N3—C2 | 1.346 (2) | C9—C13 | 1.507 (3) |
N3—C3 | 1.434 (2) | C9—C10 | 1.550 (3) |
N3—H3N | 0.8804 | C9—H9 | 1.0000 |
N4—C1 | 1.334 (2) | C10—C11 | 1.554 (2) |
N4—C7 | 1.345 (2) | C10—H10A | 0.9900 |
N5—C8 | 1.311 (2) | C10—H10B | 0.9900 |
N5—C6 | 1.393 (2) | C11—C12 | 1.495 (3) |
N6—C7 | 1.373 (2) | C11—C14 | 1.526 (3) |
N6—C8 | 1.374 (2) | C11—H11 | 1.0000 |
N6—C9 | 1.480 (2) | C12—C13 | 1.329 (3) |
C2—C6 | 1.412 (2) | C12—H12 | 0.9500 |
C3—C4 | 1.493 (3) | C13—H13 | 0.9500 |
C3—C5 | 1.503 (4) | C14—H14A | 0.9900 |
C3—H3 | 1.0000 | C14—H14B | 0.9900 |
C14—O1—H1O | 109.5 | C7—C6—C2 | 116.10 (14) |
C1—N1—H1A | 120.0 | N5—C6—C2 | 132.81 (14) |
C1—N1—H1B | 120.0 | N4—C7—N6 | 126.66 (14) |
H1A—N1—H1B | 120.0 | N4—C7—C6 | 127.64 (14) |
C2—N2—C1 | 118.76 (13) | N6—C7—C6 | 105.69 (14) |
C2—N3—C3 | 122.41 (14) | N5—C8—N6 | 114.20 (14) |
C2—N3—H3N | 118.8 | N5—C8—H8 | 122.9 |
C3—N3—H3N | 118.8 | N6—C8—H8 | 122.9 |
C1—N4—C7 | 111.41 (13) | N6—C9—C13 | 111.75 (14) |
C8—N5—C6 | 103.26 (13) | N6—C9—C10 | 113.26 (16) |
C7—N6—C8 | 105.80 (13) | C13—C9—C10 | 104.22 (15) |
C7—N6—C9 | 125.03 (13) | N6—C9—H9 | 109.2 |
C8—N6—C9 | 129.15 (14) | C13—C9—H9 | 109.2 |
N4—C1—N1 | 117.23 (14) | C10—C9—H9 | 109.2 |
N4—C1—N2 | 127.52 (14) | C9—C10—C11 | 105.93 (16) |
N1—C1—N2 | 115.24 (14) | C9—C10—H10A | 110.5 |
N3—C2—N2 | 118.91 (15) | C11—C10—H10A | 110.5 |
N3—C2—C6 | 122.56 (14) | C9—C10—H10B | 110.5 |
N2—C2—C6 | 118.54 (14) | C11—C10—H10B | 110.5 |
N3—C3—C4 | 117.6 (2) | H10A—C10—H10B | 108.7 |
N3—C3—C5 | 117.7 (2) | C12—C11—C14 | 109.71 (16) |
C4—C3—C5 | 60.57 (16) | C12—C11—C10 | 103.19 (17) |
N3—C3—H3 | 116.5 | C14—C11—C10 | 112.74 (16) |
C4—C3—H3 | 116.5 | C12—C11—H11 | 110.3 |
C5—C3—H3 | 116.5 | C14—C11—H11 | 110.3 |
C3—C4—C5 | 60.04 (16) | C10—C11—H11 | 110.3 |
C3—C4—H4A | 117.8 | C13—C12—C11 | 113.64 (19) |
C5—C4—H4A | 117.8 | C13—C12—H12 | 123.2 |
C3—C4—H4B | 117.8 | C11—C12—H12 | 123.2 |
C5—C4—H4B | 117.8 | C12—C13—C9 | 111.33 (19) |
H4A—C4—H4B | 114.9 | C12—C13—H13 | 124.3 |
C3—C5—C4 | 59.39 (16) | C9—C13—H13 | 124.3 |
C3—C5—H5B | 117.8 | O1—C14—C11 | 111.11 (17) |
C4—C5—H5B | 117.8 | O1—C14—H14A | 109.4 |
C3—C5—H5C | 117.8 | C11—C14—H14A | 109.4 |
C4—C5—H5C | 117.8 | O1—C14—H14B | 109.4 |
H5B—C5—H5C | 115.0 | C11—C14—H14B | 109.4 |
C7—C6—N5 | 111.05 (14) | H14A—C14—H14B | 108.0 |
C7—N4—C1—N1 | −179.56 (17) | C9—N6—C7—C6 | 179.02 (18) |
C7—N4—C1—N2 | −0.2 (3) | N5—C6—C7—N4 | −179.26 (18) |
C2—N2—C1—N4 | −1.3 (3) | C2—C6—C7—N4 | −1.3 (3) |
C2—N2—C1—N1 | 178.04 (17) | N5—C6—C7—N6 | −0.4 (2) |
C3—N3—C2—N2 | −5.9 (3) | C2—C6—C7—N6 | 177.52 (17) |
C3—N3—C2—C6 | 174.0 (2) | C6—N5—C8—N6 | 0.1 (2) |
C1—N2—C2—N3 | −178.59 (17) | C7—N6—C8—N5 | −0.4 (2) |
C1—N2—C2—C6 | 1.5 (3) | C9—N6—C8—N5 | −178.85 (19) |
C2—N3—C3—C4 | 142.2 (2) | C7—N6—C9—C13 | 146.99 (18) |
C2—N3—C3—C5 | 72.8 (3) | C8—N6—C9—C13 | −34.8 (3) |
N3—C3—C4—C5 | −107.9 (3) | C7—N6—C9—C10 | −95.7 (2) |
N3—C3—C5—C4 | 107.7 (2) | C8—N6—C9—C10 | 82.6 (2) |
C8—N5—C6—C7 | 0.2 (2) | N6—C9—C10—C11 | −110.14 (16) |
C8—N5—C6—C2 | −177.3 (2) | C13—C9—C10—C11 | 11.53 (19) |
N3—C2—C6—C7 | 179.77 (18) | C9—C10—C11—C12 | −12.79 (19) |
N2—C2—C6—C7 | −0.4 (3) | C9—C10—C11—C14 | 105.50 (19) |
N3—C2—C6—N5 | −2.9 (3) | C14—C11—C12—C13 | −110.41 (19) |
N2—C2—C6—N5 | 177.0 (2) | C10—C11—C12—C13 | 10.0 (2) |
C1—N4—C7—N6 | −177.05 (18) | C11—C12—C13—C9 | −2.7 (2) |
C1—N4—C7—C6 | 1.6 (3) | N6—C9—C13—C12 | 116.80 (18) |
C8—N6—C7—N4 | 179.31 (18) | C10—C9—C13—C12 | −5.9 (2) |
C9—N6—C7—N4 | −2.1 (3) | C12—C11—C14—O1 | 179.07 (17) |
C8—N6—C7—C6 | 0.4 (2) | C10—C11—C14—O1 | 64.7 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1A···N4i | 0.88 | 2.16 | 3.036 (2) | 177 |
N1—H1B···O1ii | 0.88 | 2.36 | 3.036 (2) | 134 |
N3—H3N···N5iii | 0.88 | 2.21 | 3.016 (2) | 152 |
O1—H1O···N2iv | 0.84 | 2.05 | 2.808 (2) | 150 |
Symmetry codes: (i) −x+1, y, −z+2; (ii) x−1/2, y−1/2, z; (iii) −x+1, y, −z+1; (iv) x+1/2, y+1/2, z. |
Experimental details
Crystal data | |
Chemical formula | C14H18N6O·2.5CH4O |
Mr | 366.45 |
Crystal system, space group | Monoclinic, C2 |
Temperature (K) | 173 |
a, b, c (Å) | 19.857 (4), 7.2552 (15), 13.735 (3) |
β (°) | 98.27 (3) |
V (Å3) | 1958.2 (7) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.09 |
Crystal size (mm) | 0.60 × 0.30 × 0.15 |
Data collection | |
Diffractometer | Bruker SMART Platform CCD diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 2003) |
Tmin, Tmax | 0.948, 0.987 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 10335, 2405, 2231 |
Rint | 0.024 |
(sin θ/λ)max (Å−1) | 0.650 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.036, 0.099, 1.01 |
No. of reflections | 2405 |
No. of parameters | 190 |
No. of restraints | 1 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.18, −0.19 |
Computer programs: SMART (Bruker, 2003), SAINT (Bruker, 2006), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1A···N4i | 0.88 | 2.16 | 3.036 (2) | 176.9 |
N1—H1B···O1ii | 0.88 | 2.36 | 3.036 (2) | 134.0 |
N3—H3N···N5iii | 0.88 | 2.21 | 3.016 (2) | 152.4 |
O1—H1O···N2iv | 0.84 | 2.05 | 2.808 (2) | 150.4 |
Symmetry codes: (i) −x+1, y, −z+2; (ii) x−1/2, y−1/2, z; (iii) −x+1, y, −z+1; (iv) x+1/2, y+1/2, z. |
Acknowledgements
This work was supported in part by the MRSEC Program of the National Science Foundation under Award Number DMR-0212302, Research Development Grants from the Pennsylvania State University and funding from the Drug Research Center at the University of Minnesota. The author also acknowledges Benjamin E. Kucera, Victor G. Young, Jr, Aalo Gupta and the X-ray Crystallographic Laboratory at the University of Minnesota.
References
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Abacavir is a potent anti-HIV drug which acquires its activity through inhibiting the viral reverse transcriptase. The crystal structure of this biologically important drug is not known. An X-ray powder diffraction analysis of abacavir hemisulfate, however, has been reported (Monger & Varlashkin, 2005). The structure of abacavir (Fig. 1) contains wide cylindrical channels that are parallel to the c axis (Fig. 2). The lattice is held together by hydrogen bonds (details are in Table 1). The absolute configuration around C9 and C11 of abacavir was assigned as R and S, respectively, based on the synthetic procedures. The large voids in the lattice of abacavir appear to hold methanol solvate molecules but attempts to model the solvent were unsuccessful.