Literature DB >> 25484692

Crystal structure of 5,5'-[(4-fluoro-phen-yl)methyl-ene]bis-[6-amino-1,3-di-methyl-pyrimidine-2,4(1H,3H)-dione].

Naresh Sharma1, Goutam Brahmachari2, Bubun Banerjee2, Rajni Kant1, Vivek K Gupta1.   

Abstract

In the title mol-ecule, C19H21FN6O4, the dihedral angles between the benzene ring and essentially planar pyrimidine rings [maximum deviations of 0.036 (2) and 0.056 (2) Å] are 73.32 (7) and 63.81 (8)°. The dihedral angle between the mean planes of the pyrimidine rings is 61.43 (6)°. In the crystal, N-H⋯O hydrogen bonds link mol-ecules, forming a two-dimensional network parallel to (001) and in combination with weak C-H⋯O hydrogen bonds, a three-dimensional network is formed. Weak C-H⋯π inter-actions and π-π inter-actions, with a centroid-centroid distance of 3.599 (2) Å are also observed.

Entities:  

Keywords:  biological activity; bis-uracil derivatives; crystal structure; pyrimidine scaffolds; uracil derivatives

Year:  2014        PMID: 25484692      PMCID: PMC4257154          DOI: 10.1107/S1600536814019886

Source DB:  PubMed          Journal:  Acta Crystallogr Sect E Struct Rep Online        ISSN: 1600-5368


Related literature

For the biological activity of uracil derivatives, see: Muller et al. (1993 ▶); Buckle et al. (1994 ▶). For drugs containing purine moieties, see: Zhi et al. (2003 ▶); Devi & Bhuyan (2005 ▶). For the biological activity of pyrimidine scaffolds, see: Makarov et al. (2005 ▶); Deshmukh et al. (2009 ▶); Ibrahim & El-Metwally (2010 ▶). For the synthesis of bis-uracil derivatives, see: Karimi et al. (2013 ▶). For a related structure, see: Das et al. (2009 ▶).

Experimental

Crystal data

C19H21FN6O4 M = 416.42 Orthorhombic, a = 14.6208 (6) Å b = 11.3324 (7) Å c = 22.6410 (12) Å V = 3751.4 (3) Å3 Z = 8 Mo Kα radiation μ = 0.11 mm−1 T = 293 K 0.30 × 0.20 × 0.20 mm

Data collection

Oxford Diffraction Xcalibur Sapphire3 diffractometer Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2010 ▶) T min = 0.862, T max = 1.000 9655 measured reflections 3665 independent reflections 2208 reflections with I > 2σ(I) R int = 0.047

Refinement

R[F 2 > 2σ(F 2)] = 0.052 wR(F 2) = 0.130 S = 1.04 3665 reflections 291 parameters H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.19 e Å−3 Δρmin = −0.20 e Å−3

Data collection: CrysAlis PRO (Oxford Diffraction, 2010 ▶); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012 ▶); software used to prepare material for publication: PLATON (Spek, 2009 ▶). Crystal structure: contains datablock(s) I, New_Global_Publ_Block. DOI: 10.1107/S1600536814019886/lh5725sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536814019886/lh5725Isup2.hkl Click here for additional data file. Supporting information file. DOI: 10.1107/S1600536814019886/lh5725Isup3.cml Click here for additional data file. . DOI: 10.1107/S1600536814019886/lh5725fig1.tif The mol­ecular structure with displacement ellipsoids drawn at the 40% probability level. H atoms are shown as small spheres of arbitrary radii. Click here for additional data file. a . DOI: 10.1107/S1600536814019886/lh5725fig2.tif Part of the crystal structure viewed along the a axis. Hydrogen bonds are shown as dashed lines. CCDC reference: 973485 Additional supporting information: crystallographic information; 3D view; checkCIF report
C19H21FN6O4F(000) = 1744
Mr = 416.42Dx = 1.475 Mg m3
Orthorhombic, PbcaMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2abCell parameters from 2766 reflections
a = 14.6208 (6) Åθ = 4.0–29.0°
b = 11.3324 (7) ŵ = 0.11 mm1
c = 22.6410 (12) ÅT = 293 K
V = 3751.4 (3) Å3Rectangular, white
Z = 80.30 × 0.20 × 0.20 mm
Oxford Diffraction Xcalibur Sapphire3 diffractometer3665 independent reflections
Radiation source: fine-focus sealed tube2208 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.047
Detector resolution: 16.1049 pixels mm-1θmax = 26.0°, θmin = 3.4°
ω scansh = −17→18
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2010)k = −13→10
Tmin = 0.862, Tmax = 1.000l = −27→27
9655 measured reflections
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.052Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.130H atoms treated by a mixture of independent and constrained refinement
S = 1.04w = 1/[σ2(Fo2) + (0.0402P)2 + 0.280P] where P = (Fo2 + 2Fc2)/3
3665 reflections(Δ/σ)max < 0.001
291 parametersΔρmax = 0.19 e Å3
0 restraintsΔρmin = −0.20 e Å3
Experimental. CrysAlis PRO, Agilent Technologies, Version 1.171.36.28 (release 01–02-2013 CrysAlis171. NET) (compiled Feb 1 2013,16:14:44) Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm.
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.
xyzUiso*/Ueq
O3A0.12040 (11)0.70286 (16)0.47999 (8)0.0448 (5)
O3A'0.41972 (12)0.90382 (17)0.35851 (8)0.0481 (5)
N30.21150 (13)0.67789 (19)0.56011 (9)0.0385 (5)
N1'0.27279 (15)0.63863 (19)0.28860 (9)0.0445 (6)
C5'0.28708 (16)0.7846 (2)0.36460 (10)0.0336 (6)
N10.35782 (12)0.7609 (2)0.56448 (9)0.0388 (5)
C50.26609 (15)0.7945 (2)0.47801 (10)0.0317 (6)
N180.16272 (16)0.6468 (2)0.36253 (12)0.0445 (6)
O20.29971 (14)0.6586 (2)0.64250 (9)0.0697 (7)
C40.25464 (16)0.8542 (2)0.41822 (10)0.0337 (6)
H40.29920.91870.42030.040*
C60.34765 (15)0.8050 (2)0.50801 (10)0.0328 (6)
C6'0.24099 (18)0.6903 (2)0.34020 (11)0.0374 (6)
N150.42224 (15)0.8593 (2)0.48533 (11)0.0410 (6)
C70.16385 (16)0.9204 (2)0.41091 (11)0.0323 (6)
C3A'0.37186 (18)0.8189 (2)0.34004 (11)0.0393 (6)
N3'0.40473 (15)0.7555 (2)0.29207 (9)0.0465 (6)
C3A0.19584 (17)0.7257 (2)0.50409 (11)0.0366 (6)
F20−0.06866 (11)1.12341 (16)0.39325 (9)0.0834 (7)
C20.28952 (18)0.6969 (3)0.59256 (12)0.0437 (7)
O2'0.39032 (16)0.60699 (19)0.22495 (9)0.0746 (7)
C2'0.3585 (2)0.6640 (3)0.26558 (12)0.0503 (8)
C130.44207 (17)0.7825 (3)0.59804 (11)0.0499 (8)
H13A0.49180.74040.58010.075*
H13B0.43410.75580.63800.075*
H13C0.45540.86550.59800.075*
C120.13307 (17)0.9921 (2)0.45682 (12)0.0441 (7)
H120.16510.99320.49230.053*
C80.11561 (17)0.9230 (2)0.35843 (12)0.0405 (7)
H80.13620.87860.32650.049*
C100.00938 (18)1.0575 (2)0.39853 (15)0.0505 (8)
C110.05596 (19)1.0616 (3)0.45075 (14)0.0510 (8)
H110.03631.10980.48150.061*
C90.03704 (18)0.9907 (2)0.35245 (14)0.0502 (8)
H90.00400.99000.31740.060*
C140.14123 (18)0.6033 (3)0.58682 (13)0.0536 (8)
H14A0.16770.55790.61830.080*
H14B0.11670.55090.55750.080*
H14C0.09310.65190.60220.080*
C170.4962 (2)0.7837 (3)0.26916 (14)0.0683 (10)
H17A0.54090.73510.28850.102*
H17B0.50960.86530.27660.102*
H17C0.49790.76900.22740.102*
C160.2188 (2)0.5502 (3)0.25638 (13)0.0626 (9)
H16A0.23780.54860.21580.094*
H16B0.15510.57040.25850.094*
H16C0.22830.47390.27380.094*
H600.1393 (18)0.576 (3)0.3509 (12)0.057 (9)*
H500.1483 (16)0.675 (2)0.4000 (13)0.049 (8)*
H400.4206 (17)0.880 (2)0.4441 (13)0.060 (9)*
H300.476 (2)0.856 (3)0.5011 (13)0.069 (10)*
U11U22U33U12U13U23
O3A0.0359 (10)0.0609 (13)0.0376 (10)−0.0095 (9)−0.0013 (8)0.0047 (10)
O3A'0.0439 (10)0.0557 (12)0.0446 (11)−0.0059 (10)0.0066 (9)0.0039 (11)
N30.0360 (11)0.0470 (14)0.0326 (11)−0.0023 (10)0.0028 (10)0.0068 (12)
N1'0.0635 (15)0.0365 (13)0.0335 (12)0.0040 (11)0.0064 (11)0.0008 (11)
C5'0.0385 (14)0.0364 (15)0.0259 (12)0.0042 (12)0.0025 (11)0.0036 (12)
N10.0311 (11)0.0530 (15)0.0322 (11)0.0047 (10)−0.0026 (9)0.0040 (12)
C50.0263 (12)0.0375 (15)0.0313 (12)0.0021 (11)0.0015 (11)0.0023 (12)
N180.0511 (15)0.0398 (15)0.0424 (14)−0.0043 (12)0.0052 (13)−0.0045 (13)
O20.0658 (14)0.1013 (19)0.0420 (12)−0.0168 (13)−0.0105 (11)0.0299 (13)
C40.0340 (13)0.0350 (15)0.0320 (13)0.0015 (12)−0.0005 (11)0.0012 (12)
C60.0320 (13)0.0355 (14)0.0310 (13)0.0041 (11)−0.0008 (11)−0.0001 (12)
C6'0.0450 (15)0.0349 (15)0.0324 (13)0.0090 (13)0.0004 (12)0.0048 (13)
N150.0305 (12)0.0565 (15)0.0361 (13)−0.0035 (11)−0.0025 (11)0.0055 (12)
C70.0302 (13)0.0315 (14)0.0352 (14)0.0001 (11)0.0000 (11)0.0043 (12)
C3A'0.0466 (16)0.0409 (16)0.0306 (13)0.0059 (13)0.0038 (13)0.0092 (14)
N3'0.0534 (14)0.0510 (15)0.0349 (12)0.0043 (12)0.0139 (11)0.0073 (12)
C3A0.0380 (14)0.0399 (16)0.0320 (13)0.0041 (12)0.0000 (12)−0.0005 (13)
F200.0666 (12)0.0682 (13)0.1154 (17)0.0373 (10)−0.0044 (11)0.0026 (13)
C20.0443 (16)0.0500 (18)0.0366 (15)0.0012 (14)0.0019 (13)0.0050 (15)
O2'0.1086 (18)0.0632 (15)0.0521 (13)0.0067 (13)0.0384 (13)−0.0086 (13)
C2'0.071 (2)0.0446 (18)0.0354 (15)0.0101 (16)0.0139 (15)0.0097 (15)
C130.0360 (14)0.078 (2)0.0360 (14)0.0019 (15)−0.0102 (12)0.0074 (16)
C120.0468 (16)0.0436 (17)0.0420 (16)0.0021 (13)0.0006 (13)−0.0035 (14)
C80.0459 (15)0.0344 (15)0.0414 (15)0.0067 (12)−0.0041 (13)0.0006 (13)
C100.0418 (16)0.0333 (16)0.076 (2)0.0096 (13)0.0004 (16)0.0073 (17)
C110.0578 (18)0.0398 (17)0.0554 (19)0.0045 (14)0.0075 (16)−0.0067 (16)
C90.0519 (17)0.0431 (17)0.0556 (18)0.0095 (14)−0.0143 (15)0.0051 (16)
C140.0539 (18)0.060 (2)0.0474 (17)−0.0143 (15)0.0038 (14)0.0125 (17)
C170.0648 (19)0.082 (3)0.0577 (18)0.0027 (18)0.0337 (16)0.008 (2)
C160.095 (3)0.0499 (19)0.0431 (17)−0.0025 (18)0.0072 (17)−0.0099 (17)
O3A—C3A1.257 (3)C7—C121.394 (3)
O3A'—C3A'1.261 (3)C3A'—N3'1.388 (3)
N3—C21.374 (3)N3'—C2'1.376 (3)
N3—C3A1.398 (3)N3'—C171.470 (3)
N3—C141.462 (3)F20—C101.369 (3)
N1'—C2'1.387 (3)O2'—C2'1.217 (3)
N1'—C6'1.387 (3)C13—H13A0.9600
N1'—C161.469 (3)C13—H13B0.9600
C5'—C6'1.379 (3)C13—H13C0.9600
C5'—C3A'1.413 (3)C12—C111.382 (4)
C5'—C41.523 (3)C12—H120.9300
N1—C61.381 (3)C8—C91.388 (3)
N1—C21.388 (3)C8—H80.9300
N1—C131.468 (3)C10—C91.351 (4)
C5—C61.377 (3)C10—C111.365 (4)
C5—C3A1.419 (3)C11—H110.9300
C5—C41.522 (3)C9—H90.9300
N18—C6'1.345 (3)C14—H14A0.9600
N18—H600.91 (3)C14—H14B0.9600
N18—H500.93 (3)C14—H14C0.9600
O2—C21.220 (3)C17—H17A0.9600
C4—C71.533 (3)C17—H17B0.9600
C4—H40.9800C17—H17C0.9600
C6—N151.354 (3)C16—H16A0.9600
N15—H400.96 (3)C16—H16B0.9600
N15—H300.87 (3)C16—H16C0.9600
C7—C81.382 (3)
C2—N3—C3A124.1 (2)O2—C2—N3122.8 (3)
C2—N3—C14116.9 (2)O2—C2—N1121.5 (3)
C3A—N3—C14119.0 (2)N3—C2—N1115.7 (2)
C2'—N1'—C6'122.1 (2)O2'—C2'—N3'122.8 (3)
C2'—N1'—C16116.1 (2)O2'—C2'—N1'121.3 (3)
C6'—N1'—C16121.8 (2)N3'—C2'—N1'115.9 (2)
C6'—C5'—C3A'119.0 (2)N1—C13—H13A109.5
C6'—C5'—C4124.6 (2)N1—C13—H13B109.5
C3A'—C5'—C4116.4 (2)H13A—C13—H13B109.5
C6—N1—C2122.4 (2)N1—C13—H13C109.5
C6—N1—C13120.6 (2)H13A—C13—H13C109.5
C2—N1—C13117.0 (2)H13B—C13—H13C109.5
C6—C5—C3A118.0 (2)C11—C12—C7121.4 (3)
C6—C5—C4119.7 (2)C11—C12—H12119.3
C3A—C5—C4122.3 (2)C7—C12—H12119.3
C6'—N18—H60122.2 (17)C7—C8—C9121.2 (3)
C6'—N18—H50114.3 (16)C7—C8—H8119.4
H60—N18—H50119 (2)C9—C8—H8119.4
C5—C4—C5'116.4 (2)C9—C10—C11122.6 (3)
C5—C4—C7114.11 (19)C9—C10—F20119.2 (3)
C5'—C4—C7115.9 (2)C11—C10—F20118.2 (3)
C5—C4—H4102.5C10—C11—C12118.3 (3)
C5'—C4—H4102.5C10—C11—H11120.9
C7—C4—H4102.5C12—C11—H11120.9
N15—C6—C5123.3 (2)C10—C9—C8118.8 (3)
N15—C6—N1115.4 (2)C10—C9—H9120.6
C5—C6—N1121.2 (2)C8—C9—H9120.6
N18—C6'—C5'123.3 (2)N3—C14—H14A109.5
N18—C6'—N1'116.6 (2)N3—C14—H14B109.5
C5'—C6'—N1'120.1 (2)H14A—C14—H14B109.5
C6—N15—H40117.4 (16)N3—C14—H14C109.5
C6—N15—H30124 (2)H14A—C14—H14C109.5
H40—N15—H30116 (3)H14B—C14—H14C109.5
C8—C7—C12117.6 (2)N3'—C17—H17A109.5
C8—C7—C4123.0 (2)N3'—C17—H17B109.5
C12—C7—C4119.0 (2)H17A—C17—H17B109.5
O3A'—C3A'—N3'117.6 (2)N3'—C17—H17C109.5
O3A'—C3A'—C5'124.5 (2)H17A—C17—H17C109.5
N3'—C3A'—C5'118.0 (2)H17B—C17—H17C109.5
C2'—N3'—C3A'124.1 (2)N1'—C16—H16A109.5
C2'—N3'—C17117.2 (2)N1'—C16—H16B109.5
C3A'—N3'—C17118.6 (2)H16A—C16—H16B109.5
O3A—C3A—N3117.2 (2)N1'—C16—H16C109.5
O3A—C3A—C5124.6 (2)H16A—C16—H16C109.5
N3—C3A—C5118.2 (2)H16B—C16—H16C109.5
C6—C5—C4—C5'86.2 (3)C5'—C3A'—N3'—C17−175.0 (2)
C3A—C5—C4—C5'−92.6 (3)C2—N3—C3A—O3A−178.5 (2)
C6—C5—C4—C7−134.7 (2)C14—N3—C3A—O3A1.2 (4)
C3A—C5—C4—C746.5 (3)C2—N3—C3A—C52.5 (4)
C6'—C5'—C4—C575.3 (3)C14—N3—C3A—C5−177.9 (2)
C3A'—C5'—C4—C5−102.8 (3)C6—C5—C3A—O3A−175.5 (2)
C6'—C5'—C4—C7−63.1 (3)C4—C5—C3A—O3A3.4 (4)
C3A'—C5'—C4—C7118.8 (2)C6—C5—C3A—N33.5 (4)
C3A—C5—C6—N15173.9 (2)C4—C5—C3A—N3−177.7 (2)
C4—C5—C6—N15−4.9 (4)C3A—N3—C2—O2176.5 (3)
C3A—C5—C6—N1−6.9 (4)C14—N3—C2—O2−3.2 (4)
C4—C5—C6—N1174.3 (2)C3A—N3—C2—N1−4.8 (4)
C2—N1—C6—N15−176.2 (2)C14—N3—C2—N1175.5 (2)
C13—N1—C6—N155.1 (3)C6—N1—C2—O2−180.0 (3)
C2—N1—C6—C54.6 (4)C13—N1—C2—O2−1.3 (4)
C13—N1—C6—C5−174.1 (2)C6—N1—C2—N31.3 (4)
C3A'—C5'—C6'—N18176.0 (2)C13—N1—C2—N3−179.9 (2)
C4—C5'—C6'—N18−2.1 (4)C3A'—N3'—C2'—O2'−177.2 (3)
C3A'—C5'—C6'—N1'−6.9 (4)C17—N3'—C2'—O2'0.2 (4)
C4—C5'—C6'—N1'175.0 (2)C3A'—N3'—C2'—N1'1.8 (4)
C2'—N1'—C6'—N18−171.0 (2)C17—N3'—C2'—N1'179.3 (2)
C16—N1'—C6'—N186.6 (4)C6'—N1'—C2'—O2'170.1 (2)
C2'—N1'—C6'—C5'11.7 (4)C16—N1'—C2'—O2'−7.6 (4)
C16—N1'—C6'—C5'−170.7 (2)C6'—N1'—C2'—N3'−8.9 (4)
C5—C4—C7—C8−142.5 (2)C16—N1'—C2'—N3'173.4 (2)
C5'—C4—C7—C8−3.2 (3)C8—C7—C12—C111.4 (4)
C5—C4—C7—C1244.9 (3)C4—C7—C12—C11174.4 (2)
C5'—C4—C7—C12−175.8 (2)C12—C7—C8—C9−2.7 (4)
C6'—C5'—C3A'—O3A'179.7 (2)C4—C7—C8—C9−175.4 (2)
C4—C5'—C3A'—O3A'−2.0 (4)C9—C10—C11—C12−1.6 (4)
C6'—C5'—C3A'—N3'0.1 (4)F20—C10—C11—C12177.9 (2)
C4—C5'—C3A'—N3'178.3 (2)C7—C12—C11—C100.7 (4)
O3A'—C3A'—N3'—C2'−177.2 (2)C11—C10—C9—C80.3 (4)
C5'—C3A'—N3'—C2'2.4 (4)F20—C10—C9—C8−179.2 (2)
O3A'—C3A'—N3'—C175.4 (3)C7—C8—C9—C101.9 (4)
D—H···AD—HH···AD···AD—H···A
N15—H40···O3A0.96 (3)1.96 (3)2.916 (3)174 (2)
N18—H50···O3A0.93 (3)1.88 (3)2.803 (3)170 (2)
N15—H30···O3Ai0.86 (3)2.26 (3)3.083 (3)161 (3)
N18—H60···O3Aii0.91 (3)2.14 (3)3.007 (3)159 (2)
C13—H13A···O3Ai0.962.413.154 (3)134
C13—H13A···Cgiii0.962.983.744 (3)138
Table 1

Hydrogen-bond geometry (Å, °)

Cg is the centroid of the C7–C12 ring.

D—H⋯A D—HH⋯A DA D—H⋯A
N15—H40⋯O3A0.96 (3)1.96 (3)2.916 (3)174 (2)
N18—H50⋯O3A 0.93 (3)1.88 (3)2.803 (3)170 (2)
N15—H30⋯O3A i 0.86 (3)2.26 (3)3.083 (3)161 (3)
N18—H60⋯O3Aii 0.91 (3)2.14 (3)3.007 (3)159 (2)
C13—H13A⋯O3A i 0.962.413.154 (3)134
C13—H13ACg iii 0.962.983.744 (3)138

Symmetry codes: (i) ; (ii) ; (iii) .

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Authors:  George M Sheldrick
Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

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Authors:  M B Deshmukh; S M Salunkhe; D R Patil; P V Anbhule
Journal:  Eur J Med Chem       Date:  2008-10-26       Impact factor: 6.514

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Journal:  Eur J Med Chem       Date:  2009-12-21       Impact factor: 6.514

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Journal:  J Med Chem       Date:  2003-06-19       Impact factor: 7.446

8.  Structure validation in chemical crystallography.

Authors:  Anthony L Spek
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-01-20
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