organic compounds
N-(4-Methoxyphenyl)-N′-(5-nitro-1,3-thiazol-2-yl)urea
aDepartment of Chemistry, University of Toronto, 80 St George Street, Toronto, Ontario, Canada M5S 3H6, bPET Centre, Centre for Addiction and Mental Health and Department of Psychiatry, University of Toronto, 250 College Street, Toronto, Ontario, Canada M5T 1R8, and cDepartments of Chemistry and Chemical Biology, and Medical Physics and Applied Radiation Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1
*Correspondence e-mail: alough@chem.utoronto.ca
The title compound, C11H10N4O4S, is a derivative of N-(4-methoxybenzyl)-N′-(5-nitro-1,3-thiazol-2-yl)urea (AR-A014418), a known glycogen synthase kinase 3β (GSK-3β) inhibitor. All non-H atoms in the molecule are essentially coplanar, with an r.m.s. deviation of 0.045 Å and a maximum deviation of 0.115 (2) Å for the carbonyl O atom. In the molecules are linked via N—H⋯O hydrogen bonds into one-dimensional chains along [101].
Related literature
For background information on the preparation and activity of AR-A014418, see: Bhat et al. (2003); Inestrosa et al. (2006). For the radiolabelling procedure of AR-A014418 with carbon-11, see: Vasdev et al. (2005). For the of AR-A014418, see: Vasdev et al. (2007).
Experimental
Crystal data
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Refinement
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Data collection: COLLECT (Nonius, 2002); cell DENZO-SMN (Otwinowski & Minor, 1997); data reduction: DENZO-SMN; program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2009); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).
Supporting information
https://doi.org/10.1107/S1600536810032186/su2205sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536810032186/su2205Isup2.hkl
The title compound, C11H10N4O4S, was obtained by heating equimolar amounts of 2-amino-5-nitrothiazole (0.65 mmol) and 4-methoxyphenyl isocyanate (0.65 mmol) in dry N,N-dimethyl formamide (5 ml) in a Biotage Initiator Microwave for 1 h at 403 K under nitrogen. Upon cooling, the reaction mixture was partitioned between ethyl acetate and water and the aqueous layer was further extracted with more ethyl acetate (15 ml). The combined organic layers were washed with brine (3 × 30 ml), dried (MgSO4), filtered, and concentrated prior to purification by silica δ 11.75 (s, 1 H, NH), 9.28 (s, 1H, NH), 8.53 (s, 1H, thiazole), 7.41 (d, J = 8.9 Hz, 2H, Ar), 6.91 (d, J = 8.9 Hz, 2H, Ar), 3.73 (s, 3H, CH3). HRMS (ESI) m/z calcd for C11H11N4O4S, 295.0495; found 295.0483 (M++H), m.p. = 454–456 K.
(Biotage Isolera Flash system, 98% dichloromethane and 2% methanol). C11H10N4O4S was obtained as a red solid in 39% yield (not optimized). X-ray quality crystals were obtained by slow evaporation of a solution of the title compound in ethyl acetate/hexane (50/50) containing 5% ethanol. 1H NMR (DMSO d6, 400 MHz)H atoms bonded to C atoms were placed in calculated positions with C—H = 0.95Å or 0.98Å for methyl groups and included in the
with Uiso(H) = 1.2Ueq(C) or 1.2Ueq(Cmethyl). H atoms bonded to N atoms were refined independently with isotropic displacement parameters.N-(4-methoxybenzyl)-N'--(5-nitro-1,3-thiazol-2-yl)urea (AR-A014418, Bhat et al., 2003) is a selective glycogen synthase kinase-3β (GSK-3β) inhibitor (Inestrosa et al., 2006). Our initial work on AR-A014418 was to radiolabel this compound with carbon-11 at the methoxy position for positron emission tomography (PET) imaging of brain pathologies (Vasdev et al., 2005). To our surprise, [11C]-AR-A014418 had insignificant brain uptake in rodents despite literature precedence (Bhat et al., 2003). To further understand the role of AR-A014418 and GSK-3β, a single-crystal X-ray structure of AR-A014418 was obtained (Vasdev et al., 2007) and overlaid with the structural determination of the of GSK-3β and AR-A014418 (Bhat et al., 2003). For that structure, the benyzl ring was bent out of the binding pocket of the kinase. We now endeavour to explore the binding affinity of an analogous molecule which has reduced flexibility (i.e. the benzyl group is replaced with a phenyl group). Biological assays are underway to determine whether the increased rigidity decreases the binding affinity for GSK-3β. Data from these biological studies as well as the determinations will assist in designing future ligands for imaging GSK-3β with PET.
The molecular structure of the title compound is shown in Fig. 1. All non-hydrogen atoms in the molecule are essentially co-planar with a r.m.s. deviation of 0.045 Å and a maximum deviation of 0.115 (2)Å for atom O1.
In the crystal symmetry related molecules are linked via N—H···O hydrogen bonds, to form one-dimensional chains propagating along [101] (Table 1, Fig. 2).
For background information on the preparation and activity of AR-A014418, see: Bhat et al. (2003); Inestrosa et al. (2006). For the radiolabelling procedure of AR-A014418 with carbon-11, see: Vasdev et al. (2005). For the
of AR-A014418, see: Vasdev et al. (2007).Data collection: COLLECT (Nonius, 2002); cell
DENZO-SMN (Otwinowski & Minor, 1997); data reduction: DENZO-SMN (Otwinowski & Minor, 1997); program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2009); software used to prepare material for publication: SHELXTL (Version 6.1; Sheldrick, 2008).C11H10N4O4S | F(000) = 608 |
Mr = 294.29 | Dx = 1.571 Mg m−3 |
Monoclinic, P21/n | Melting point: 454 K |
Hall symbol: -P 2yn | Mo Kα radiation, λ = 0.71073 Å |
a = 6.8740 (3) Å | Cell parameters from 3592 reflections |
b = 12.5840 (7) Å | θ = 2.6–27.5° |
c = 14.6861 (5) Å | µ = 0.28 mm−1 |
β = 101.622 (3)° | T = 150 K |
V = 1244.34 (10) Å3 | Block, red |
Z = 4 | 0.28 × 0.24 × 0.22 mm |
Nonius KappaCCD diffractometer | 2825 independent reflections |
Radiation source: fine-focus sealed tube | 1979 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.053 |
Detector resolution: 9 pixels mm-1 | θmax = 27.5°, θmin = 2.8° |
φ scans and ω scans with κ offsets | h = −8→8 |
Absorption correction: multi-scan (SORTAV; Blessing, 1995) | k = −14→16 |
Tmin = 0.718, Tmax = 0.948 | l = −17→19 |
8106 measured reflections |
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)] = 0.050 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.145 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.07 | w = 1/[σ2(Fo2) + (0.0755P)2 + 0.3053P] where P = (Fo2 + 2Fc2)/3 |
2825 reflections | (Δ/σ)max < 0.001 |
190 parameters | Δρmax = 0.38 e Å−3 |
0 restraints | Δρmin = −0.51 e Å−3 |
C11H10N4O4S | V = 1244.34 (10) Å3 |
Mr = 294.29 | Z = 4 |
Monoclinic, P21/n | Mo Kα radiation |
a = 6.8740 (3) Å | µ = 0.28 mm−1 |
b = 12.5840 (7) Å | T = 150 K |
c = 14.6861 (5) Å | 0.28 × 0.24 × 0.22 mm |
β = 101.622 (3)° |
Nonius KappaCCD diffractometer | 2825 independent reflections |
Absorption correction: multi-scan (SORTAV; Blessing, 1995) | 1979 reflections with I > 2σ(I) |
Tmin = 0.718, Tmax = 0.948 | Rint = 0.053 |
8106 measured reflections |
R[F2 > 2σ(F2)] = 0.050 | 0 restraints |
wR(F2) = 0.145 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.07 | Δρmax = 0.38 e Å−3 |
2825 reflections | Δρmin = −0.51 e Å−3 |
190 parameters |
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 expr ession 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. |
x | y | z | Uiso*/Ueq | ||
S1 | 0.12900 (8) | 0.68571 (5) | 0.41433 (3) | 0.0246 (2) | |
O1 | 0.2254 (2) | 0.48461 (14) | 0.47569 (10) | 0.0306 (4) | |
O2 | 0.5006 (3) | 0.00530 (13) | 0.62455 (11) | 0.0340 (4) | |
O3 | −0.0126 (3) | 0.97318 (14) | 0.33409 (11) | 0.0347 (4) | |
O4 | 0.0063 (3) | 0.82488 (15) | 0.25900 (11) | 0.0367 (5) | |
N1 | 0.2026 (3) | 0.79137 (16) | 0.57084 (12) | 0.0277 (5) | |
N2 | 0.2668 (3) | 0.61085 (16) | 0.58904 (13) | 0.0268 (5) | |
H2N | 0.327 (4) | 0.627 (2) | 0.6449 (19) | 0.042 (8)* | |
N3 | 0.3514 (3) | 0.44014 (16) | 0.62860 (13) | 0.0253 (5) | |
H3N | 0.380 (4) | 0.466 (2) | 0.6845 (19) | 0.037 (8)* | |
N4 | 0.0257 (3) | 0.87648 (16) | 0.33258 (13) | 0.0270 (5) | |
C1 | 0.0930 (3) | 0.82155 (19) | 0.41566 (14) | 0.0232 (5) | |
C2 | 0.1399 (3) | 0.8632 (2) | 0.50308 (15) | 0.0267 (5) | |
H2A | 0.1292 | 0.9369 | 0.5153 | 0.032* | |
C3 | 0.2033 (3) | 0.69504 (18) | 0.53334 (15) | 0.0224 (5) | |
C4 | 0.2790 (3) | 0.50759 (19) | 0.55815 (15) | 0.0243 (5) | |
C5 | 0.3832 (3) | 0.32879 (18) | 0.62462 (15) | 0.0223 (5) | |
C6 | 0.3583 (3) | 0.2717 (2) | 0.54193 (15) | 0.0245 (5) | |
H6A | 0.3153 | 0.3064 | 0.4839 | 0.029* | |
C7 | 0.3970 (3) | 0.1640 (2) | 0.54544 (15) | 0.0258 (5) | |
H7A | 0.3791 | 0.1245 | 0.4892 | 0.031* | |
C8 | 0.4620 (3) | 0.11186 (19) | 0.63008 (15) | 0.0253 (5) | |
C9 | 0.4842 (4) | 0.1688 (2) | 0.71214 (16) | 0.0281 (6) | |
H9A | 0.5265 | 0.1342 | 0.7702 | 0.034* | |
C10 | 0.4439 (4) | 0.2773 (2) | 0.70889 (16) | 0.0277 (5) | |
H10A | 0.4583 | 0.3164 | 0.7651 | 0.033* | |
C11 | 0.5519 (4) | −0.0525 (2) | 0.70992 (17) | 0.0360 (6) | |
H11A | 0.5715 | −0.1276 | 0.6965 | 0.054* | |
H11B | 0.4446 | −0.0460 | 0.7445 | 0.054* | |
H11C | 0.6749 | −0.0236 | 0.7472 | 0.054* |
U11 | U22 | U33 | U12 | U13 | U23 | |
S1 | 0.0269 (3) | 0.0260 (4) | 0.0198 (3) | 0.0001 (2) | 0.0024 (2) | −0.0017 (2) |
O1 | 0.0405 (10) | 0.0273 (10) | 0.0225 (9) | 0.0016 (8) | 0.0028 (7) | −0.0024 (7) |
O2 | 0.0482 (11) | 0.0242 (9) | 0.0304 (9) | 0.0047 (8) | 0.0097 (8) | 0.0018 (7) |
O3 | 0.0418 (11) | 0.0279 (10) | 0.0335 (10) | 0.0046 (8) | 0.0057 (8) | 0.0080 (8) |
O4 | 0.0450 (11) | 0.0437 (12) | 0.0193 (8) | 0.0073 (9) | 0.0015 (7) | −0.0019 (8) |
N1 | 0.0368 (12) | 0.0251 (11) | 0.0214 (10) | 0.0020 (9) | 0.0059 (8) | −0.0009 (8) |
N2 | 0.0352 (12) | 0.0240 (11) | 0.0205 (10) | 0.0011 (9) | 0.0040 (8) | −0.0033 (9) |
N3 | 0.0315 (11) | 0.0238 (11) | 0.0204 (10) | 0.0003 (9) | 0.0048 (8) | −0.0014 (9) |
N4 | 0.0239 (11) | 0.0318 (12) | 0.0250 (10) | 0.0008 (9) | 0.0041 (8) | 0.0044 (9) |
C1 | 0.0226 (12) | 0.0249 (13) | 0.0223 (11) | 0.0005 (10) | 0.0049 (9) | 0.0036 (10) |
C2 | 0.0310 (13) | 0.0242 (13) | 0.0246 (12) | 0.0003 (10) | 0.0046 (9) | −0.0005 (10) |
C3 | 0.0241 (12) | 0.0231 (13) | 0.0206 (11) | −0.0022 (9) | 0.0063 (8) | −0.0015 (9) |
C4 | 0.0243 (12) | 0.0251 (13) | 0.0247 (12) | −0.0007 (10) | 0.0079 (9) | −0.0009 (10) |
C5 | 0.0206 (11) | 0.0247 (13) | 0.0226 (11) | −0.0003 (9) | 0.0070 (8) | 0.0002 (10) |
C6 | 0.0233 (12) | 0.0285 (14) | 0.0219 (11) | 0.0006 (10) | 0.0051 (9) | 0.0007 (10) |
C7 | 0.0253 (12) | 0.0293 (14) | 0.0233 (11) | −0.0025 (10) | 0.0063 (9) | −0.0030 (10) |
C8 | 0.0257 (12) | 0.0214 (12) | 0.0309 (12) | 0.0006 (10) | 0.0105 (9) | 0.0002 (10) |
C9 | 0.0310 (13) | 0.0314 (14) | 0.0231 (11) | 0.0006 (11) | 0.0087 (9) | 0.0044 (10) |
C10 | 0.0338 (14) | 0.0273 (13) | 0.0235 (12) | 0.0006 (11) | 0.0097 (10) | −0.0020 (10) |
C11 | 0.0477 (16) | 0.0261 (14) | 0.0345 (14) | 0.0045 (12) | 0.0089 (11) | 0.0074 (11) |
S1—C3 | 1.723 (2) | C1—C2 | 1.364 (3) |
S1—C1 | 1.728 (2) | C2—H2A | 0.9500 |
O1—C4 | 1.227 (3) | C5—C10 | 1.385 (3) |
O2—C8 | 1.373 (3) | C5—C6 | 1.391 (3) |
O2—C11 | 1.431 (3) | C6—C7 | 1.381 (3) |
O3—N4 | 1.246 (3) | C6—H6A | 0.9500 |
O4—N4 | 1.245 (2) | C7—C8 | 1.397 (3) |
N1—C3 | 1.332 (3) | C7—H7A | 0.9500 |
N1—C2 | 1.349 (3) | C8—C9 | 1.384 (3) |
N2—C3 | 1.356 (3) | C9—C10 | 1.391 (3) |
N2—C4 | 1.384 (3) | C9—H9A | 0.9500 |
N2—H2N | 0.86 (3) | C10—H10A | 0.9500 |
N3—C4 | 1.353 (3) | C11—H11A | 0.9800 |
N3—C5 | 1.421 (3) | C11—H11B | 0.9800 |
N3—H3N | 0.87 (3) | C11—H11C | 0.9800 |
N4—C1 | 1.398 (3) | ||
C3—S1—C1 | 86.27 (11) | C10—C5—C6 | 120.0 (2) |
C8—O2—C11 | 117.49 (19) | C10—C5—N3 | 116.5 (2) |
C3—N1—C2 | 109.40 (18) | C6—C5—N3 | 123.5 (2) |
C3—N2—C4 | 124.68 (19) | C7—C6—C5 | 119.0 (2) |
C3—N2—H2N | 115.2 (19) | C7—C6—H6A | 120.5 |
C4—N2—H2N | 118.6 (19) | C5—C6—H6A | 120.5 |
C4—N3—C5 | 128.5 (2) | C6—C7—C8 | 121.3 (2) |
C4—N3—H3N | 117.8 (18) | C6—C7—H7A | 119.4 |
C5—N3—H3N | 113.6 (18) | C8—C7—H7A | 119.4 |
O4—N4—O3 | 122.61 (19) | O2—C8—C9 | 124.7 (2) |
O4—N4—C1 | 117.3 (2) | O2—C8—C7 | 115.9 (2) |
O3—N4—C1 | 120.09 (19) | C9—C8—C7 | 119.4 (2) |
C2—C1—N4 | 127.3 (2) | C8—C9—C10 | 119.5 (2) |
C2—C1—S1 | 112.58 (17) | C8—C9—H9A | 120.3 |
N4—C1—S1 | 120.16 (17) | C10—C9—H9A | 120.3 |
N1—C2—C1 | 114.6 (2) | C5—C10—C9 | 120.8 (2) |
N1—C2—H2A | 122.7 | C5—C10—H10A | 119.6 |
C1—C2—H2A | 122.7 | C9—C10—H10A | 119.6 |
N1—C3—N2 | 119.29 (19) | O2—C11—H11A | 109.5 |
N1—C3—S1 | 117.15 (17) | O2—C11—H11B | 109.5 |
N2—C3—S1 | 123.53 (17) | H11A—C11—H11B | 109.5 |
O1—C4—N3 | 126.7 (2) | O2—C11—H11C | 109.5 |
O1—C4—N2 | 121.2 (2) | H11A—C11—H11C | 109.5 |
N3—C4—N2 | 112.05 (19) | H11B—C11—H11C | 109.5 |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2N···O4i | 0.86 (3) | 1.97 (3) | 2.817 (3) | 168 (3) |
N3—H3N···O3i | 0.87 (3) | 2.30 (3) | 3.168 (2) | 174 (2) |
Symmetry code: (i) x+1/2, −y+3/2, z+1/2. |
Experimental details
Crystal data | |
Chemical formula | C11H10N4O4S |
Mr | 294.29 |
Crystal system, space group | Monoclinic, P21/n |
Temperature (K) | 150 |
a, b, c (Å) | 6.8740 (3), 12.5840 (7), 14.6861 (5) |
β (°) | 101.622 (3) |
V (Å3) | 1244.34 (10) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.28 |
Crystal size (mm) | 0.28 × 0.24 × 0.22 |
Data collection | |
Diffractometer | Nonius KappaCCD |
Absorption correction | Multi-scan (SORTAV; Blessing, 1995) |
Tmin, Tmax | 0.718, 0.948 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 8106, 2825, 1979 |
Rint | 0.053 |
(sin θ/λ)max (Å−1) | 0.649 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.050, 0.145, 1.07 |
No. of reflections | 2825 |
No. of parameters | 190 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.38, −0.51 |
Computer programs: COLLECT (Nonius, 2002), DENZO-SMN (Otwinowski & Minor, 1997), SIR92 (Altomare et al., 1994), SHELXL97 (Sheldrick, 2008), PLATON (Spek, 2009), SHELXTL (Version 6.1; Sheldrick, 2008).
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2N···O4i | 0.86 (3) | 1.97 (3) | 2.817 (3) | 168 (3) |
N3—H3N···O3i | 0.87 (3) | 2.30 (3) | 3.168 (2) | 174 (2) |
Symmetry code: (i) x+1/2, −y+3/2, z+1/2. |
Acknowledgements
We thank Dr Sylvain Houle for allowing the CAMH PET Centre facilities to be used for this research. Funding was provided by the Ontario Ministry for Research and Innovation (Early Researcher Award to NV).
References
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N-(4-methoxybenzyl)-N'--(5-nitro-1,3-thiazol-2-yl)urea (AR-A014418, Bhat et al., 2003) is a selective glycogen synthase kinase-3β (GSK-3β) inhibitor (Inestrosa et al., 2006). Our initial work on AR-A014418 was to radiolabel this compound with carbon-11 at the methoxy position for positron emission tomography (PET) imaging of brain pathologies (Vasdev et al., 2005). To our surprise, [11C]-AR-A014418 had insignificant brain uptake in rodents despite literature precedence (Bhat et al., 2003). To further understand the role of AR-A014418 and GSK-3β, a single-crystal X-ray structure of AR-A014418 was obtained (Vasdev et al., 2007) and overlaid with the structural determination of the co-crystal of GSK-3β and AR-A014418 (Bhat et al., 2003). For that structure, the benyzl ring was bent out of the binding pocket of the kinase. We now endeavour to explore the binding affinity of an analogous molecule which has reduced flexibility (i.e. the benzyl group is replaced with a phenyl group). Biological assays are underway to determine whether the increased rigidity decreases the binding affinity for GSK-3β. Data from these biological studies as well as the crystal structure determinations will assist in designing future ligands for imaging GSK-3β with PET.
The molecular structure of the title compound is shown in Fig. 1. All non-hydrogen atoms in the molecule are essentially co-planar with a r.m.s. deviation of 0.045 Å and a maximum deviation of 0.115 (2)Å for atom O1.
In the crystal symmetry related molecules are linked via N—H···O hydrogen bonds, to form one-dimensional chains propagating along [101] (Table 1, Fig. 2).