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organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 66| Part 11| November 2010| Page o2955
https://doi.org/10.1107/S1600536810042753

N-(2-Chloro­pyrimidin-4-yl)-N,2-di­methyl-2H-indazol-6-amine

Hao-Fei Qi,a Bing-Ni Liu,b* Mo Liub and Deng-Ke Liub

aMaterials Science and Engineering, Tianjin Polytechnic University, Tianjin 300160, People's Republic of China, and bTianjin Institute of Pharmaceutical Research, Tianjin 300193, People's Republic of China
*Correspondence e-mail: lbn_1111@yahoo.com.cn

(Received 11 October 2010; accepted 21 October 2010; online 30 October 2010)

In the title compound, C13H12ClN5, which is a derivative of the anti­tumor agent pazopanib {systematic name: 5-[[4-[(2,3-di­methyl-2H-indazol-6-yl)methylamino]-2-pyrimidinyl]amino]-2-methylbenzolsulfonamide}, the indazole and pyrim­idine fragments form a dihedral angle of 62.63 (5)°. In the crystal, pairs of mol­ecules related by twofold rotational symmetry are linked into dimers through π–π inter­actions between the indazole ring systems [centroid–centroid distance = 3.720 (2) Å]. Weak inter­molecular C—H⋯N hydrogen bonds further assemble these dimers into columns propagated in [001].

Related literature

For background to the pharmacokinetics and clinical studies of the anti­tumor agent pazopanib, see: Limvorasak & Posadas (2009[Limvorasak, S. & Posadas, E. M. (2009). Expert Opin. Pharmacother. 10, 3091-3102.]); Sloan & Scheinfeld 2008[Sloan, B. & Scheinfeld, N. S. (2008). Curr. Opin. Investig. Drugs, 9, 1324-1335.]; Sonpavde et al. (2007[Sonpavde, G. M. D., Hutson, T. E. D. O. & Pharm, D. (2007). Curr. Oncol. Rep. 9, 115-119.]). For the synthesis of pazopanib, see: Sorbera et al. (2006[Sorbera, L. A., Bolos, J. & Serradell, N. (2006). Drugs. Fut. 31, 585-589.]).

[Scheme 1]

Experimental

Crystal data

  • C13H12ClN5

  • Mr = 273.73

  • Monoclinic, C 2/c

  • a = 21.432 (4) Å

  • b = 9.836 (2) Å

  • c = 12.542 (3) Å

  • β = 90.25 (3)°

  • V = 2644.1 (9) Å3

  • Z = 8

  • Mo Kα radiation

  • μ = 0.28 mm−1

  • T = 113 K

  • 0.20 × 0.18 × 0.12 mm
Data collection

  • Rigaku Saturn CCD area-detector diffractometer

  • Absorption correction: multi-scan (CrystalClear; Rigaku/MSC, 2005[Rigaku/MSC (2005). CrystalClear. Rigaku/MSC Inc., The Woodlands, Texas, USA.]) Tmin = 0.946, Tmax = 0.967

  • 10576 measured reflections

  • 2323 independent reflections

  • 1982 reflections with I > 2σ(I)

  • Rint = 0.043
Refinement

  • R[F2 > 2σ(F2)] = 0.036

  • wR(F2) = 0.100

  • S = 1.01

  • 2323 reflections

  • 175 parameters

  • H-atom parameters constrained

  • Δρmax = 0.21 e Å−3

  • Δρmin = −0.25 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
C13—H13B⋯N2i 0.98 2.56 3.517 (2) 166
Symmetry code: (i) -x, -y+1, -z+2.

Data collection: CrystalClear (Rigaku/MSC, 2005[Rigaku/MSC (2005). CrystalClear. Rigaku/MSC Inc., The Woodlands, Texas, USA.]); cell refinement: CrystalClear; data reduction: CrystalClear; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL.

Supporting information

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S1600536810042753/cv2775sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536810042753/cv2775Isup2.hkl

checkCIF report


Comment top

Pazopanib is an oral, second-generation multi-targeted tyrosine kinase inhibitor that targets VEGFR, platelet-derived growth factor receptor and c-kit, key proteins responsible for tumor growth and survival (Limvorasak et al., 2009; Sloan et al., 2008; Sonpavde et al., 2007). The crystal structure of the title compound (I), a derivative of pazopanib, synthesized through the transformation of pazopanib (Sorbera et al., 2006), is reported here.

In (I) (Fig. 1), the indazole and pyrimidine fragments form a dihedral angle of 62.63 (5)°. In the crystal structure, The π–π contacts between the indazole systems from the adjacent molecules (Table 1) link them into dimers. Weak intermolecular C—H···N hydrogen bonds (Table 2) link further the dimers into columns propagated in direction [001].

Related literature top

For background to the pharmacokinetics and clinical studies of the antitumor agent pazopanib, see: Limvorasak & Posadas (2009); Sloan & Scheinfeld 2008; Sonpavde et al. (2007). For the synthesis of pazopanib, see: Sorbera et al. (2006).

Experimental top

To a stirred solution of the N-(2-chloropyrimidin-4-yl)-2 -methyl-2H-indazol-6-amine 5 g (0.02 mol) in DMF (30 ml) was added Cs2CO3 9.8 g (0.03 mol) and iodomethane 2.5 ml (5.7 g, 0.04 mol) at room temperature. The mixture was stirred for 5 h. The reaction mixture was then poured into an ice-water bath, and the precipitate was collected via filtration and washed with water. The precipitate was air-dried to get off-white solid as crude product. The solid was dissolved in ethyl acetate 30 ml at 278 k, then white crystals were generated slowly.

Refinement top

C-bound H atoms were geometrically positioned (C—H 0.95–0.98 Å), and refined as riding with Uiso = 1.2-1.5 Ueq(C).

Structure description top

Pazopanib is an oral, second-generation multi-targeted tyrosine kinase inhibitor that targets VEGFR, platelet-derived growth factor receptor and c-kit, key proteins responsible for tumor growth and survival (Limvorasak et al., 2009; Sloan et al., 2008; Sonpavde et al., 2007). The crystal structure of the title compound (I), a derivative of pazopanib, synthesized through the transformation of pazopanib (Sorbera et al., 2006), is reported here.

In (I) (Fig. 1), the indazole and pyrimidine fragments form a dihedral angle of 62.63 (5)°. In the crystal structure, The π–π contacts between the indazole systems from the adjacent molecules (Table 1) link them into dimers. Weak intermolecular C—H···N hydrogen bonds (Table 2) link further the dimers into columns propagated in direction [001].

For background to the pharmacokinetics and clinical studies of the antitumor agent pazopanib, see: Limvorasak & Posadas (2009); Sloan & Scheinfeld 2008; Sonpavde et al. (2007). For the synthesis of pazopanib, see: Sorbera et al. (2006).

Computing details top

Data collection: CrystalClear (Rigaku/MSC, 2005); cell refinement: CrystalClear (Rigaku/MSC, 2005); data reduction: CrystalClear (Rigaku/MSC, 2005); 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).

Figures top
[Figure 1] Fig. 1. The molecular structure of (I). Displacement ellipsoids are drawn at the 50% probability level.
N-(2-Chloropyrimidin-4-yl)-N,2-dimethyl-2H-indazol-6-amine top
Crystal data top
C13H12ClN5F(000) = 1136
Mr = 273.73Dx = 1.375 Mg m−3
Monoclinic, C2/cMo Kα radiation, λ = 0.71073 Å
a = 21.432 (4) ÅCell parameters from 4286 reflections
b = 9.836 (2) Åθ = 1.9–27.9°
c = 12.542 (3) ŵ = 0.28 mm−1
β = 90.25 (3)°T = 113 K
V = 2644.1 (9) Å3Block, white
Z = 80.20 × 0.18 × 0.12 mm
Data collection top
Rigaku Saturn CCD area-detector
diffractometer		2323 independent reflections
Radiation source: rotating anode1982 reflections with I > 2σ(I)
Confocal monochromatorRint = 0.043
Detector resolution: 7.31 pixels mm-1θmax = 25.0°, θmin = 1.9°
ω and φ scansh = −25→25
Absorption correction: multi-scan
(CrystalClear; Rigaku/MSC, 2005)		k = −11→11
Tmin = 0.946, Tmax = 0.967l = −14→14
10576 measured reflections
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.036H-atom parameters constrained
wR(F2) = 0.100 w = 1/[σ2(Fo2) + (0.070P)2]
where P = (Fo2 + 2Fc2)/3
S = 1.01(Δ/σ)max = 0.001
2323 reflectionsΔρmax = 0.21 e Å−3
175 parametersΔρmin = −0.25 e Å−3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0191 (14)
Crystal data top
C13H12ClN5V = 2644.1 (9) Å3
Mr = 273.73Z = 8
Monoclinic, C2/cMo Kα radiation
a = 21.432 (4) ŵ = 0.28 mm−1
b = 9.836 (2) ÅT = 113 K
c = 12.542 (3) Å0.20 × 0.18 × 0.12 mm
β = 90.25 (3)°
Data collection top
Rigaku Saturn CCD area-detector
diffractometer		2323 independent reflections
Absorption correction: multi-scan
(CrystalClear; Rigaku/MSC, 2005)		1982 reflections with I > 2σ(I)
Tmin = 0.946, Tmax = 0.967Rint = 0.043
10576 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0360 restraints
wR(F2) = 0.100H-atom parameters constrained
S = 1.01Δρmax = 0.21 e Å−3
2323 reflectionsΔρmin = −0.25 e Å−3
175 parameters
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Cl10.227613 (19)0.06867 (4)0.79285 (3)0.0308 (2)
N10.13815 (6)0.18363 (13)0.68576 (10)0.0268 (4)
N20.18239 (6)0.30697 (12)0.83256 (10)0.0206 (3)
N30.14793 (6)0.52060 (13)0.88097 (10)0.0206 (3)
N4−0.06548 (6)0.69175 (13)0.92048 (10)0.0223 (3)
N5−0.08472 (6)0.82333 (13)0.91397 (10)0.0218 (3)
C10.17633 (7)0.20335 (15)0.76669 (12)0.0211 (4)
C20.10043 (8)0.29266 (17)0.66821 (13)0.0284 (4)
H20.07200.28800.61010.034*
C30.10066 (8)0.40761 (16)0.72803 (12)0.0235 (4)
H30.07360.48150.71240.028*
C40.14298 (7)0.41252 (15)0.81461 (12)0.0189 (4)
C50.19380 (7)0.52028 (18)0.96815 (13)0.0295 (4)
H5A0.17760.46711.02800.044*
H5B0.20160.61390.99150.044*
H5C0.23290.47970.94320.044*
C60.10170 (7)0.62570 (16)0.88222 (11)0.0194 (4)
C70.12160 (7)0.76193 (16)0.86613 (13)0.0252 (4)
H70.16440.78010.85290.030*
C80.07992 (7)0.86753 (17)0.86940 (13)0.0267 (4)
H80.09350.95850.85920.032*
C90.01641 (7)0.83811 (15)0.88831 (12)0.0209 (4)
C10−0.00297 (7)0.70070 (15)0.90426 (11)0.0188 (4)
C110.04067 (7)0.59365 (15)0.90219 (12)0.0195 (4)
H110.02820.50230.91420.023*
C12−0.03903 (7)0.91238 (17)0.89500 (12)0.0246 (4)
H12−0.04341.00800.88750.030*
C13−0.15098 (7)0.85326 (18)0.92276 (13)0.0286 (4)
H13A−0.15730.95190.92010.043*
H13B−0.16670.81790.99060.043*
H13C−0.17350.81020.86360.043*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.0287 (3)0.0271 (3)0.0365 (3)0.00976 (17)−0.00266 (19)−0.00407 (17)
N10.0329 (8)0.0226 (8)0.0250 (8)0.0042 (6)−0.0049 (6)−0.0020 (6)
N20.0177 (7)0.0222 (8)0.0220 (7)0.0014 (6)0.0025 (5)0.0001 (6)
N30.0176 (7)0.0228 (7)0.0214 (7)0.0028 (6)−0.0009 (5)−0.0045 (6)
N40.0207 (7)0.0194 (8)0.0267 (8)0.0035 (6)0.0006 (6)0.0018 (5)
N50.0223 (7)0.0204 (7)0.0226 (7)0.0049 (6)−0.0011 (5)0.0004 (6)
C10.0205 (8)0.0200 (9)0.0228 (9)0.0009 (7)0.0050 (7)0.0024 (7)
C20.0344 (9)0.0284 (10)0.0225 (9)0.0018 (8)−0.0080 (7)0.0005 (7)
C30.0274 (9)0.0220 (9)0.0210 (8)0.0041 (7)−0.0025 (7)0.0036 (7)
C40.0181 (8)0.0203 (9)0.0184 (8)−0.0010 (6)0.0052 (6)0.0028 (6)
C50.0229 (9)0.0349 (10)0.0307 (10)0.0057 (8)−0.0078 (7)−0.0107 (8)
C60.0206 (8)0.0214 (9)0.0163 (8)0.0019 (7)−0.0011 (6)−0.0024 (6)
C70.0212 (8)0.0254 (9)0.0290 (9)−0.0040 (7)0.0022 (7)−0.0015 (7)
C80.0278 (9)0.0194 (9)0.0328 (10)−0.0036 (7)0.0007 (7)0.0011 (7)
C90.0239 (8)0.0188 (8)0.0200 (8)−0.0002 (7)−0.0013 (6)0.0001 (6)
C100.0201 (8)0.0199 (8)0.0164 (8)−0.0004 (6)−0.0025 (6)−0.0002 (6)
C110.0225 (8)0.0176 (8)0.0185 (8)−0.0005 (6)−0.0001 (6)−0.0003 (6)
C120.0303 (10)0.0180 (8)0.0255 (9)0.0009 (7)−0.0013 (7)0.0003 (7)
C130.0223 (9)0.0308 (10)0.0328 (10)0.0082 (7)0.0023 (7)0.0053 (7)
Geometric parameters (Å, º) top
Cl1—C11.7515 (16)C5—H5B0.9800
N1—C11.315 (2)C5—H5C0.9800
N1—C21.360 (2)C6—C111.370 (2)
N2—C11.3182 (19)C6—C71.421 (2)
N2—C41.3564 (19)C7—C81.371 (2)
N3—C41.3540 (19)C7—H70.9500
N3—C61.4321 (19)C8—C91.413 (2)
N3—C51.467 (2)C8—H80.9500
N4—C101.3586 (19)C9—C121.398 (2)
N4—N51.3607 (17)C9—C101.428 (2)
N5—C121.336 (2)C10—C111.409 (2)
N5—C131.4551 (19)C11—H110.9500
C2—C31.357 (2)C12—H120.9500
C2—H20.9500C13—H13A0.9800
C3—C41.413 (2)C13—H13B0.9800
C3—H30.9500C13—H13C0.9800
C5—H5A0.9800
Cg1···Cg2i3.720 (2)
C1—N1—C2112.08 (13)C11—C6—C7122.04 (14)
C1—N2—C4115.36 (12)C11—C6—N3119.81 (14)
C4—N3—C6121.42 (12)C7—C6—N3118.11 (13)
C4—N3—C5120.45 (13)C8—C7—C6120.96 (15)
C6—N3—C5117.04 (12)C8—C7—H7119.5
C10—N4—N5103.19 (12)C6—C7—H7119.5
C12—N5—N4114.34 (13)C7—C8—C9118.58 (15)
C12—N5—C13126.67 (14)C7—C8—H8120.7
N4—N5—C13118.92 (13)C9—C8—H8120.7
N1—C1—N2131.07 (14)C12—C9—C8136.31 (15)
N1—C1—Cl1114.88 (12)C12—C9—C10103.78 (14)
N2—C1—Cl1114.05 (11)C8—C9—C10119.90 (14)
C3—C2—N1124.52 (14)N4—C10—C11127.55 (14)
C3—C2—H2117.7N4—C10—C9111.71 (13)
N1—C2—H2117.7C11—C10—C9120.74 (14)
C2—C3—C4117.01 (15)C6—C11—C10117.78 (14)
C2—C3—H3121.5C6—C11—H11121.1
C4—C3—H3121.5C10—C11—H11121.1
N3—C4—N2116.87 (13)N5—C12—C9106.98 (14)
N3—C4—C3123.20 (14)N5—C12—H12126.5
N2—C4—C3119.91 (14)C9—C12—H12126.5
N3—C5—H5A109.5N5—C13—H13A109.5
N3—C5—H5B109.5N5—C13—H13B109.5
H5A—C5—H5B109.5H13A—C13—H13B109.5
N3—C5—H5C109.5N5—C13—H13C109.5
H5A—C5—H5C109.5H13A—C13—H13C109.5
H5B—C5—H5C109.5H13B—C13—H13C109.5
C10—N4—N5—C120.03 (17)C11—C6—C7—C8−0.4 (2)
C10—N4—N5—C13177.21 (12)N3—C6—C7—C8−178.15 (13)
C2—N1—C1—N21.9 (2)C6—C7—C8—C9−0.5 (2)
C2—N1—C1—Cl1−178.80 (12)C7—C8—C9—C12−178.16 (16)
C4—N2—C1—N1−0.3 (2)C7—C8—C9—C100.4 (2)
C4—N2—C1—Cl1−179.62 (10)N5—N4—C10—C11−179.72 (13)
C1—N1—C2—C3−1.4 (2)N5—N4—C10—C90.32 (16)
N1—C2—C3—C4−0.4 (3)C12—C9—C10—N4−0.53 (17)
C6—N3—C4—N2−168.27 (13)C8—C9—C10—N4−179.54 (12)
C5—N3—C4—N2−0.5 (2)C12—C9—C10—C11179.50 (13)
C6—N3—C4—C313.5 (2)C8—C9—C10—C110.5 (2)
C5—N3—C4—C3−178.74 (15)C7—C6—C11—C101.3 (2)
C1—N2—C4—N3179.92 (13)N3—C6—C11—C10179.02 (12)
C1—N2—C4—C3−1.8 (2)N4—C10—C11—C6178.69 (14)
C2—C3—C4—N3−179.73 (15)C9—C10—C11—C6−1.3 (2)
C2—C3—C4—N22.1 (2)N4—N5—C12—C9−0.37 (18)
C4—N3—C6—C1157.33 (19)C13—N5—C12—C9−177.29 (13)
C5—N3—C6—C11−110.80 (17)C8—C9—C12—N5179.28 (16)
C4—N3—C6—C7−124.86 (16)C10—C9—C12—N50.52 (16)
C5—N3—C6—C767.01 (18)
Symmetry code: (i) −x, y, −z+3/2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C13—H13B···N2ii0.982.563.517 (2)166
Symmetry code: (ii) −x, −y+1, −z+2.

Experimental details

Crystal data
Chemical formulaC13H12ClN5
Mr273.73
Crystal system, space groupMonoclinic, C2/c
Temperature (K)113
a, b, c (Å)21.432 (4), 9.836 (2), 12.542 (3)
β (°) 90.25 (3)
V (Å3)2644.1 (9)
Z8
Radiation typeMo Kα
µ (mm−1)0.28
Crystal size (mm)0.20 × 0.18 × 0.12
Data collection
DiffractometerRigaku Saturn CCD area-detector
Absorption correctionMulti-scan
(CrystalClear; Rigaku/MSC, 2005)
Tmin, Tmax0.946, 0.967
No. of measured, independent and
observed [I > 2σ(I)] reflections		10576, 2323, 1982
Rint0.043
(sin θ/λ)max (Å−1)0.595
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.036, 0.100, 1.01
No. of reflections2323
No. of parameters175
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å−3)0.21, −0.25

Computer programs: CrystalClear (Rigaku/MSC, 2005), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C13—H13B···N2i0.982.563.517 (2)165.7
Symmetry code: (i) −x, −y+1, −z+2.
 

Acknowledgements

The authors thank Mr Hai-Bin Song of Nankai University and Mr Shuai Mu of Tianjin University for their helpful suggestions.

References

First citationLimvorasak, S. & Posadas, E. M. (2009). Expert Opin. Pharmacother. 10, 3091–3102.  Web of Science CrossRef PubMed CAS Google Scholar
 First citationRigaku/MSC (2005). CrystalClear. Rigaku/MSC Inc., The Woodlands, Texas, USA.  Google Scholar
 First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
 First citationSloan, B. & Scheinfeld, N. S. (2008). Curr. Opin. Investig. Drugs, 9, 1324–1335.  Web of Science PubMed CAS Google Scholar
 First citationSonpavde, G. M. D., Hutson, T. E. D. O. & Pharm, D. (2007). Curr. Oncol. Rep. 9, 115–119.  CrossRef PubMed CAS Google Scholar
 First citationSorbera, L. A., Bolos, J. & Serradell, N. (2006). Drugs. Fut. 31, 585–589.  Web of Science CrossRef CAS Google Scholar

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ISSN: 2056-9890
Volume 66| Part 11| November 2010| Page o2955
https://doi.org/10.1107/S1600536810042753
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