Synthesis, spectroscopic characterization, structural studies, thermal analysis and mol­ecular docking of N-(2-methyl-5-nitro­phen­yl)-4-(pyridin-2-yl)pyrimidin-2-amine, a precursor for drug design against chronic myeloid leukemia

Moreno-Fuquen, R.; Arango-Daraviña, K.; Kennedy, A.R.

doi:10.1107/S2053229621009487

Synthesis, spectroscopic characterization, structural studies, thermal analysis and molecular docking of N-(2-methyl-5-nitrophenyl)-4-(pyridin-2-yl)pyrimidin-2-amine, a precursor for drug design against chronic myeloid leukemia

R. Moreno-Fuquen, K. Arango-Daraviña and A. R. Kennedy

The synthesis, crystal structure and spectroscopic and electronic properties of N-(2-methyl-5-nitrophenyl)-4-(pyridin-2-yl)pyrimidin-2-amine (NPPA), C₁₆H₁₃N₅O₂, a potential template for drug design against chronic myelogenous leukemia (CML), is reported. The design and construction of the target molecule were carried out starting from the guanidinium nitrate salt (previously synthesized) and the corresponding enaminone. X-ray diffraction analysis and a study of the Hirshfeld surfaces revealed important interactions between the nitro-group O atoms and the H atoms of the pyridine and pyrimidine rings. A crystalline ordering in layers, by the stacking of rings through interactions of the π–π type, was observed and confirmed by a study of the shape-index surfaces and dispersion energy calculations. Quantitative electrostatic potential studies revealed the most positive value of the molecule on regions close to the N—H groups (34.8 kcal mol⁻¹); nevertheless, steric impediments and the planarity of the molecule do not allow the formation of hydrogen bonds from this group. This interaction is however activated when the molecule takes on a new extended conformation in the active pocket of the enzyme kinase (PDB ID 2hyy), interacting with protein residues that are fundamental in the inhibition process of CML. The most negative values of the molecule are seen in regions close to the nitro group (−35.4 and −34.0 kcal mol⁻¹). A molecular docking study revealed an energy affinity of ΔG = −10.3 kcal mol⁻¹ for NPPA which, despite not having a more negative value than the control molecule (Imatinib; ΔG = −12.8 kcal mol⁻¹), shows great potential to be used as a template for new drugs against CML.

Keywords: chronic myeloid leukemia; CML; Hirshfeld surface; molecular electrostatic potential; molecular docking; supramolecular chemistry; crystal structure.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S2053229621009487/eq3001sup1.cif Contains datablocks I, global
	Structure factor file (CIF format) https://doi.org/10.1107/S2053229621009487/eq3001Isup2.hkl Contains datablock I
	Chemical Markup Language (CML) file https://doi.org/10.1107/S2053229621009487/eq3001Isup3.cml Supplementary material

CCDC reference: 2109438

Computing details top

Data collection: CrysAlis PRO (Oxford Diffraction, 2010); cell refinement: CrysAlis PRO (Oxford Diffraction, 2010); data reduction: CrysAlis PRO (Oxford Diffraction, 2010); program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: Mercury (Macrae et al., 2020); software used to prepare material for publication: publCIF (Westrip, 2010).

(I) top

Crystal data top

C₁₆H₁₃N₅O₂	F(000) = 640
M_r = 307.31	D_x = 1.489 Mg m⁻³
Monoclinic, P2₁/n	Cu Kα radiation, λ = 1.54184 Å
a = 8.0616 (5) Å	Cell parameters from 4950 reflections
b = 17.8873 (8) Å	θ = 5.0–73.1°
c = 9.5504 (4) Å	µ = 0.85 mm⁻¹
β = 95.490 (4)°	T = 123 K
V = 1370.85 (12) Å³	Block, brown
Z = 4	0.45 × 0.20 × 0.10 mm

Data collection top

Oxford Diffraction Gemini S diffractometer	2684 independent reflections
Radiation source: fine-focus sealed tube	2326 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.020
ω scans	θ_max = 73.1°, θ_min = 5.0°
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2010)	h = −7→9
T_min = 0.687, T_max = 1.000	k = −18→21
4948 measured reflections	l = −11→11

Refinement top

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)] = 0.043	Hydrogen site location: mixed
wR(F²) = 0.123	H atoms treated by a mixture of independent and constrained refinement
S = 1.01	w = 1/[σ²(F_o²) + (0.0719P)² + 0.3901P] where P = (F_o² + 2F_c²)/3
2684 reflections	(Δ/σ)_max = 0.001
213 parameters	Δρ_max = 0.28 e Å⁻³
0 restraints	Δρ_min = −0.22 e Å⁻³

Special details top

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. All non-H atoms were modelled anisotropically and the structure was refined to convergence using SHELXL (Sheldrick, 2015) as included in WinGx software (Farrugia, 2012).

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
O1	1.16103 (14)	1.01117 (7)	0.92354 (12)	0.0339 (3)
O2	0.99304 (18)	1.07275 (7)	0.77704 (15)	0.0469 (4)
N1	0.51884 (16)	0.91344 (7)	0.27391 (14)	0.0287 (3)
N2	0.67099 (15)	1.00859 (7)	0.40847 (13)	0.0242 (3)
N3	0.59142 (16)	1.19155 (7)	0.25969 (13)	0.0267 (3)
N4	0.69772 (17)	0.88107 (7)	0.46299 (14)	0.0274 (3)
N5	1.05088 (17)	1.01392 (7)	0.82592 (15)	0.0293 (3)
C1	0.62803 (18)	0.93787 (9)	0.37969 (15)	0.0247 (3)
C2	0.4500 (2)	0.96675 (9)	0.19020 (17)	0.0304 (3)
H2	0.3732	0.9523	0.1133	0.036*
C3	0.48455 (19)	1.04235 (9)	0.20924 (16)	0.0284 (3)
H3	0.4331	1.0793	0.1482	0.034*
C4	0.59806 (18)	1.06101 (8)	0.32205 (15)	0.0242 (3)
C5	0.64673 (18)	1.14002 (8)	0.35555 (15)	0.0242 (3)
C6	0.74363 (18)	1.15826 (9)	0.47974 (15)	0.0264 (3)
H6	0.7798	1.1205	0.5457	0.032*
C7	0.78625 (19)	1.23231 (9)	0.50530 (16)	0.0286 (3)
H7	0.8525	1.2462	0.5889	0.034*
C8	0.73079 (19)	1.28577 (9)	0.40709 (17)	0.0285 (3)
H8	0.7580	1.3370	0.4216	0.034*
C9	0.6348 (2)	1.26264 (9)	0.28737 (16)	0.0282 (3)
H9	0.5971	1.2996	0.2203	0.034*
C10	0.80883 (18)	0.88211 (8)	0.58471 (15)	0.0240 (3)
C11	0.87791 (18)	0.94771 (8)	0.64248 (16)	0.0256 (3)
H11	0.8531	0.9945	0.5984	0.031*
C12	0.98348 (18)	0.94365 (8)	0.76537 (16)	0.0252 (3)
C13	1.02617 (19)	0.87739 (9)	0.83338 (16)	0.0277 (3)
H13	1.0991	0.8763	0.9176	0.033*
C14	0.9580 (2)	0.81246 (8)	0.77344 (16)	0.0273 (3)
H14	0.9860	0.7660	0.8178	0.033*
C15	0.85026 (18)	0.81275 (8)	0.65066 (16)	0.0250 (3)
C16	0.7805 (2)	0.74006 (8)	0.59130 (17)	0.0293 (3)
H161	0.8189	0.6989	0.6540	0.044*
H162	0.8188	0.7318	0.4982	0.044*
H163	0.6585	0.7421	0.5831	0.044*
H4N	0.660 (2)	0.8382 (12)	0.435 (2)	0.031 (5)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0339 (6)	0.0326 (6)	0.0330 (6)	−0.0025 (5)	−0.0075 (5)	−0.0019 (5)
O2	0.0614 (8)	0.0200 (6)	0.0536 (8)	−0.0030 (6)	−0.0236 (6)	0.0029 (5)
N1	0.0318 (7)	0.0229 (7)	0.0306 (7)	−0.0008 (5)	−0.0018 (5)	−0.0026 (5)
N2	0.0276 (6)	0.0199 (6)	0.0248 (6)	0.0002 (5)	0.0006 (5)	0.0001 (5)
N3	0.0315 (6)	0.0217 (6)	0.0265 (6)	0.0032 (5)	0.0004 (5)	0.0017 (5)
N4	0.0343 (7)	0.0159 (6)	0.0308 (7)	−0.0024 (5)	−0.0036 (5)	−0.0014 (5)
N5	0.0331 (7)	0.0229 (7)	0.0310 (7)	−0.0021 (5)	−0.0014 (5)	0.0006 (5)
C1	0.0265 (7)	0.0225 (7)	0.0249 (7)	0.0012 (5)	0.0021 (5)	−0.0013 (5)
C2	0.0314 (8)	0.0294 (8)	0.0289 (8)	−0.0007 (6)	−0.0048 (6)	−0.0037 (6)
C3	0.0316 (8)	0.0255 (8)	0.0273 (7)	0.0041 (6)	−0.0014 (6)	0.0020 (6)
C4	0.0265 (7)	0.0215 (7)	0.0251 (7)	0.0014 (6)	0.0045 (6)	−0.0002 (5)
C5	0.0256 (7)	0.0213 (7)	0.0261 (7)	0.0027 (5)	0.0045 (6)	0.0016 (5)
C6	0.0302 (7)	0.0225 (7)	0.0263 (7)	0.0024 (6)	0.0011 (6)	0.0030 (6)
C7	0.0297 (7)	0.0275 (8)	0.0279 (7)	0.0002 (6)	−0.0012 (6)	−0.0023 (6)
C8	0.0324 (8)	0.0192 (7)	0.0344 (8)	0.0001 (6)	0.0051 (6)	−0.0013 (6)
C9	0.0339 (8)	0.0207 (7)	0.0298 (8)	0.0037 (6)	0.0024 (6)	0.0049 (6)
C10	0.0254 (7)	0.0206 (7)	0.0259 (7)	0.0008 (5)	0.0033 (6)	0.0005 (5)
C11	0.0290 (7)	0.0186 (7)	0.0288 (7)	0.0011 (6)	0.0006 (6)	0.0032 (5)
C12	0.0266 (7)	0.0202 (7)	0.0288 (7)	−0.0007 (6)	0.0021 (6)	−0.0001 (6)
C13	0.0308 (7)	0.0257 (8)	0.0263 (7)	0.0011 (6)	0.0002 (6)	0.0030 (6)
C14	0.0335 (8)	0.0206 (7)	0.0281 (7)	0.0028 (6)	0.0041 (6)	0.0046 (5)
C15	0.0286 (7)	0.0187 (7)	0.0286 (7)	0.0011 (5)	0.0073 (6)	0.0011 (5)
C16	0.0392 (8)	0.0185 (7)	0.0302 (8)	0.0000 (6)	0.0035 (6)	0.0012 (6)

Geometric parameters (Å, º) top

O1—N5	1.2255 (18)	C6—C7	1.384 (2)
O2—N5	1.2252 (18)	C6—H6	0.9500
N1—C2	1.331 (2)	C7—C8	1.383 (2)
N1—C1	1.348 (2)	C7—H7	0.9500
N2—N2	0.000 (2)	C8—C9	1.381 (2)
N2—C1	1.3333 (19)	C8—H8	0.9500
N2—C4	1.3466 (19)	C9—H9	0.9500
N3—C9	1.338 (2)	C10—C11	1.390 (2)
N3—C5	1.3448 (19)	C10—C15	1.417 (2)
N4—C1	1.377 (2)	C11—C12	1.384 (2)
N4—C10	1.398 (2)	C11—H11	0.9500
N4—H4N	0.86 (2)	C12—C13	1.379 (2)
N5—C12	1.4661 (19)	C13—C14	1.385 (2)
C1—N2	1.3333 (19)	C13—H13	0.9500
C2—C3	1.389 (2)	C14—C15	1.391 (2)
C2—H2	0.9500	C14—H14	0.9500
C3—C4	1.386 (2)	C15—C16	1.506 (2)
C3—H3	0.9500	C16—H161	0.9800
C4—N2	1.3466 (19)	C16—H162	0.9800
C4—C5	1.493 (2)	C16—H163	0.9800
C5—C6	1.395 (2)

C2—N1—C1	115.01 (13)	C9—C8—C7	118.25 (14)
C1—N2—C4	116.41 (13)	C9—C8—H8	120.9
C9—N3—C5	116.97 (13)	C7—C8—H8	120.9
C1—N4—C10	131.63 (13)	N3—C9—C8	124.27 (14)
C1—N4—H4N	111.4 (13)	N3—C9—H9	117.9
C10—N4—H4N	116.9 (13)	C8—C9—H9	117.9
O2—N5—O1	123.09 (13)	C11—C10—N4	122.80 (13)
O2—N5—C12	118.23 (13)	C11—C10—C15	119.62 (14)
O1—N5—C12	118.68 (13)	N4—C10—C15	117.58 (13)
N2—C1—N1	126.89 (14)	C12—C11—C10	118.87 (14)
N2—C1—N4	119.83 (13)	C12—C11—H11	120.6
N1—C1—N4	113.27 (13)	C10—C11—H11	120.6
N1—C2—C3	123.51 (14)	C13—C12—C11	123.35 (14)
N1—C2—H2	118.2	C13—C12—N5	118.99 (14)
C3—C2—H2	118.2	C11—C12—N5	117.65 (13)
C4—C3—C2	116.44 (14)	C12—C13—C14	117.05 (14)
C4—C3—H3	121.8	C12—C13—H13	121.5
C2—C3—H3	121.8	C14—C13—H13	121.5
N2—C4—C3	121.73 (14)	C13—C14—C15	122.44 (14)
N2—C4—C5	115.94 (13)	C13—C14—H14	118.8
C3—C4—C5	122.34 (14)	C15—C14—H14	118.8
N3—C5—C6	122.73 (14)	C14—C15—C10	118.66 (14)
N3—C5—C4	116.08 (13)	C14—C15—C16	119.66 (13)
C6—C5—C4	121.19 (14)	C10—C15—C16	121.68 (14)
C7—C6—C5	118.88 (14)	C15—C16—H161	109.5
C7—C6—H6	120.6	C15—C16—H162	109.5
C5—C6—H6	120.6	H161—C16—H162	109.5
C8—C7—C6	118.89 (14)	C15—C16—H163	109.5
C8—C7—H7	120.6	H161—C16—H163	109.5
C6—C7—H7	120.6	H162—C16—H163	109.5

C4—N2—C1—N2	0 (100)	N2—C4—C5—C6	−8.5 (2)
N2—N2—C1—N1	0.0 (3)	C3—C4—C5—C6	171.36 (14)
C4—N2—C1—N1	−0.4 (2)	N3—C5—C6—C7	−0.6 (2)
N2—N2—C1—N4	0.0 (3)	C4—C5—C6—C7	179.57 (13)
C4—N2—C1—N4	179.78 (13)	C5—C6—C7—C8	0.2 (2)
C2—N1—C1—N2	0.8 (2)	C6—C7—C8—C9	0.0 (2)
C2—N1—C1—N2	0.8 (2)	C5—N3—C9—C8	−0.3 (2)
C2—N1—C1—N4	−179.37 (13)	C7—C8—C9—N3	0.0 (2)
C10—N4—C1—N2	2.9 (2)	C1—N4—C10—C11	−3.0 (3)
C10—N4—C1—N2	2.9 (2)	C1—N4—C10—C15	176.64 (14)
C10—N4—C1—N1	−176.90 (14)	N4—C10—C11—C12	178.33 (13)
C1—N1—C2—C3	−0.8 (2)	C15—C10—C11—C12	−1.3 (2)
N1—C2—C3—C4	0.4 (2)	C10—C11—C12—C13	0.9 (2)
C1—N2—C4—N2	0 (100)	C10—C11—C12—N5	−178.38 (13)
N2—N2—C4—C3	0.0 (3)	O2—N5—C12—C13	−169.19 (15)
C1—N2—C4—C3	0.0 (2)	O1—N5—C12—C13	10.2 (2)
N2—N2—C4—C5	0.0 (3)	O2—N5—C12—C11	10.1 (2)
C1—N2—C4—C5	179.83 (12)	O1—N5—C12—C11	−170.51 (14)
C2—C3—C4—N2	0.0 (2)	C11—C12—C13—C14	−0.1 (2)
C2—C3—C4—N2	0.0 (2)	N5—C12—C13—C14	179.22 (13)
C2—C3—C4—C5	−179.82 (14)	C12—C13—C14—C15	−0.4 (2)
C9—N3—C5—C6	0.6 (2)	C13—C14—C15—C10	0.0 (2)
C9—N3—C5—C4	−179.53 (13)	C13—C14—C15—C16	−179.92 (14)
N2—C4—C5—N3	171.65 (13)	C11—C10—C15—C14	0.9 (2)
N2—C4—C5—N3	171.65 (13)	N4—C10—C15—C14	−178.77 (13)
C3—C4—C5—N3	−8.5 (2)	C11—C10—C15—C16	−179.22 (14)
N2—C4—C5—C6	−8.5 (2)	N4—C10—C15—C16	1.1 (2)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C2—H2···O1ⁱ	0.95	2.59	3.3777 (19)	140
C9—H9···O2ⁱⁱ	0.95	2.51	3.1565 (19)	125
C11—H11···N2	0.95	2.24	2.8723 (19)	124

Symmetry codes: (i) x−1, y, z−1; (ii) x−1/2, −y+5/2, z−1/2.

Interaction energies of pairs of molecules (kJ mol^-1) obtained from energy lattice calculations for NPPA top

Colour	N	Symmetry code	R	Electron density	E_ele	E_pol	E_disp	E_rep	E_tot
i	2	-x+1/2, y+1/2, -z+1/2	13.04	B3LYP/6-31G(d,p)	0.2	0.0	-1.1	0.0	-0.8
ii	1	-x, -y, -z	18.15	B3LYP/6-31G(d,p)	0.0	0.0	0.1	0.0	-0.1
iii	1	-x, -y, -z	15.22	B3LYP/6-31G(d,p)	0.0	0.0	-0.3	0.0	-0.2
iv	2	x+1/2, -y+1/2, z+1/2	10.51	B3LYP/6-31G(d,p)	-14.3	-4.1	-20	23.5	-21.0
v	2	x, y, z	11.89	B3LYP/6-31G(d,p)	-4.9	-1.4	-5.8	5.1	-8.2
vi	2	x, y, z	17.89	B3LYP/6-31G(d,p)	0.2	0.0	-0.1	0.0	0.1
vii	1	-x, -y, -z	10.54	B3LYP/6-31G(d,p)	-0.9	-0.2	-8.7	2.3	-7.3
viii	2	-x+1/2, y+1/2, -z+1/2	10.35	B3LYP/6-31G(d,p)	-6.8	-1.6	-20.1	15.5	-16.3
ix	1	-x, -y, -z	18.00	B3LYP/6-31G(d,p)	0.0	0.0	-0.1	0.0	-0.1
x	2	x+1/2, -y+1/2, z+1/2	10.97	B3LYP/6-31G(d,p)	-4.1	-2.4	-18.4	13.2	-14.0
xi	2	-x+1/2, y+1/2, -z+1/2	12.31	B3LYP/6-31G(d,p)	-2.4	-0.2	-1.2	0.0	-3.7
xii	1	-x, -y, -z	3.74	B3LYP/6-31G(d,p)	-7.8	-2.8	-99.2	54.4	-63.1
xiii	1	-x, -y, -z	4.39	B3LYP/6-31G(d,p)	-13.8	-2.3	-95.4	56.4	-64.6
xiv	2	-x+1/2, y+1/2, -z+1/2	9.96	B3LYP/6-31G(d,p)	-5.3	-0.9	-18.2	11.4	-15.1
xv	1	-x, -y, -z	9.48	B3LYP/6-31G(d,p)	-5.4	-2.3	-16.1	8.3	-16.4
xvi	1	-x ,-y, -z	18.69	B3LYP/6-31G(d,p)	0.4	0.0	-0.1	0.0	0.3
xvii	1	-x, -y, -z	18.54	B3LYP/6-31G(d,p)	0.4	0.0	-0.1	0.0	0.3
xviii	1	-x, -y, -z	14.14	B3LYP/6-31G(d,p)	1.3	-0.1	-0.4	0.0	1.0

Notes: (*) scaling factors used for the determination of the total energy E_tot: E_ele = 1.057, E_pol = 0.740, E_dis = 0.871 and E_rep = 0.618, R is the distance between molecule centroids (Å), N is the number of pairs of molecules in the cluster with that particular interaction energy.

IR assignments and distribution of percent potential energy (%PED) top

Assignments (PED%)	Exp (cm^-1)	6311G++(d,p) (cm^-1)
		Without sc.	Sc.
ν NH (100)	3448	3631	3481
ν CH (99)	3145	3288	3152
ν CH (91)	3090	3115	2986
ν CH (100)	3063	3054	2928
ν CC (55)	1578	1655	1587
ν CC (14) + ν NC (12)	1553	1619	1553
ν_as ON (59)	1518	1575	1510
ν ON (16) + β HCC (22)	1474	1557	1492
β HCN (56)	1452	1514	1452
β HCC (42) + β HCH(78)+ τ HCCC(15)	1430	1491	1429
ν NC (43)	1399	1459	1399
β HCN (42)	1380	1435	1376
ν_s ON (64)	1342	1367	1310
ν CC (12)	1308	1338	1283
ν NC (37) + β HCN(19)	1285	1322	1267
ν NC (30) + ν CC(10)	1263	1280	1227
ν NC (34) + β HCN(10)	1238	1264	1212
β CNC(51)	1115	1130	1083
ν CC (30) + β HCC (50)	1096	1119	1073
ν CC (33) + β HCH (11)	1077	1092	1047
ν CC (45)	1055	1065	1021
ν CC (21) + β CCC (45)	989	1012	970
ν NC (10) + τ HCCC (13) + β CCC(17)	963	981	941
τ HCCC (81)	888	924	886
τ HCNC (76)	847	880	843
δ ONO (43) + ν ON(11)	825	846	811
τ HCCC (79)	800	831	797
τ HCCC (70)	781	819	785
β CNC (52) + ν CC(11)	742	768	736
τ HCCC (10) + τ HCCN(69)	734	760	729
γ CCNC (70)	649	687	659
β CCC (68)	617	632	606

ν is stretching, β is in-plane deformation, δ is scissors, γ is out-of-plane deformation, τ is torsion, s is symmetric, as is asymmetric, r is rocking and t is twisting.

The most relevant hydrogen bonds (Å, °) formed by the protein residues of 2HYY with imatinib and NPPA top

Imatinib					NPPA
Residue	Amino acid	H···A	D···A	D—H···A	H···A	D···A	D—H···A
286C	Glu	2.24	3.09	143.11
315C	Thr	2.34	3.01	124.55	2.46	3.19	143.37
318C	Met	2.00	2.94	158.24

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Synthesis, spectroscopic characterization, structural studies, thermal analysis and mol­ecular docking of N-(2-methyl-5-nitro­phen­yl)-4-(pyridin-2-yl)pyrimidin-2-amine, a precursor for drug design against chronic myeloid leukemia

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Synthesis, spectroscopic characterization, structural studies, thermal analysis and molecular docking of N-(2-methyl-5-nitrophenyl)-4-(pyridin-2-yl)pyrimidin-2-amine, a precursor for drug design against chronic myeloid leukemia