Crystal structure of 1-phenyl-1H-pyrazolo­[3,4-d]pyrimidin-4(5H)-one

Akhmedova, N.; Ortikov, I.; Khasanova, N.; Zokhidov, K.; Turgunov, K.; Elmuradov, B.

doi:10.1107/S205698902500934X

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Volume 81| Part 11| November 2025| Pages 1076-1079

https://doi.org/10.1107/S205698902500934X

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Crystal structure of 1-phenyl-1H-pyrazolo[3,4-d]pyrimidin-4(5H)-one

Nilufar Akhmedova,^a Ilkhom Ortikov,^b Nilufar Khasanova,^b Kosim Zokhidov,^c Kambarali Turgunov ^a,^d ^* and Burkhon Elmuradov ^a

^aS. Yunusov Institute of the Chemistry of Plant Substances, Academy of Sciences of Uzbekistan, Mirzo Ulugbek Str., 77, Tashkent 100170, Uzbekistan, ^bAlfraganus University, Yukori Korakamysh str., 2, Tashkent 100190, Uzbekistan, ^cSamarkand State University, 15, University blv., 140104, Samarkand, Uzbekistan, and ^dTurin Polytechnic University in Tashkent, Kichik Khalka yuli str. 17, 100095 Tashkent, Uzbekistan
^*Correspondence e-mail: [email protected]

Edited by M. Weil, Vienna University of Technology, Austria (Received 10 October 2025; accepted 22 October 2025; online 28 October 2025)

Heating of 5-amino-1-phenyl-1H-pyrazole-4-carbonitrile in the presence of formic acid yielded the title compound, C₁₁H₈N₄O. The pyrazolo[3,4-d]pyrimidine ring system forms a dihedral angle of 34.72 (6)° with the phenyl ring. In the crystal, classical N—H⋯O and non-classical C—H⋯O and C—H⋯N intermolecular interactions result in the formation of supramolecular bands extending parallel to the a axis. Additional π⋯π interactions between pyrimidine and pyrazole rings, and C—H⋯π interactions between neighboring phenyl rings consolidate the packing.

Keywords: crystal structure; molecular structure; 1-phenyl-1H-pyrazolo[3,4-d]pyrimidin-4(5H)-one.

CCDC reference: 2497282

1. Chemical context

Cancer is one of the most difficult to treat and rapidly increasing diseases worldwide. The number of cancer types is increasing every year, which worries the World Health Organization and specialists in the field. One of the urgent tasks facing chemists and pharmacists is therefore to create and implement new, effective drugs against cancer. An analysis of the literature shows that pyrazolopyrimidines, a class of compounds we have selected for our research, are among the pharmaceutically active substances. Synthetic pyrazolopyrimidines are widely used in medicine. In particular, drugs based on these compounds are used to repair cells damaged by viruses, microbes, and cancer. Examples of such drugs include allopurinol, istrafilin, and ruxolitinib. Research in the field of pyrazolopyrimidines is advancing with the design, screening, synthesis, and biological evaluation of potential cancer drugs that inhibit tumor growth and induce apoptosis (He et al., 2011 ; Gillespie et al., 2008 ; Schenone et al., 2004 ; Tintori et al., 2015 ; Gaber et al., 2022 ; Trivedi et al., 2012 ). Among these, compounds containing a pyrazolo[3,4-d]pyrimidine moiety exhibit broad anticancer activity in vitro. These derivatives are of further interest due to their high similarity to the adenine moiety of ATP. To obtain new pyrazolo[3,4-d]pyrimidine-4-one derivatives, we carried out the reaction of 5-amino-1-phenyl-1H-pyrazole-4-carbonitrile with formic acid, yielding 1-phenyl-1H-pyrazolo[3,4-d]pyrimidin-4(5H)-one, C₁₁H₈N₄O, the crystal structure of which is reported here.

2. Structural commentary

The asymmetric unit consist of one formula unit (Fig. 1). Selected N—N and N—C bond lengths given in Table 1 correspond to those observed in related structures [Cambridge Structure Database (CSD; Groom et al., 2016 ) refcodes CICPAG, NIFGUF, UBAVUS and VICGOD (Yathirajan et al., 2007a ,b ; Wang et al., 2021 ; Ferroni et al., 1990 , respectively)]. In the unsubstituted base, 1H-pyrazolo[3,4-d]pyrimidin-4(5H)-one, the N—N and N—C bond lengths within the pyrazole ring are slightly shorter (N1—N2 = 1.363 Å, N1—C7A = 1.343 Å and N2—C3 = 1.313 Å; ALOPUR01, Tang et al., 2023 ). The pyrazolo[3,4-d]pyrimidine ring system is planar with an r.m.s. deviation of 0.012 Å for the ring atoms. The phenyl ring (C8–C13) forms a dihedral angle of 34.72 (6)° with the mean plane of the pyrazolo[3,4-d]pyrimidine ring system.

Table 1
Selected bond lengths (Å)

N1—C7A	1.358 (2)	N2—C3	1.321 (2)
N1—N2	1.376 (2)	N5—C6	1.355 (2)
N1—C8	1.428 (2)	N7—C6	1.304 (2)

Figure 1
The molecular structure of the title compound, with displacement ellipsoids drawn at the 50% probability level.

3. Supramolecular features

In the crystal of the title compound, intermolecular N—H⋯O hydrogen bonds link the molecules into centrosymmetric dimers, forming R₂²(8) motifs. Other centrosymmetric R₂²(10) motifs are formed by weak intermolecular C—H⋯O bonds, and a weak C—H⋯N hydrogen bond participates in the formation of R₃²(8) ring motifs (Table 2). These hydrogen bonds generate supramolecular bands running parallel to the a axis (Fig. 2). The bands are further packed along the b-axis direction through pairs of π–π stacking interactions (Fig. 3) [Cg2⋯Cg3^v and Cg3⋯Cg2^v, centroid-to-centroid distances of 3.4644 (11) and 3.6444 (11) Å and a slippage of 0.860 and 1.471 Å, respectively; Cg2 is the pyrimidine ring centroid, Cg3 is the pyrazole ring centroid; symmetry code: (v) $[{3\over 2}]$ − x, − $[{1\over 2}]$ + y, z). In addition, an intermolecular C_ar—H⋯π interaction is observed between the phenyl ring and the centroid of a neighboring phenyl ring (Cg1; Table 2).

Table 2
Hydrogen-bond geometry (Å, °)

Cg1 is the centroid of the C8–C13 ring.

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N5—H5⋯O1ⁱ	0.94 (3)	1.94 (3)	2.862 (2)	166 (2)
C3—H3⋯O1ⁱⁱ	0.93	2.28	3.180 (2)	162
C6—H6⋯N2ⁱⁱⁱ	0.93	2.48	3.374 (2)	162
C9—H9⋯Cg1^iv	0.93	2.94	3.767 (2)	150
Symmetry codes: (i) ; (ii) ; (iii) ; (iv) $[-x+{\script{3\over 2}}, y-{\script{1\over 2}}, z]$ .

Figure 2
Formation of supramolecular bands running parallel to the a axis.

Figure 3
Packing of the supramolecular bands along the b axis.

4. Database survey

A search of the Cambridge Structural Database (CSD; updated 16 May 2025; Groom et al., 2016) revealed 91 relevant entries containing the 1H-pyrazolo[3,4-d]pyrimidin-4(5H)-one moiety. Two of these, namely ALOPUR (Prusiner & Sundaralingam, 1972 ) and ALOPUR01 (Tang et al., 2023), correspond to allopurinol, i.e., the 1H-pyrazolo[3,4-d]pyrimidin-4(5H)-one structure. Two other entries, SUTRUX and SUTSAE (Dai et al., 2020 ), are co-crystals of allopurinol. The structures of allopurinol salts with maleic and oxalic acids were determined by powder X-ray diffraction analysis (Varsa et al., 2023 ). Among the retrieved entries, more than 20 correspond to metal-containing structures.

5. Synthesis and crystallization

The reaction scheme is displayed in Fig. 4. Amino-1-phenyl-1H-pyrazole-4-carbonitrile (4. 2 g, 10.8 mmol) was heated in 10 ml of formic acid at 383–385 K for 6 h. Then, the mixture was poured into a 250 ml beaker of ice–water and the resulting precipitate was filtered off and dried. Recrystallization from ethanol yielded 1.98 g (86%) of 1-phenyl-1H-pyrazolo[3,4-d]pyrimidin-4(5H)-one in form of rod-shaped crystals (Fig. 5), m.p. 577–578 K, R_f = 0.38.

Figure 4
Synthesis scheme for the title compound.

Figure 5
Screenshot from the face-indexing procedure showing the a and b axes of the rod-shaped crystal.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 3. Hydrogen atoms bonded to carbon atoms were placed in calculated positions and refined to ride on their parent atoms with C—H = 0.93 Å and U_iso(H) = 1.2U_eq(C). The H atom attached to N5 was located in a difference-Fourier map, and its coordinates and isotropic displacement parameter were refined freely.

Table 3
Experimental details

Crystal data
Chemical formula	C₁₁H₈N₄O
M_r	212.21
Crystal system, space group	Orthorhombic, Pbca
Temperature (K)	293
a, b, c (Å)	7.7822 (2), 6.8848 (2), 36.8514 (10)
V (Å³)	1974.46 (9)
Z	8
Radiation type	Cu Kα
μ (mm⁻¹)	0.81
Crystal size (mm)	0.44 × 0.12 × 0.05

Data collection
Diffractometer	Bruker D8 VENTURE dual wavelength Mo/Cu
Absorption correction	Numerical (SADABS; Krause et al., 2015 )
T_min, T_max	0.659, 0.753
No. of measured, independent and observed [I > 2σ(I)] reflections	20676, 1807, 1619
R_int	0.054
(sin θ/λ)_max (Å⁻¹)	0.602

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.046, 0.120, 1.13
No. of reflections	1807
No. of parameters	150
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.25, −0.19
Computer programs: APEX5 and SAINT (Bruker, 2023 ), SHELXT (Sheldrick, 2015a ), SHELXL (Sheldrick, 2015b ), Mercury (Macrae et al., 2020 ) and publCIF (Westrip, 2010 ).

Supporting information

CCDC reference: 2497282

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S205698902500934X/wm5773sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S205698902500934X/wm5773Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S205698902500934X/wm5773Isup3.cml

checkCIF report

Computing details top

1-Phenyl-1H-pyrazolo[3,4-d]pyrimidin-4(5H)-one top

Crystal data top

C₁₁H₈N₄O	D_x = 1.428 Mg m⁻³
M_r = 212.21	Melting point: 577(2) K
Orthorhombic, Pbca	Cu Kα radiation, λ = 1.54178 Å
a = 7.7822 (2) Å	Cell parameters from 3849 reflections
b = 6.8848 (2) Å	θ = 7.2–66.9°
c = 36.8514 (10) Å	µ = 0.81 mm⁻¹
V = 1974.46 (9) Å³	T = 293 K
Z = 8	Prism, colourless
F(000) = 880	0.44 × 0.12 × 0.05 mm

Data collection top

Bruker D8 VENTURE dual wavelength Mo/Cu diffractometer	1807 independent reflections
Radiation source: microfocus X-ray source, Incoatec IµS 3.0 Microfocus Source	1619 reflections with I > 2σ(I)
Mirror monochromator	R_int = 0.054
ω–φ scans	θ_max = 68.1°, θ_min = 7.2°
Absorption correction: numerical (SADABS; Krause et al., 2015)	h = −9→9
T_min = 0.659, T_max = 0.753	k = −8→8
20676 measured reflections	l = −44→44

Refinement top

Refinement on F²	Hydrogen site location: mixed
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F² > 2σ(F²)] = 0.046	w = 1/[σ²(F_o²) + (0.0495P)² + 0.8037P] where P = (F_o² + 2F_c²)/3
wR(F²) = 0.120	(Δ/σ)_max < 0.001
S = 1.13	Δρ_max = 0.25 e Å⁻³
1807 reflections	Δρ_min = −0.19 e Å⁻³
150 parameters	Extinction correction: SHELXL-2014/7 (Sheldrick 2015b), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
0 restraints	Extinction coefficient: 0.0042 (6)

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.

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

	x	y	z	U_iso*/U_eq
O1	0.78192 (17)	0.5391 (2)	0.49996 (3)	0.0534 (4)
N1	0.56134 (18)	0.6999 (2)	0.38824 (4)	0.0416 (4)
N2	0.42164 (19)	0.6696 (3)	0.41042 (5)	0.0489 (4)
N5	0.9606 (2)	0.6158 (2)	0.45274 (4)	0.0450 (4)
H5	1.056 (3)	0.582 (3)	0.4669 (6)	0.064 (7)*
N7	0.87219 (19)	0.7013 (2)	0.39334 (4)	0.0434 (4)
C3	0.4855 (2)	0.6268 (3)	0.44265 (5)	0.0446 (5)
H3	0.4195	0.5980	0.4630	0.053*
C3A	0.6660 (2)	0.6305 (3)	0.44230 (5)	0.0392 (4)
C4	0.7984 (2)	0.5914 (3)	0.46802 (5)	0.0415 (4)
C6	0.9895 (2)	0.6677 (3)	0.41782 (5)	0.0431 (5)
H6	1.1035	0.6805	0.4106	0.052*
C7A	0.7101 (2)	0.6778 (2)	0.40708 (5)	0.0371 (4)
C8	0.5349 (2)	0.7457 (3)	0.35086 (5)	0.0442 (5)
C9	0.6491 (3)	0.6783 (3)	0.32524 (6)	0.0538 (5)
H9	0.7413	0.6008	0.3321	0.065*
C10	0.6254 (3)	0.7269 (4)	0.28933 (6)	0.0640 (6)
H10	0.7030	0.6827	0.2720	0.077*
C11	0.4895 (4)	0.8388 (4)	0.27881 (7)	0.0696 (7)
H11	0.4747	0.8705	0.2545	0.083*
C12	0.3746 (4)	0.9045 (4)	0.30437 (7)	0.0718 (7)
H12	0.2817	0.9803	0.2972	0.086*
C13	0.3959 (3)	0.8587 (3)	0.34074 (6)	0.0585 (6)
H13	0.3182	0.9031	0.3580	0.070*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0433 (8)	0.0746 (10)	0.0423 (7)	−0.0024 (7)	−0.0020 (6)	0.0144 (6)
N1	0.0323 (8)	0.0477 (9)	0.0448 (9)	0.0009 (6)	−0.0018 (6)	0.0030 (6)
N2	0.0320 (8)	0.0594 (10)	0.0554 (10)	−0.0011 (7)	0.0015 (7)	0.0061 (8)
N5	0.0341 (8)	0.0538 (9)	0.0471 (9)	−0.0006 (7)	−0.0045 (7)	0.0068 (7)
N7	0.0336 (8)	0.0521 (9)	0.0446 (9)	0.0012 (7)	0.0013 (6)	0.0027 (7)
C3	0.0334 (9)	0.0531 (11)	0.0472 (10)	−0.0011 (8)	0.0032 (8)	0.0065 (8)
C3A	0.0331 (9)	0.0417 (9)	0.0427 (10)	0.0002 (7)	−0.0015 (7)	0.0029 (7)
C4	0.0369 (9)	0.0427 (10)	0.0449 (10)	−0.0007 (7)	−0.0004 (7)	0.0028 (7)
C6	0.0314 (9)	0.0516 (10)	0.0464 (10)	−0.0002 (8)	0.0016 (8)	0.0028 (8)
C7A	0.0318 (9)	0.0366 (9)	0.0428 (9)	−0.0004 (7)	−0.0023 (7)	0.0006 (7)
C8	0.0473 (10)	0.0412 (9)	0.0441 (10)	−0.0039 (8)	−0.0090 (8)	0.0035 (8)
C9	0.0563 (12)	0.0558 (12)	0.0491 (12)	0.0041 (10)	−0.0073 (9)	−0.0021 (9)
C10	0.0704 (15)	0.0753 (15)	0.0464 (12)	−0.0061 (12)	−0.0033 (11)	−0.0041 (10)
C11	0.0880 (18)	0.0724 (15)	0.0483 (12)	−0.0084 (13)	−0.0192 (12)	0.0098 (11)
C12	0.0732 (16)	0.0726 (15)	0.0696 (16)	0.0122 (13)	−0.0266 (13)	0.0112 (12)
C13	0.0536 (12)	0.0649 (13)	0.0571 (13)	0.0087 (11)	−0.0106 (10)	0.0011 (10)

Geometric parameters (Å, º) top

O1—C4	1.237 (2)	C3A—C4	1.426 (2)
N1—C7A	1.358 (2)	C6—H6	0.9300
N1—N2	1.376 (2)	C8—C9	1.377 (3)
N1—C8	1.428 (2)	C8—C13	1.384 (3)
N2—C3	1.321 (2)	C9—C10	1.377 (3)
N5—C6	1.355 (2)	C9—H9	0.9300
N5—C4	1.392 (2)	C10—C11	1.365 (4)
N5—H5	0.94 (3)	C10—H10	0.9300
N7—C6	1.304 (2)	C11—C12	1.376 (4)
N7—C7A	1.369 (2)	C11—H11	0.9300
C3—C3A	1.405 (2)	C12—C13	1.387 (3)
C3—H3	0.9300	C12—H12	0.9300
C3A—C7A	1.381 (2)	C13—H13	0.9300

C7A—N1—N2	110.66 (14)	N1—C7A—C3A	107.17 (15)
C7A—N1—C8	129.83 (16)	N7—C7A—C3A	127.16 (16)
N2—N1—C8	119.51 (15)	C9—C8—C13	120.60 (19)
C3—N2—N1	105.69 (14)	C9—C8—N1	119.61 (17)
C6—N5—C4	124.55 (16)	C13—C8—N1	119.79 (18)
C6—N5—H5	117.5 (15)	C8—C9—C10	119.4 (2)
C4—N5—H5	117.6 (15)	C8—C9—H9	120.3
C6—N7—C7A	111.62 (15)	C10—C9—H9	120.3
N2—C3—C3A	111.35 (17)	C11—C10—C9	120.9 (2)
N2—C3—H3	124.3	C11—C10—H10	119.5
C3A—C3—H3	124.3	C9—C10—H10	119.5
C7A—C3A—C3	105.13 (16)	C10—C11—C12	119.7 (2)
C7A—C3A—C4	119.32 (16)	C10—C11—H11	120.2
C3—C3A—C4	135.49 (18)	C12—C11—H11	120.2
O1—C4—N5	120.94 (16)	C11—C12—C13	120.6 (2)
O1—C4—C3A	127.74 (17)	C11—C12—H12	119.7
N5—C4—C3A	111.31 (16)	C13—C12—H12	119.7
N7—C6—N5	125.98 (17)	C8—C13—C12	118.8 (2)
N7—C6—H6	117.0	C8—C13—H13	120.6
N5—C6—H6	117.0	C12—C13—H13	120.6
N1—C7A—N7	125.67 (16)

C7A—N1—N2—C3	−0.7 (2)	C6—N7—C7A—C3A	1.9 (3)
C8—N1—N2—C3	178.78 (16)	C3—C3A—C7A—N1	0.0 (2)
N1—N2—C3—C3A	0.7 (2)	C4—C3A—C7A—N1	177.64 (16)
N2—C3—C3A—C7A	−0.4 (2)	C3—C3A—C7A—N7	179.11 (18)
N2—C3—C3A—C4	−177.5 (2)	C4—C3A—C7A—N7	−3.2 (3)
C6—N5—C4—O1	178.24 (18)	C7A—N1—C8—C9	34.0 (3)
C6—N5—C4—C3A	−0.8 (3)	N2—N1—C8—C9	−145.37 (19)
C7A—C3A—C4—O1	−176.59 (18)	C7A—N1—C8—C13	−145.4 (2)
C3—C3A—C4—O1	0.2 (4)	N2—N1—C8—C13	35.2 (3)
C7A—C3A—C4—N5	2.3 (2)	C13—C8—C9—C10	1.0 (3)
C3—C3A—C4—N5	179.1 (2)	N1—C8—C9—C10	−178.44 (19)
C7A—N7—C6—N5	0.0 (3)	C8—C9—C10—C11	−0.7 (4)
C4—N5—C6—N7	−0.4 (3)	C9—C10—C11—C12	0.1 (4)
N2—N1—C7A—N7	−178.70 (17)	C10—C11—C12—C13	0.3 (4)
C8—N1—C7A—N7	1.9 (3)	C9—C8—C13—C12	−0.6 (3)
N2—N1—C7A—C3A	0.5 (2)	N1—C8—C13—C12	178.8 (2)
C8—N1—C7A—C3A	−178.97 (17)	C11—C12—C13—C8	0.0 (4)
C6—N7—C7A—N1	−179.11 (17)

Hydrogen-bond geometry (Å, º) top

Cg1 is the centroid of the C8–C13 ring.

D—H···A	D—H	H···A	D···A	D—H···A
N5—H5···O1ⁱ	0.94 (3)	1.94 (3)	2.862 (2)	166 (2)
C3—H3···O1ⁱⁱ	0.93	2.28	3.180 (2)	162
C6—H6···N2ⁱⁱⁱ	0.93	2.48	3.374 (2)	162
C9—H9···Cg1^iv	0.93	2.94	3.767 (2)	150

Symmetry codes: (i) −x+2, −y+1, −z+1; (ii) −x+1, −y+1, −z+1; (iii) x+1, y, z; (iv) −x+3/2, y−1/2, z.

Acknowledgements

This work was carried out within the framework of the Basic Scientific Research Program of the Academy of Sciences of the Republic of Uzbekistan.

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