Crystal structure of (S)-4-carbamoyl-4-(1,3-dioxo­isoindolin-2-yl)butanoic acid

Otogawa, K.; Ishikawa, K.; Shiro, M.; Asahi, T.

doi:10.1107/S2056989014027121

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Volume 71| Part 1| January 2015| Pages 107-109

https://doi.org/10.1107/S2056989014027121

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Crystal structure of (S)-4-carbamoyl-4-(1,3-dioxoisoindolin-2-yl)butanoic acid¹

Kohei Otogawa,^a Kazuhiko Ishikawa,^a Motoo Shiro ^b and Toru Asahi ^a,^b ^*

^aGraduate school of Advanced Science and Engineering, Waseda University (TWIns), Tokyo 162-8480, Japan, and ^bConsolidated Research Institute for Advanced Science and Medical Care, Waseda University (ASMeW), Tokyo 162-0041, Japan
^*Correspondence e-mail: tasahi@waseda.jp

Edited by H. Ishida, Okayama University, Japan (Received 29 October 2014; accepted 11 December 2014; online 1 January 2015)

In the title compound, C₁₃H₁₂N₂O₅, the phthalimide ring system is essentially planar, with a maximum deviation of 0.0479 (14) Å. In the crystal, each molecule is linked via six neighbouring molecules into a three-dimensional network through N—H⋯O and O—H⋯O hydrogen bonds, which form an R₃²(8) ring motif.

Keywords: crystal structure; thalidomide; hydrogen bonds.

CCDC reference: 1038803

1. Chemical context

The title compound, 5-(aminoxy)-4-(3-oxo-2H-isoindol-2-oyl)valeric acid (phthaloylisoglutamine), is one of the first-step hydrolysis products of thalidomide. Thalidomide was first synthesized in 1953 and was marketed as a hypnotic medicine in 1956. After that, the teratogenic side effect of thalidomide was proved and caused serious drug disaster (Lenz, 1961 ). Blashke et al. (1979 ) reported that only (S)-thalidomide exhibits teratogenicity while (R)-thalidomide exhibits sedative effects. In other words, the hypnotic and teratogenic mechanisms of thalidomide are different. For a long time, the target protein of thalidomide has not been clarified. However in 2010, the protein cereblon, which is one of the E3 ubiquitin ligase proteins, was identified as the primary target of thalidomide teratogenicity (Ito et al., 2010 ). Furthermore, the conformation of a Cereblon and thalidomide complex has been reported (Fischer et al., 2014 ).

Hydrolysis compounds of thalidomide are generated rapidly in vivo (Schumacher et al., 1965 ; Nishimura et al., 1994 ) and some of these showed TNF-α production-inhibitory activity (Nakamura et al., 2007 ). Although the crystal structures of racemic and enantiomeric thalidomide were solved and reported earlier (Allen & Trotter, 1971 ; Suzuki et al., 2010 ), the crystal structures of hydrolysis compounds of thalidomide have not been reported. Considering that knowing the structure of the molecule enables us to calculate the affinity between ligand and receptor using computer simulation, our report herein will be helpful in clarifying the differences between the biological effects of thalidomide and phthaloylisoglutamine.

2. Structural commentary

The molecular structure of the title molecule is shown in Fig. 1. The asymmetric center is S for atom C9. The phthalimide ring (N1/C1–C8) is essentially planar, with a maximum deviation of 0.0479 (14) Å for N1. The carbon–oxygen distances in the carboxy group (COOH) show different lengths [C13—O4 = 1.206 (2) and C13—O5 = 1.316 (2) Å]. This difference indicates that the C—O bonds in the carboxy group are non-delocalized. These bonds are slightly strengthened by intermolecular O5—H12⋯O3 and O4⋯H7A—N2 hydrogen bonding (Fig. 2). The conformation of C9—C11—C12—C13 chain is slightly twisted gauche [torsion angle = 77.4 (2)°].

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

Figure 2
A trimer structure of the title compound and an R₃²(8) ring motif formed through O5ⁱⁱⁱ—H12ⁱⁱⁱ⋯O3ⁱⁱ, N2—H6B⋯O3ⁱⁱ and N2—H7A⋯O4ⁱⁱⁱ hydrogen bonds. [Symmetry codes: (ii) x + $[{1\over 2}]$ , −y + $[{1\over 2}]$ , −z + 1; (iii) −x + 1, y − $[{1\over 2}]$ , −z + $[{3\over 2}]$ .]

3. Supramolecular features

In the crystal structure, each molecule has six hydrogen bonds, which are divided into three types (Table 1). The three hydrogen bonds form a hydrogen-bonded ring with an R₃²(8) ring motif, which unites three molecules (Fig. 2). Taken together as shown in Fig. 3, one molecule (yellow) is linked to another six molecules (blue, red, and green) by three sets of circular hydrogen bonds.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O5—H12⋯O3ⁱ	0.83	1.80	2.6230 (19)	172
N2—H6B⋯O3ⁱⁱ	0.87	2.32	2.891 (2)	123
N2—H7A⋯O4ⁱⁱⁱ	0.87	2.05	2.886 (2)	161
Symmetry codes: (i) $[-x+{\script{1\over 2}}, -y+1, z+{\script{1\over 2}}]$ ; (ii) $[x+{\script{1\over 2}}, -y+{\script{1\over 2}}, -z+1]$ ; (iii) $[-x+1, y-{\script{1\over 2}}, -z+{\script{3\over 2}}]$ .

Figure 3
A crystal packing view of the title compound, showing the intermolecular hydrogen bonds. A yellow molecule is linked with two red, two green and two blue molecules.

4. Database survey

A search of the Cambridge Structural Database (Version 5.35 update in 2014; Groom & Allen, 2014 ) for the structure of thalidomide gave 11 hits, but there was no hydrolysis compound of thalidomide.

5. Synthesis and crystallization

The title compound was purchased from WuXi AppTec. The title compound (2 mg) was dissolved in ethanol (500 µl). After a few days of slow evaporation at 278 K, colourless single crystals suitable for X-ray diffraction were obtained.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. All H atoms were included in calculated positions [C—H (aromatic) = 0.93, C—H (methine) = 0.98, C—H (methylene) = 0.97, N—H = 0.87 and O—H = 0.82 Å] and treated as riding atoms with U_iso(H) = 1.2U_eq(C) and 1.5U_eq(N, O).

Table 2
Experimental details

Crystal data
Chemical formula	C₁₃H₁₂N₂O₅
M_r	276.25
Crystal system, space group	Orthorhombic, P2₁2₁2₁
Temperature (K)	223
a, b, c (Å)	8.4790 (3), 9.6751 (3), 15.4488 (5)
V (Å³)	1267.35 (7)
Z	4
Radiation type	Cu Kα
μ (mm⁻¹)	0.96
Crystal size (mm)	0.63 × 0.20 × 0.10

Data collection
Diffractometer	Rigaku R-AXIS RAPID
Absorption correction	Multi-scan (ABSCOR; Rigaku, 1995 )
T_min, T_max	0.766, 0.908
No. of measured, independent and observed [F² > 2σ(F²)] reflections	23228, 2320, 2245
R_int	0.058
(sin θ/λ)_max (Å⁻¹)	0.602

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.027, 0.067, 1.08
No. of reflections	2320
No. of parameters	183
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.16, −0.16
Absolute structure	Flack x determined using 914 quotients [(I⁺)−(I⁻)]/[(I⁺)+(I⁻)] (Parsons et al., 2013 )
Absolute structure parameter	0.06 (4)
Computer programs: RAPID-AUTO (Rigaku, 1998 ), SHELXS2013 and SHELXL2013 (Sheldrick, 2008 ) and CrystalStructure (Rigaku, 2014 ).

Supporting information

CCDC reference: 1038803

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S2056989014027121/is5381sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989014027121/is5381Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989014027121/is5381Isup3.cml

checkCIF report

Computing details top

Data collection: RAPID-AUTO (Rigaku, 1998); cell refinement: RAPID-AUTO (Rigaku, 1998); data reduction: RAPID-AUTO (Rigaku, 1998); program(s) used to solve structure: SHELXS2013 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2013 (Sheldrick, 2008); molecular graphics: CrystalStructure (Rigaku, 2014); software used to prepare material for publication: CrystalStructure (Rigaku, 2014).

(S)-4-Carbamoyl-4-(1,3-dioxoisoindolin-2-yl)butanoic acid top

Crystal data top

C₁₃H₁₂N₂O₅	D_x = 1.448 Mg m⁻³
M_r = 276.25	Cu Kα radiation, λ = 1.54187 Å
Orthorhombic, P2₁2₁2₁	Cell parameters from 12101 reflections
a = 8.4790 (3) Å	θ = 4.6–68.3°
b = 9.6751 (3) Å	µ = 0.96 mm⁻¹
c = 15.4488 (5) Å	T = 223 K
V = 1267.35 (7) Å³	Needle, colorless
Z = 4	0.63 × 0.20 × 0.10 mm
F(000) = 576.00

Data collection top

Rigaku R-AXIS RAPID diffractometer	2245 reflections with F² > 2σ(F²)
Detector resolution: 10.000 pixels mm^-1	R_int = 0.058
ω scans	θ_max = 68.2°, θ_min = 5.4°
Absorption correction: multi-scan (ABSCOR; Rigaku, 1995)	h = −10→10
T_min = 0.766, T_max = 0.908	k = −11→11
23228 measured reflections	l = −18→18
2320 independent reflections

Refinement top

Refinement on F²	H-atom parameters constrained
R[F² > 2σ(F²)] = 0.027	w = 1/[σ²(F_o²) + (0.0326P)² + 0.1235P] where P = (F_o² + 2F_c²)/3
wR(F²) = 0.067	(Δ/σ)_max < 0.001
S = 1.08	Δρ_max = 0.16 e Å⁻³
2320 reflections	Δρ_min = −0.16 e Å⁻³
183 parameters	Extinction correction: SHELXL2013 (Sheldrick, 2008)
0 restraints	Extinction coefficient: 0.0357 (16)
Primary atom site location: structure-invariant direct methods	Absolute structure: Flack x determined using 914 quotients [(I⁺)-(I^-)]/[(I⁺)+(I^-)] (Parsons et al., 2013)
Secondary atom site location: difference Fourier map	Absolute structure parameter: 0.06 (4)
Hydrogen site location: inferred from neighbouring sites

Special details top

Refinement. Refinement was performed using all reflections. The weighted R-factor (wR) and goodness of fit (S) are based on F². R-factor (gt) are based on F. The threshold expression of F² > 2.0 σ(F²) is used only for calculating R-factor (gt).

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

	x	y	z	U_iso*/U_eq
O1	0.60120 (16)	0.50832 (14)	0.65955 (9)	0.0380 (4)
O2	0.22423 (15)	0.29086 (15)	0.81979 (8)	0.0354 (3)
O3	0.28367 (17)	0.34228 (17)	0.49573 (8)	0.0435 (4)
O4	0.32128 (15)	0.66161 (14)	0.78685 (8)	0.0353 (3)
O5	0.08071 (16)	0.6519 (2)	0.84322 (9)	0.0498 (4)
N1	0.39627 (16)	0.38300 (15)	0.71946 (9)	0.0246 (3)
N2	0.48080 (19)	0.24502 (17)	0.57047 (10)	0.0342 (4)
C1	0.7414 (2)	0.4824 (2)	0.84759 (13)	0.0358 (4)
C2	0.7647 (2)	0.4539 (2)	0.93501 (13)	0.0416 (5)
C3	0.6535 (2)	0.3840 (2)	0.98308 (13)	0.0395 (5)
C4	0.5124 (2)	0.3393 (2)	0.94584 (11)	0.0326 (4)
C5	0.4892 (2)	0.36838 (17)	0.85916 (11)	0.0255 (4)
C6	0.6010 (2)	0.43761 (18)	0.81107 (11)	0.0274 (4)
C7	0.5420 (2)	0.45217 (18)	0.72098 (11)	0.0266 (4)
C8	0.3518 (2)	0.33864 (17)	0.80233 (11)	0.0250 (4)
C9	0.2867 (2)	0.38767 (19)	0.64668 (11)	0.0269 (4)
C10	0.3548 (2)	0.32287 (19)	0.56467 (11)	0.0281 (4)
C11	0.2218 (2)	0.5328 (2)	0.62906 (12)	0.0337 (4)
C12	0.1075 (2)	0.5854 (2)	0.69751 (13)	0.0396 (5)
C13	0.1827 (2)	0.63585 (19)	0.77980 (12)	0.0311 (4)
H1	0.81748	0.52994	0.8148	0.0429*
H2	0.85847	0.48296	0.96185	0.0499*
H3	0.67296	0.36605	1.04192	0.0475*
H4	0.43628	0.2915	0.97838	0.0392*
H5	0.19512	0.32999	0.66336	0.0323*
H6B	0.51794	0.20427	0.52459	0.0513*
H7A	0.52731	0.23407	0.62019	0.0513*
H8A	0.31049	0.59737	0.62494	0.0404*
H9B	0.16801	0.53233	0.5729	0.0404*
H10A	0.04576	0.66122	0.67253	0.0475*
H11B	0.03387	0.51082	0.71193	0.0475*
H12	0.1288	0.66053	0.8897	0.0747*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0368 (7)	0.0480 (8)	0.0294 (7)	−0.0115 (7)	0.0044 (6)	0.0064 (6)
O2	0.0285 (7)	0.0478 (8)	0.0299 (7)	−0.0078 (6)	0.0024 (6)	0.0079 (6)
O3	0.0411 (8)	0.0673 (10)	0.0221 (7)	0.0098 (8)	−0.0079 (6)	−0.0063 (6)
O4	0.0307 (7)	0.0439 (7)	0.0313 (7)	−0.0037 (6)	−0.0003 (6)	−0.0053 (6)
O5	0.0331 (7)	0.0856 (12)	0.0306 (8)	−0.0014 (8)	0.0020 (6)	−0.0085 (8)
N1	0.0237 (7)	0.0314 (7)	0.0188 (7)	−0.0022 (6)	−0.0007 (6)	0.0021 (6)
N2	0.0352 (9)	0.0442 (9)	0.0233 (8)	0.0063 (7)	−0.0016 (7)	−0.0053 (7)
C1	0.0269 (9)	0.0432 (10)	0.0373 (11)	−0.0013 (9)	−0.0037 (8)	−0.0049 (9)
C2	0.0322 (10)	0.0538 (12)	0.0388 (11)	0.0062 (10)	−0.0146 (9)	−0.0102 (10)
C3	0.0436 (12)	0.0508 (11)	0.0243 (10)	0.0134 (10)	−0.0094 (9)	−0.0036 (9)
C4	0.0362 (10)	0.0392 (10)	0.0225 (9)	0.0074 (9)	0.0008 (8)	0.0014 (8)
C5	0.0262 (9)	0.0286 (9)	0.0219 (9)	0.0046 (7)	0.0000 (7)	−0.0023 (7)
C6	0.0257 (8)	0.0315 (8)	0.0251 (9)	0.0030 (8)	−0.0013 (7)	−0.0024 (8)
C7	0.0239 (8)	0.0315 (8)	0.0244 (9)	−0.0024 (7)	0.0012 (7)	0.0001 (8)
C8	0.0272 (9)	0.0268 (8)	0.0210 (8)	0.0026 (7)	0.0004 (7)	0.0023 (7)
C9	0.0242 (8)	0.0364 (9)	0.0203 (9)	−0.0034 (7)	−0.0031 (7)	0.0016 (8)
C10	0.0259 (9)	0.0366 (9)	0.0217 (9)	−0.0053 (8)	−0.0027 (7)	0.0003 (7)
C11	0.0376 (10)	0.0409 (10)	0.0226 (9)	0.0074 (9)	−0.0064 (8)	0.0017 (8)
C12	0.0318 (9)	0.0517 (12)	0.0351 (11)	0.0115 (9)	−0.0089 (9)	−0.0073 (9)
C13	0.0321 (10)	0.0321 (9)	0.0291 (10)	0.0051 (8)	−0.0018 (8)	0.0016 (8)

Geometric parameters (Å, º) top

O1—C7	1.203 (2)	C9—C10	1.527 (2)
O2—C8	1.207 (2)	C9—C11	1.532 (3)
O3—C10	1.238 (2)	C11—C12	1.522 (3)
O4—C13	1.206 (2)	C12—C13	1.503 (3)
O5—C13	1.316 (2)	O5—H12	0.830
N1—C7	1.405 (2)	N2—H6B	0.870
N1—C8	1.402 (2)	N2—H7A	0.870
N1—C9	1.460 (2)	C1—H1	0.940
N2—C10	1.310 (2)	C2—H2	0.940
C1—C2	1.393 (3)	C3—H3	0.940
C1—C6	1.387 (3)	C4—H4	0.940
C2—C3	1.378 (3)	C9—H5	0.990
C3—C4	1.396 (3)	C11—H8A	0.980
C4—C5	1.382 (2)	C11—H9B	0.980
C5—C6	1.378 (2)	C12—H10A	0.980
C5—C8	1.487 (2)	C12—H11B	0.980
C6—C7	1.486 (2)

C7—N1—C8	111.52 (14)	O4—C13—C12	123.81 (17)
C7—N1—C9	123.92 (14)	O5—C13—C12	112.90 (16)
C8—N1—C9	122.81 (14)	C13—O5—H12	109.469
C2—C1—C6	117.00 (17)	C10—N2—H6B	120.005
C1—C2—C3	121.55 (19)	C10—N2—H7A	120.001
C2—C3—C4	121.08 (18)	H6B—N2—H7A	119.994
C3—C4—C5	117.28 (17)	C2—C1—H1	121.519
C4—C5—C6	121.54 (16)	C6—C1—H1	121.506
C4—C5—C8	130.11 (16)	C1—C2—H2	119.202
C6—C5—C8	108.34 (15)	C3—C2—H2	119.210
C1—C6—C5	121.54 (16)	C2—C3—H3	119.482
C1—C6—C7	129.83 (16)	C4—C3—H3	119.476
C5—C6—C7	108.63 (15)	C3—C4—H4	121.355
O1—C7—N1	124.67 (16)	C5—C4—H4	121.352
O1—C7—C6	129.86 (16)	N1—C9—H5	106.340
N1—C7—C6	105.47 (14)	C10—C9—H5	106.336
O2—C8—N1	124.22 (16)	C11—C9—H5	106.343
O2—C8—C5	130.12 (16)	C9—C11—H8A	108.681
N1—C8—C5	105.63 (14)	C9—C11—H9B	108.685
N1—C9—C10	112.66 (14)	C12—C11—H8A	108.682
N1—C9—C11	113.19 (15)	C12—C11—H9B	108.682
C10—C9—C11	111.39 (14)	H8A—C11—H9B	107.616
O3—C10—N2	122.91 (17)	C11—C12—H10A	108.474
O3—C10—C9	117.83 (16)	C11—C12—H11B	108.468
N2—C10—C9	119.20 (15)	C13—C12—H10A	108.470
C9—C11—C12	114.32 (16)	C13—C12—H11B	108.470
C11—C12—C13	115.22 (16)	H10A—C12—H11B	107.495
O4—C13—O5	123.27 (17)

C7—N1—C8—O2	171.27 (15)	C4—C5—C6—C7	179.74 (15)
C7—N1—C8—C5	−6.74 (17)	C4—C5—C8—O2	5.8 (3)
C8—N1—C7—O1	−174.78 (15)	C4—C5—C8—N1	−176.37 (17)
C8—N1—C7—C6	5.92 (17)	C6—C5—C8—O2	−172.97 (16)
C7—N1—C9—C10	63.76 (19)	C6—C5—C8—N1	4.88 (17)
C7—N1—C9—C11	−63.74 (19)	C8—C5—C6—C1	178.32 (13)
C9—N1—C7—O1	−9.5 (3)	C8—C5—C6—C7	−1.38 (18)
C9—N1—C7—C6	171.19 (13)	C1—C6—C7—O1	−1.5 (3)
C8—N1—C9—C10	−132.59 (14)	C1—C6—C7—N1	177.71 (17)
C8—N1—C9—C11	99.91 (17)	C5—C6—C7—O1	178.13 (16)
C9—N1—C8—O2	5.8 (2)	C5—C6—C7—N1	−2.62 (18)
C9—N1—C8—C5	−172.20 (13)	N1—C9—C10—O3	−167.77 (14)
C2—C1—C6—C5	0.2 (3)	N1—C9—C10—N2	15.1 (2)
C2—C1—C6—C7	179.85 (16)	N1—C9—C11—C12	−70.37 (18)
C6—C1—C2—C3	0.2 (3)	C10—C9—C11—C12	161.47 (13)
C1—C2—C3—C4	−0.2 (3)	C11—C9—C10—O3	−39.3 (2)
C2—C3—C4—C5	−0.1 (3)	C11—C9—C10—N2	143.54 (15)
C3—C4—C5—C6	0.5 (3)	C9—C11—C12—C13	77.4 (2)
C3—C4—C5—C8	−178.13 (16)	C11—C12—C13—O4	15.2 (3)
C4—C5—C6—C1	−0.6 (3)	C11—C12—C13—O5	−166.20 (15)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O5—H12···O3ⁱ	0.83	1.80	2.6230 (19)	172
N2—H6B···O3ⁱⁱ	0.87	2.32	2.891 (2)	123
N2—H7A···O4ⁱⁱⁱ	0.87	2.05	2.886 (2)	161

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

Footnotes

¹Trivial name (S)-phthaloylisoglutamine, one of the hydrolysis products of thalidomide.

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