Home The crystal structure of 5-amino-5-oxo-4-(1-oxo-4-(2-oxopyrrolidin-1-yl)isoindolin-2-yl)pentanoic acid, C17H19N3O5
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The crystal structure of 5-amino-5-oxo-4-(1-oxo-4-(2-oxopyrrolidin-1-yl)isoindolin-2-yl)pentanoic acid, C17H19N3O5

  • Qing Wang , Yanrong Gao , Hongjuan Tong ORCID logo and Wenqiang Tang ORCID logo EMAIL logo
Published/Copyright: November 15, 2023
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Zeitschrift für Kristallographie - New Crystal Structures
From the journal Zeitschrift für Kristallographie - New Crystal Structures Volume 239 Issue 1

Abstract

C17H19N3O5, triclinic, P 1 ‾ (no. 2), a = 8.3683(3) Å, b = 9.1873(3) Å, c = 11.3782(4) Å, α = 96.553(1)°, β = 108.368(1)°, γ = 92.429(1)°, V = 821.94(5) Å3, Z = 2, R gt (F) = 0.0450, wR ref (F2) = 0.1175, T = 170 K.

CCDC no.: 2292587

The molecular structure is shown in the figure. Table 1 contains crystallographic data and Table 2 contains the list of the atoms including atomic coordinates and displacement parameters.

Table 1:

Data collection and handling.

Crystal: Colourless block
Size: 0.12 × 0.08 × 0.05 mm
Wavelength: Mo Kα radiation (0.71073 Å)
μ: 0.10 mm−1
Diffractometer, scan mode: D8 VENTURE, φ and ω
θmax, completeness: 26.4°, >99 %
N(hkl)measured, N(hkl)unique, Rint: 9545, 3343, 0.049
Criterion for Iobs, N(hkl)gt: Iobs > 2σ(Iobs), 2528
N(param)refined: 227
Programs: Bruker [1], SHELX [2, 3], Olex2 [4]
Table 2:

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

Atom x y z Uiso*/Ueq
C1 0.2862 (2) 0.9589 (2) 0.22399 (19) 0.0311 (5)
H1A 0.308889 0.914396 0.148001 0.037*
H1B 0.374918 1.038936 0.268497 0.037*
C2 0.1103 (3) 1.0146 (2) 0.1920 (2) 0.0391 (5)
H2A 0.105517 1.095633 0.255826 0.047*
H2B 0.076876 1.049482 0.109141 0.047*
C3 −0.0021 (2) 0.8796 (2) 0.1915 (2) 0.0358 (5)
H3C −0.097598 0.908077 0.220521 0.043*
H3D −0.047640 0.823651 0.106623 0.043*
C4 0.1134 (2) 0.7896 (2) 0.28104 (17) 0.0261 (4)
C5 0.4231 (2) 0.78458 (19) 0.37368 (16) 0.0225 (4)
C6 0.5601 (2) 0.7746 (2) 0.32857 (18) 0.0287 (4)
H6 0.552054 0.808699 0.251302 0.034*
C7 0.7082 (2) 0.7162 (2) 0.39375 (18) 0.0300 (5)
H7 0.798872 0.710672 0.360405 0.036*
C8 0.7240 (2) 0.6661 (2) 0.50681 (18) 0.0270 (4)
H8 0.823670 0.624865 0.551640 0.032*
C9 0.5885 (2) 0.67854 (19) 0.55227 (17) 0.0227 (4)
C10 0.4404 (2) 0.73710 (19) 0.48870 (16) 0.0212 (4)
C11 0.3249 (2) 0.7415 (2) 0.56653 (16) 0.0237 (4)
H11A 0.300058 0.843520 0.588659 0.028*
H11B 0.217382 0.680921 0.522527 0.028*
C12 0.5774 (2) 0.64364 (19) 0.67298 (17) 0.0221 (4)
C13 0.4279 (2) 0.81687 (19) 0.87301 (16) 0.0209 (4)
C14 0.3728 (2) 0.67029 (19) 0.78794 (16) 0.0206 (4)
H14 0.432252 0.590957 0.833275 0.025*
C15 0.1824 (2) 0.6355 (2) 0.75472 (17) 0.0230 (4)
H15A 0.122669 0.706199 0.700209 0.028*
H15B 0.150455 0.535723 0.707140 0.028*
C16 0.1254 (2) 0.6432 (2) 0.87012 (17) 0.0244 (4)
H16A 0.147842 0.745616 0.912810 0.029*
H16B 0.001865 0.618076 0.842705 0.029*
C17 0.2099 (2) 0.5435 (2) 0.96203 (17) 0.0238 (4)
N1 0.27630 (18) 0.84785 (17) 0.30557 (14) 0.0246 (4)
N2 0.42371 (18) 0.67976 (16) 0.67728 (13) 0.0207 (3)
N3 0.5523 (2) 0.81464 (17) 0.97887 (15) 0.0298 (4)
H3A 0.588989 0.895769 1.031824 0.036*
H3B 0.598233 0.732024 0.996313 0.036*
O1 0.07119 (16) 0.68343 (15) 0.32244 (12) 0.0318 (3)
O2 0.35670 (16) 0.92824 (13) 0.84154 (12) 0.0286 (3)
O3 0.68721 (16) 0.59542 (15) 0.75635 (12) 0.0303 (3)
O4 0.28085 (18) 0.43750 (15) 0.93747 (13) 0.0340 (3)
O5 0.19910 (18) 0.58426 (15) 1.07467 (12) 0.0349 (4)
H5 0.248094 0.526080 1.123532 0.052*

1 Source of materials

A mixture of methyl 5-amino-5-oxo-4-(1-oxo-4-(2-oxopyrrolidin-1-yl) isoindolin-2-yl)pentanoate (3.6 g, 10 mmol), H2O (10 mL), and sodium hydroxide (1.6 g, 40 mmol) was stirred in tetrahydrofuran (30 mL) at 40 °C for 2 h. The reaction was monitored by thin-layer chromatography. The solution was concentrated and diluted with water, and the pH was adjusted to three by adding hydrochloric acid solution (4 mol/L). The mixture was extracted with ethyl acetate and washed with brine. The organic layer was concentrated under reduced pressure, and the residue was purified by column chromatography using dichloromethane and methanol (15:1, v/v). Crystals of the title compound were obtained by slow evaporation of the aforementioned mixed solution at room temperature after a week.

2 Experimental details

Hydrogen atoms were positioned ideally and refined as riding atoms, with Uiso values set to 1.2 Ueq of the parent atoms. The structure was solved with ShelXT [2] and refined using ShelXL [3] in Olex2 software [4].

3 Comment

Isoindole derivatives are a prominent class of heterocyclic compounds with significant biological activity [5]. To date, numerous research reports have explored the crystal structures of isoindoles, which play a significant role in studying their activity and aiding in the development of new drugs [6], [7], [8], [9], [10], [11].

The crystal structure analysis reveals that a pyrrolidin-2-one group substitutes a hydrogen atom on the phenyl ring within the isoindole framework. Notably, the atoms within the pyrrolidin-2-one moiety exhibit non-coplanar arrangement, exemplified by the dihedral angle of 32.05(19)° for the N1–C1–C2–C3 atoms. Conversely, the atoms within the isoindole moiety demonstrate nearly coplanar alignment, with minimal torsional angles, consistent with previously reported structures [12], [13], [14]. This investigation encompasses a discussion on the crystal packing of the studied compound, revealing that the molecules primarily form stacks through hydrogen bonds. Specifically, two crystallographically dependent N3–H3A⋯O2 bonds and one O5–H5⋯O3 bond are involved in the intermolecular interactions. These hydrogen bonds display angles close to 180° and bond lengths below 2 Å, indicating strong hydrogen bonding interactions.

Corresponding author: Wenqiang Tang, Xianyang Key Laboratory of Molecular Imaging and Drug Synthesis, School of Pharmacy, Shaanxi Institute of International Trade & Commerce, Xianyang, Shaanxi, China, E-mail:

Funding source: key laboratory of molecular imaging and drug synthesis of Xianyang city

Award Identifier / Grant number: 2021QXNL–PT-0008

Funding source: Natural Science Foundation of Shaanxi Province

Award Identifier / Grant number: 2021SF-386

Funding source: the scientific research plan project of Shaanxi provincial department of education

Award Identifier / Grant number: 21JK0517

Funding source: Shaanxi University Association of Science and Technology Young Talents Lifting Plan Project

Award Identifier / Grant number: 20210313

  1. Author contribution: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.

  2. Research funding: This work was financially supported by the projects of key laboratory of molecular imaging and drug synthesis of Xianyang city (2021QXNL–PT-0008), the Natural Science Foundation of Shaanxi Province (2021SF-386), the scientific research plan project of Shaanxi provincial department of education (21JK0517) and Shaanxi University Association of Science and Technology Young Talents Lifting Plan Project (20210313).

  3. Competing interests: The authors declare no conflicts of interest regarding this article.

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Received: 2023-09-30
Accepted: 2023-11-03
Published Online: 2023-11-15
Published in Print: 2024-02-26

© 2023 the author(s), published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution 4.0 International License.

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  1. Frontmatter
  2. New Crystal Structures
  3. Crystal structure of poly[diaqua-(μ4-3,3′-di(1H-1,2,4-triazol-1-yl)-[1,1′-biphenyl]-4,4′-dicarboxylate-N:N′:O:O′)cadmium(II)], C18H14N6O6Cd
  4. Crystal structure of (8R,8′S,13S,13′R)-8,8′-bis(hydroxymethyl)-9,9′,10,10′-tetramethoxy-5,5′,6,6′,8,8′,13,13′-octahydro-[13,13′-bi[1,3]dioxolo[4,5-g]isoquinolino[3,2-a]isoquinoline]-7,7′-diium chloride-methanol (1/2), C46H58N2O14Cl2
  5. The crystal structure of 8-methoxy-2,2-diphenyl-tosyl-1,2-dihydro-2λ4,3λ4-[1,3,2]diazaborolo[4,5,1-ig]quinoline, C29H25BN2O3S
  6. Crystal structure of aqua-(5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane-κ4N,N′,N″,N‴)copper(II) 5-carboxyisophthalate tetrahydrate, C25H50N4CuO11
  7. The crystal structure of 1-(naphthalen-2-ylsulfonyl)-2,2-diphenyl-1,2-dihydro-2λ4,3λ4-[1,3,2]diazaborolo[4,5,1-ij]quinoline, C31H23BN2O2S
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  9. The crystal structure of 1-(3-oxo-1-phenyl-3-(p-tolyl) propylidene)-1,3-dihydro-2H-inden-2-one, C25H20O2
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  11. Crystal structure of [triaqua-(8-carboxymethoxy-quinoline-2-carboxylate-κ4N,O,O,O)cadmium(II)]monohydrate, C12H15NO9Cd
  12. Crystal structure of ethyl 2-((4-(3,5-dimethylisoxazol-4-yl)-2,6-difluorophenyl)amino)benzoate, C20H18F2N2O3
  13. The crystal structure of 2-(hydroxymethyl)-2-(4H-1,2,4-triazol-4-yl)propane-1,3-diol, C6H11N3O3
  14. The crystal structure of 1,2-bis(2,4-dinitrophenyl) hydrazine, C12H8N6O8
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  16. The crystal structure of 5-amino-5-oxo-4-(1-oxo-4-(2-oxopyrrolidin-1-yl)isoindolin-2-yl)pentanoic acid, C17H19N3O5
  17. Crystal structure of N2,N6-bis(2-(((Z)-5-bromo-2-hydroxybenzylidene)amino) phenyl)pyridine-2,6-dicarboxamide, C33H23Br2N5O4
  18. The crystal structure of (E)-2-methoxy-6-(((5-methyl-1,3,4-thiadiazol-2-yl)imino)methyl)phenol, C11H11N3O2S
  19. The crystal structure of 3-((tert-butyldiphenylsilyl)methyl)-5,5-diphenyl-6-(p-tolyl) tetrahydro-2H-pyran-2-one, C41H42O2Si
  20. Crystal structure of 9-fluoro-4-(6-methoxypyridin-3-yl)-5,6-dihydrobenzo[h]quinazolin-2-amine, C18H15FN4O
  21. The crystal structure of 2-bromo-5-(4-cyanophenoxy)benzyl 1-methyl-1,2,5,6-tetrahydropyridine-3-carboxylate, C21H19BrN2O3
  22. Crystal structure of 3,3′-(1,4-phenylenebis(methylene))bis(1-isopropyl-1H-imidazol-3-ium) bis(hexafluorophosphate(V)), C10H14F6N2P
  23. The crystal structure of 2,2-di(thiophen-3-yl)-1-tosyl-1,2-dihydro-2λ4,3λ4-[1,3,2]diazaborolo[4,5,1-ig]quinoline, C24H19BN2O2S3
  24. Crystal structure of 5-bromo-1-(2-iodobenzoyl)-1H-indole-3-carbaldehyde, C16H9BrINO2
  25. The crystal structure of monocarbonyl-2-carboxypyridinato-κ2N,O-triphenylphosphine-rhodium(I) acetonitrile solvate, C26H20.50N1.50O3PRh
  26. Crystal structure of dichlorido-tetrakis(1-(2,4-dichlorophenyl)-4,4-dimethyl-2-(1,2,4-triazol-1-yl)pent-1-en-3-ol-κ1N)manganese(II), C60H68O4N12Cl10Mn
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  28. Crystal structure of langite from Mine du Pradet (France)
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https://doi.org/10.1515/ncrs-2023-0431
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Articles in the same Issue

  1. Frontmatter
  2. New Crystal Structures
  3. Crystal structure of poly[diaqua-(μ4-3,3′-di(1H-1,2,4-triazol-1-yl)-[1,1′-biphenyl]-4,4′-dicarboxylate-N:N′:O:O′)cadmium(II)], C18H14N6O6Cd
  4. Crystal structure of (8R,8′S,13S,13′R)-8,8′-bis(hydroxymethyl)-9,9′,10,10′-tetramethoxy-5,5′,6,6′,8,8′,13,13′-octahydro-[13,13′-bi[1,3]dioxolo[4,5-g]isoquinolino[3,2-a]isoquinoline]-7,7′-diium chloride-methanol (1/2), C46H58N2O14Cl2
  5. The crystal structure of 8-methoxy-2,2-diphenyl-tosyl-1,2-dihydro-2λ4,3λ4-[1,3,2]diazaborolo[4,5,1-ig]quinoline, C29H25BN2O3S
  6. Crystal structure of aqua-(5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane-κ4N,N′,N″,N‴)copper(II) 5-carboxyisophthalate tetrahydrate, C25H50N4CuO11
  7. The crystal structure of 1-(naphthalen-2-ylsulfonyl)-2,2-diphenyl-1,2-dihydro-2λ4,3λ4-[1,3,2]diazaborolo[4,5,1-ij]quinoline, C31H23BN2O2S
  8. Crystal structure of iodido-(η6-benzene) (1-(pyridin-2-yl)-N-(p-fluoro-methanamine)-κ2N,Nʹ)ruthenium(II) hexaflourophosphate, (C18H15F7IN2RuP)
  9. The crystal structure of 1-(3-oxo-1-phenyl-3-(p-tolyl) propylidene)-1,3-dihydro-2H-inden-2-one, C25H20O2
  10. Crystal structure of tricyclohexyl[4-(4H-1,2,4-triazol-4-yl)-benzoato-κO]tin(IV), C27H39N3O2Sn
  11. Crystal structure of [triaqua-(8-carboxymethoxy-quinoline-2-carboxylate-κ4N,O,O,O)cadmium(II)]monohydrate, C12H15NO9Cd
  12. Crystal structure of ethyl 2-((4-(3,5-dimethylisoxazol-4-yl)-2,6-difluorophenyl)amino)benzoate, C20H18F2N2O3
  13. The crystal structure of 2-(hydroxymethyl)-2-(4H-1,2,4-triazol-4-yl)propane-1,3-diol, C6H11N3O3
  14. The crystal structure of 1,2-bis(2,4-dinitrophenyl) hydrazine, C12H8N6O8
  15. Crystal structure of 1-(2,6-dichloro-4-(3,5-dimethylisoxazol-4-yl)phenyl)-1,2-dihydro-4H-benzo[d][1,3]oxazin-4-one, C19H14Cl2N2O3
  16. The crystal structure of 5-amino-5-oxo-4-(1-oxo-4-(2-oxopyrrolidin-1-yl)isoindolin-2-yl)pentanoic acid, C17H19N3O5
  17. Crystal structure of N2,N6-bis(2-(((Z)-5-bromo-2-hydroxybenzylidene)amino) phenyl)pyridine-2,6-dicarboxamide, C33H23Br2N5O4
  18. The crystal structure of (E)-2-methoxy-6-(((5-methyl-1,3,4-thiadiazol-2-yl)imino)methyl)phenol, C11H11N3O2S
  19. The crystal structure of 3-((tert-butyldiphenylsilyl)methyl)-5,5-diphenyl-6-(p-tolyl) tetrahydro-2H-pyran-2-one, C41H42O2Si
  20. Crystal structure of 9-fluoro-4-(6-methoxypyridin-3-yl)-5,6-dihydrobenzo[h]quinazolin-2-amine, C18H15FN4O
  21. The crystal structure of 2-bromo-5-(4-cyanophenoxy)benzyl 1-methyl-1,2,5,6-tetrahydropyridine-3-carboxylate, C21H19BrN2O3
  22. Crystal structure of 3,3′-(1,4-phenylenebis(methylene))bis(1-isopropyl-1H-imidazol-3-ium) bis(hexafluorophosphate(V)), C10H14F6N2P
  23. The crystal structure of 2,2-di(thiophen-3-yl)-1-tosyl-1,2-dihydro-2λ4,3λ4-[1,3,2]diazaborolo[4,5,1-ig]quinoline, C24H19BN2O2S3
  24. Crystal structure of 5-bromo-1-(2-iodobenzoyl)-1H-indole-3-carbaldehyde, C16H9BrINO2
  25. The crystal structure of monocarbonyl-2-carboxypyridinato-κ2N,O-triphenylphosphine-rhodium(I) acetonitrile solvate, C26H20.50N1.50O3PRh
  26. Crystal structure of dichlorido-tetrakis(1-(2,4-dichlorophenyl)-4,4-dimethyl-2-(1,2,4-triazol-1-yl)pent-1-en-3-ol-κ1N)manganese(II), C60H68O4N12Cl10Mn
  27. Crystal structure of 3-(tert-butyldiphenylsilyl)-1-(2,6-dichlorophenyl)-2,2-diphenylpropan-1-ol, C37H36Cl2OSi
  28. Crystal structure of langite from Mine du Pradet (France)
  29. The crystal structure of 5′-(furan-2-yl)-3′-((4-methylphenyl)sulfonamido)-3′,4′,5′,6′-tetrahydro-[1,1′:3′,1″-terphenyl]-4′-carboxylic acid, C30H27NO5S
  30. Synthesis and crystal structure of bis{2-(((4-acetophenone)imino)methyl)-4-fluorophenolato-κ2N,O}zinc(II), C30H22F2N2O4Zn
  31. The crystal structure of poly[(tripyridine-κ3N,N′,N″) μ3-(pyridine-3,4-dicarboxylate-κ3N:O:O′) manganese(II)], C22H22N4O8Mn
  32. The crystal structure of (E)-4-chloro-N′-(1-(4-hydroxyphenyl)propylidene)benzohydrazide, C16H15ClN2O2
  33. Synthesis and crystal structure of bis{2-(tert-butyl)-6-((E)-((4-((E)-1-(methoxyimino) ethyl)phenyl)imino)methyl)phenolato-κ2N,O}cobalt(II), C40H46CoN4O4
  34. Crystal structure of tetraaqua-[(1-(carboxymethyl)-1H-pyrazole-3-carboxylato-κ2N,O)cobalt(II)], C6H12CoN2O8
  35. (6R,7S)-2,3,13-trimethoxy-6,7-dimethyl-5,6,7,8-tetrahydrobenzo[3′,4′]cycloocta [1′,2′:4,5]benzo[1,2-d][1,3]dioxol-1-ol, C22H26O6
  36. Crystal structure of 2-((2,6-dichloro-4-(3,5-dimethylisoxazol-4-yl)phenyl)amino)benzoic acid, C18H14Cl2N2O3
  37. Crystal structure of (5aS,6aS,8aR,9R,11aS, 11bS,13R,13aS)-1,1,8a,11a-tetramethyl-9-((S)-1-((S)-5-methyl-6-oxo-3,6-dihydro-2H-pyran-2-yl)ethyl)-3-oxo-1,7,8,8a,9,10,11,11a,11b,12,13,13a-dodecahydro-3H,6H-cyclopenta[5,6]cyclopropa[1,8a]naphtho[2,1-c]oxepin-13-yl acetate, C32H44O6
  38. Crystal structure of catena-poly[triaqua-(μ2-1-(4-carboxylatophenyl)-4-oxo-1,4-dihydropyridazine-3-carboxylato-O,O′:O″)cobalt(II)], C12H12N2O8Co
  39. Crystal structure of 3-[(furan-2-ylmethyl)-amino]-2-(2,3,4,5-tetrafluoro-benzoyl)-acrylic acid ethyl ester, C17H13F4NO4
  40. Crystal structure of methyl 4-(2-ethoxy-2-oxoethoxy)-3-methoxybenzoate, C13H16O6
  41. Crystal structure of 4-bromo-2-(4-chlorophenyl)-1-methyl-5-(trifluoromethyl)-1H-pyrrole-3-carbonitrile, C13H7BrClF3N2
  42. The crystal structure of triaqua-(8-carboxymethoxy-quinoline-2-carboxylate-κ3N,O,O)nickel(II) monohydrate, C12H15NO9Ni
  43. Crystal structure of dihydroxy(2,4,6-triisopro-pylphenyl)telluronium trifluoromethanesulfonate, C16H25F3O5STe
  44. The crystal structure of 1-(carboxymethyl)-1H-imidazole 3-oxide
  45. The crystal structure of 1,3,5-tris(dibromomethyl)benzene, C9H6Br6
  46. Crystal structure of (Z)-3-(4-methoxyphenyl)-4-(5-methyl-1-phenyl-1H-1,2,3-triazol-4-yl)-N-phenylthiazol-2(3H)-imine, C25H21N5OS
  47. Crystal structure of (Z)-3-(3-(4-hydroxyphenyl)-2-(phenylimino)-2,3-dihydrothiazol-4-yl)-2H-chromen-2-one, C24H16N2O3S
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