SMTL ID : 4ixh.1

Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Cryptosporidium parvum

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

homo-tetramer

Ligands

4 x IMP: INOSINIC ACID(Non-covalent)

IMP.1: 22 residues within 4Å: Chain A: S.51, M.53, N.152, G.177, S.178, I.179, C.180, D.213, G.214, G.215, M.234, I.235, G.236, S.237, Y.260, G.262, M.263, G.264, S.265, E.290, G.291 Ligands: Q21.6 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.51, A:N.152, A:S.178, A:D.213, A:G.215, A:G.236, A:S.237, A:Y.260, A:M.263, A:G.264, A:E.290 Water bridges: A:G.175, A:G.214, A:I.216, A:I.216, A:S.237, A:I.238, B:H.348 IMP.7: 22 residues within 4Å: Chain B: S.51, M.53, N.152, G.177, S.178, I.179, C.180, D.213, G.214, G.215, M.234, I.235, G.236, S.237, Y.260, G.262, M.263, G.264, S.265, E.290, G.291 Ligands: Q21.8 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:S.51, B:N.152, B:S.178, B:D.213, B:G.215, B:G.236, B:S.237, B:M.263, B:G.264, B:E.290 Water bridges: B:G.175, B:G.177, B:T.182, B:G.214, B:G.214, B:G.215, B:I.216, B:S.237, B:I.238 IMP.9: 22 residues within 4Å: Chain C: S.51, M.53, N.152, G.177, S.178, I.179, C.180, D.213, G.214, G.215, M.234, I.235, G.236, S.237, Y.260, G.262, M.263, G.264, S.265, E.290, G.291 Ligands: Q21.10 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:S.51, C:N.152, C:S.178, C:D.213, C:G.215, C:I.216, C:G.236, C:S.237, C:M.263, C:G.264, C:E.290 Water bridges: C:G.175, C:G.177, C:G.214, C:G.214, C:I.216, C:S.237, C:S.237, C:I.238 IMP.13: 22 residues within 4Å: Chain D: S.51, M.53, N.152, G.177, S.178, I.179, C.180, D.213, G.214, G.215, M.234, I.235, G.236, S.237, Y.260, G.262, M.263, G.264, S.265, E.290, G.291 Ligands: Q21.4 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:S.51, D:N.152, D:S.178, D:D.213, D:G.215, D:G.236, D:S.237, D:Y.260, D:M.263, D:G.264, D:E.290 Water bridges: D:G.175, D:G.177, D:G.214, D:G.215, D:I.216, D:I.216, D:S.237, D:I.238

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 4 residues within 4Å: Chain A: T.36, K.37, S.231, W.329 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.37, A:S.231, A:S.231 Water bridges: A:I.325 EDO.3: 4 residues within 4Å: Chain A: V.185, V.288, P.289 Chain B: Q.308 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:G.291 Hydrogen bonds: B:Q.308 EDO.5: 4 residues within 4Å: Chain A: Q.308 Chain D: V.185, V.288, P.289 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:P.289, A:Q.308 Water bridges: D:G.291 EDO.11: 4 residues within 4Å: Chain C: S.200, S.204, G.229, W.329 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.200, C:G.229 Water bridges: C:S.204 EDO.12: 5 residues within 4Å: Chain C: T.36, K.37, S.231, I.325, W.329 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.36, C:T.36, C:K.37, C:S.231 Water bridges: C:I.325

4 x Q21: (2S)-2-(naphthalen-1-yloxy)-N-[2-(pyridin-4-yl)-1,3-benzoxazol-5-yl]propanamide(Non-covalent)

Q21.4: 17 residues within 4Å: Chain A: S.25, V.27, L.28, P.29, S.315, G.318, Y.319 Chain D: A.126, S.130, T.182, M.263, G.264, M.269, M.287, V.288, E.290 Ligands: IMP.13 11 PLIP interactions: 7 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: D:A.126, D:M.263, D:E.290, A:L.28, A:P.29, A:Y.319 Hydrogen bonds: D:S.130, D:E.290, A:Y.319 Water bridges: D:A.126, D:L.131 Q21.6: 16 residues within 4Å: Chain A: A.126, S.130, T.182, M.263, G.264, M.287, V.288, E.290 Chain B: S.25, V.27, L.28, P.29, S.315, G.318, Y.319 Ligands: IMP.1 12 PLIP interactions: 7 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:A.126, A:M.263, A:E.290, B:L.28, B:P.29, B:Y.319 Hydrogen bonds: A:S.130, A:E.290, B:Y.319 Water bridges: A:A.126, A:L.131, B:S.315 Q21.8: 17 residues within 4Å: Chain B: A.126, S.130, N.132, T.182, M.263, G.264, M.287, V.288, E.290 Chain C: S.25, V.27, L.28, P.29, S.315, G.318, Y.319 Ligands: IMP.7 10 PLIP interactions: 3 interactions with chain C, 7 interactions with chain B Hydrophobic interactions: C:L.28, C:P.29, C:Y.319, B:A.126, B:M.263, B:E.290 Hydrogen bonds: B:S.130, B:E.290 Water bridges: B:A.126, B:L.131 Q21.10: 16 residues within 4Å: Chain C: A.126, S.130, N.132, T.182, M.263, G.264, V.288, E.290 Chain D: S.25, V.27, L.28, P.29, S.315, G.318, Y.319 Ligands: IMP.9 11 PLIP interactions: 3 interactions with chain D, 8 interactions with chain C Hydrophobic interactions: D:L.28, D:P.29, D:Y.319, C:A.126, C:M.263, C:E.290 Hydrogen bonds: C:S.130, C:E.290 Water bridges: C:A.126, C:L.131, C:E.290

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gorla, S.K. et al., Optimization of Benzoxazole-Based Inhibitors of Cryptosporidium parvum Inosine 5'-Monophosphate Dehydrogenase. J.Med.Chem. (2013)

Release Date

2013-04-03

Peptides

Inosine-5'-monophosphate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Inosine-5'-monophosphate dehydrogenase

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