SMTL ID : 4qj1.1

Co-crystal structure of the catalytic domain of the inosine monophosphate dehydrogenase from Cryptosporidium parvum with inhibitor N109

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.42 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: N09.2 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:S.51, A:N.152, A:S.178, A:D.213, A:G.215, A:I.216, A:G.236, A:S.237, A:S.237, A:M.263, A:G.264, A:E.290 Water bridges: A:K.171, A:G.177, A:G.177, A:S.237, A:S.237 IMP.3: 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: N09.4 22 PLIP interactions: 22 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:S.237, B:Y.260, B:M.263, B:G.264, B:E.290 Water bridges: B:A.52, B:K.171, B:G.175, B:G.177, B:T.182, B:I.216, B:I.216, B:S.237, B:S.237, B:I.238 IMP.7: 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: N09.5 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:S.51, C:N.152, C:S.178, C:D.213, C:G.215, C:G.236, C:S.237, C:S.237, C:Y.260, C:M.263, C:G.264, C:E.290 IMP.9: 23 residues within 4Å: Chain D: S.51, M.53, N.152, G.177, S.178, I.179, C.180, T.182, 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: N09.10 18 PLIP interactions: 18 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:S.237, D:M.263, D:G.264, D:E.290 Water bridges: D:G.175, D:G.175, D:G.177, D:G.214, D:G.214, D:S.237, D:S.237

4 x N09: N-(4-chloro-3-methoxyphenyl)-2-(4-oxochromeno[4,3-c]pyrazol-1(4H)-yl)acetamide(Non-covalent)

N09.2: 12 residues within 4Å: Chain A: A.126, H.127, T.182, M.263, G.264, M.269, E.290 Chain D: P.29, S.315, G.318, Y.319 Ligands: IMP.1 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:A.126, A:E.290 Hydrogen bonds: A:E.290 pi-Stacking: D:Y.319 N09.4: 13 residues within 4Å: Chain A: P.29, S.315, G.318, Y.319 Chain B: S.125, A.126, H.127, T.182, M.263, G.264, M.269, E.290 Ligands: IMP.3 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:P.29, A:Y.319, B:A.126, B:E.290 Hydrogen bonds: B:E.290 N09.5: 13 residues within 4Å: Chain B: V.27, P.29, S.315, G.318, Y.319 Chain C: S.125, A.126, H.127, T.182, M.263, G.264, E.290 Ligands: IMP.7 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:A.126, B:P.29, B:Y.319 Hydrogen bonds: C:E.290 N09.10: 13 residues within 4Å: Chain C: L.28, P.29, S.315, G.318, Y.319 Chain D: A.126, H.127, T.182, M.263, G.264, M.269, E.290 Ligands: IMP.9 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:A.126, D:E.290, C:P.29, C:Y.319 Hydrogen bonds: D:E.290 Water bridges: D:A.126

1 x ACY: ACETIC ACID(Non-functional Binders)

ACY.6: 6 residues within 4Å: Chain A: T.338 Chain B: K.11, E.336, I.337, T.338 Chain C: K.11 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:E.336, B:T.338, C:K.11 Hydrogen bonds: B:E.336 Salt bridges: B:K.11

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

EDO.8: 8 residues within 4Å: Chain C: T.338, T.339, S.340 Chain D: E.16, D.17, I.337, T.338, T.339 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:S.340, C:S.340, D:E.16, D:D.17, D:T.339, D:T.339 Water bridges: C:T.339 EDO.11: 5 residues within 4Å: Chain D: R.217, I.238, K.299, M.357, N.358 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.299, D:K.299, D:N.358 EDO.13: 5 residues within 4Å: Chain A: G.5 Chain D: I.9, G.10, K.11, T.194 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.5, A:G.5

1 x FMT: FORMIC ACID(Non-functional Binders)

FMT.12: 4 residues within 4Å: Chain D: R.217, Y.218, I.238, S.360 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Co-crystal structure of the catalytic domain of the inosine monophosphate dehydrogenase from Cryptosporidium parvum with inhibitor N109. To be Published

Release Date

2014-08-06

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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