SMTL ID : 8r3u.1

Crystal structure of DHPS in complex with an inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

homo-tetramer

Ligands

4 x XTQ: 2-[(2~{R})-1-azanyl-4-methyl-pentan-2-yl]-5-pyridin-3-yl-isoquinolin-1-one(Non-covalent)

XTQ.1: 16 residues within 4Å: Chain A: T.238, D.239, G.240, D.244 Chain B: V.130, F.233, P.235, I.260, D.263, L.264, I.267, N.268, A.271, V.286, V.287, R.298 10 PLIP interactions: 2 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:D.239, B:V.130, B:P.235, B:L.264, B:I.267, B:A.271, B:V.287 Hydrogen bonds: A:D.239 Water bridges: B:K.288, B:R.298 XTQ.7: 16 residues within 4Å: Chain A: V.130, F.233, P.235, I.260, D.263, L.264, I.267, N.268, A.271, V.286, V.287, R.298 Chain B: T.238, D.239, G.240, D.244 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.130, A:P.235, A:L.264, A:L.264, A:I.267, A:A.271, A:V.287, B:D.239 Water bridges: A:K.288, A:K.288 Hydrogen bonds: B:D.239 XTQ.12: 15 residues within 4Å: Chain C: T.238, D.239, G.240, D.244 Chain D: V.130, F.233, P.235, I.260, D.263, L.264, I.267, A.271, V.286, V.287, R.298 13 PLIP interactions: 10 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:V.130, D:P.235, D:L.264, D:I.267, D:A.271, D:V.287, C:D.239 Water bridges: D:D.263, D:K.288, D:K.288, D:K.288, C:D.244 Hydrogen bonds: C:D.239 XTQ.20: 14 residues within 4Å: Chain C: V.130, F.233, P.235, I.260, D.263, L.264, I.267, A.271, V.286, V.287, R.298 Chain D: T.238, D.239, D.244 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:V.130, C:P.235, C:L.264, C:I.267, C:A.271, C:V.287, D:D.239 Water bridges: C:K.288, C:K.288 Hydrogen bonds: D:D.239

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

EDO.2: 7 residues within 4Å: Chain A: E.181, D.244, M.245, F.248 Chain B: N.293, N.295, L.296 Ligand excluded by PLIP EDO.3: 5 residues within 4Å: Chain A: C.143, L.144, W.183, I.215, N.217 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: K.142, C.143, L.144, A.145, P.146 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain A: Y.306, P.337, K.339 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: N.293, N.295 Chain B: E.181, D.244, M.245, F.248 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain B: C.143, L.144, I.215, N.217 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain B: K.142, L.144, A.145, P.146 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain B: H.289, Y.306, P.337, K.339 Ligand excluded by PLIP EDO.11: 1 residues within 4Å: Chain B: N.196 Ligand excluded by PLIP EDO.13: 2 residues within 4Å: Chain C: G.40, V.41 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain C: P.218, Y.223, W.224, K.227 Ligands: DMS.18 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain C: C.143, L.144, I.215, N.217 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain C: K.142, L.144, A.145, P.146 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain C: Y.306, P.337, K.339 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain C: E.181, D.244, M.245, F.248 Chain D: N.293, N.295, L.296 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain C: N.293, N.295 Chain D: E.181, D.244, F.248 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain D: C.143, L.144, I.215, N.217 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain D: H.289, Y.306, E.312, K.339 Ligand excluded by PLIP

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.18: 4 residues within 4Å: Chain C: N.216, P.218, Y.223 Ligands: EDO.14 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.223 DMS.24: 3 residues within 4Å: Chain D: N.216, P.218, Y.223 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.216

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Turnbull, A.P., Crystal structure of DHPS in complex with an inhibitor. To Be Published

Release Date

2024-11-20

Peptides

Deoxyhypusine synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

C
CCC

D
DDD

Deoxyhypusine synthase