SMTL ID : 6w0t.1

Co-crystal structures of CHIKV nsP3 macrodomain with pyrimidone fragments

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

4 x S6Y: 6-(2-methylpropyl)-2-oxidanylidene-5~{H}-pyrimidine-4-carboxylic acid(Non-covalent)

S6Y.1: 14 residues within 4Å: Chain A: A.30, A.31, N.32, C.42, A.76, V.77, G.78, L.116, L.117, S.118, T.119, G.120, V.121, Y.122 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.121, A:Y.122, A:Y.122 Hydrogen bonds: A:G.78, A:S.118, A:T.119, A:G.120, A:Y.122 pi-Stacking: A:Y.122 S6Y.2: 15 residues within 4Å: Chain B: A.30, A.31, N.32, G.38, D.39, C.42, A.76, G.78, L.116, L.117, S.118, T.119, G.120, V.121, Y.122 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.121 Hydrogen bonds: B:G.78, B:S.118, B:T.119, B:G.120, B:Y.122 pi-Stacking: B:Y.122 S6Y.3: 15 residues within 4Å: Chain C: A.30, A.31, N.32, D.39, C.42, A.76, V.77, G.78, L.116, L.117, S.118, T.119, G.120, V.121, Y.122 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:V.121, C:Y.122, C:Y.122 Hydrogen bonds: C:G.78, C:S.118, C:T.119, C:G.120, C:Y.122 pi-Stacking: C:Y.122 S6Y.4: 14 residues within 4Å: Chain D: A.30, A.31, N.32, D.39, C.42, A.76, G.78, L.116, L.117, S.118, T.119, G.120, V.121, Y.122 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:V.121, D:Y.122, D:Y.122 Hydrogen bonds: D:G.78, D:L.116, D:S.118, D:T.119, D:G.120, D:Y.122 pi-Stacking: D:Y.122

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, S. et al., Pyrimidone inhibitors targeting Chikungunya Virus nsP3 macrodomain by fragment-based drug design. Plos One (2021)

Release Date

2021-01-13

Peptides

Non-structural protein 3: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Non-structural protein 3

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