SMTL ID : 4cdu.3 (3 other biounits)

Crystal structure of human Enterovirus 71 in complex with the uncoating inhibitor GPP3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-6-6-6-6-mer

Ligands

6 x YM2: 1-[(3S)-5-[4-[(E)-ETHOXYIMINOMETHYL]PHENOXY]-3-METHYL-PENTYL]-3-PYRIDIN-4-YL-IMIDAZOLIDIN-2-ONE(Non-covalent)

YM2.1: 20 residues within 4Å: Chain A: I.111, D.112, I.113, T.114, F.135, F.137, Y.153, F.155, P.177, S.178, V.179, V.192, M.195, Y.201, Q.202, W.203, N.228, M.230, F.233 Chain C: I.24 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:I.111, A:I.111, A:T.114, A:F.135, A:F.155, A:V.179, A:V.192, A:W.203, A:W.203, A:N.228, C:I.24 Hydrogen bonds: A:D.112, A:I.113 pi-Stacking: A:F.135, A:F.155 YM2.5: 20 residues within 4Å: Chain E: I.111, D.112, I.113, T.114, F.135, F.137, Y.153, F.155, P.177, S.178, V.179, V.192, M.195, Y.201, Q.202, W.203, N.228, M.230, F.233 Chain G: I.24 15 PLIP interactions: 14 interactions with chain E, 1 interactions with chain G Hydrophobic interactions: E:I.111, E:I.111, E:T.114, E:F.135, E:F.155, E:V.179, E:V.192, E:W.203, E:W.203, E:N.228, G:I.24 Hydrogen bonds: E:D.112, E:I.113 pi-Stacking: E:F.135, E:F.155 YM2.9: 20 residues within 4Å: Chain I: I.111, D.112, I.113, T.114, F.135, F.137, Y.153, F.155, P.177, S.178, V.179, V.192, M.195, Y.201, Q.202, W.203, N.228, M.230, F.233 Chain K: I.24 14 PLIP interactions: 13 interactions with chain I, 1 interactions with chain K Hydrophobic interactions: I:I.111, I:I.111, I:T.114, I:F.135, I:F.155, I:V.179, I:V.192, I:W.203, I:W.203, I:N.228, K:I.24 Hydrogen bonds: I:I.113 pi-Stacking: I:F.135, I:F.155 YM2.13: 20 residues within 4Å: Chain M: I.111, D.112, I.113, T.114, F.135, F.137, Y.153, F.155, P.177, S.178, V.179, V.192, M.195, Y.201, Q.202, W.203, N.228, M.230, F.233 Chain O: I.24 14 PLIP interactions: 13 interactions with chain M, 1 interactions with chain O Hydrophobic interactions: M:I.111, M:I.111, M:T.114, M:F.135, M:F.155, M:V.179, M:V.192, M:W.203, M:W.203, M:N.228, O:I.24 Hydrogen bonds: M:I.113 pi-Stacking: M:F.135, M:F.155 YM2.17: 20 residues within 4Å: Chain Q: I.111, D.112, I.113, T.114, F.135, F.137, Y.153, F.155, P.177, S.178, V.179, V.192, M.195, Y.201, Q.202, W.203, N.228, M.230, F.233 Chain S: I.24 15 PLIP interactions: 14 interactions with chain Q, 1 interactions with chain S Hydrophobic interactions: Q:I.111, Q:I.111, Q:T.114, Q:F.135, Q:F.155, Q:V.179, Q:V.192, Q:W.203, Q:W.203, Q:N.228, S:I.24 Hydrogen bonds: Q:D.112, Q:I.113 pi-Stacking: Q:F.135, Q:F.155 YM2.21: 20 residues within 4Å: Chain U: I.111, D.112, I.113, T.114, F.135, F.137, Y.153, F.155, P.177, S.178, V.179, V.192, M.195, Y.201, Q.202, W.203, N.228, M.230, F.233 Chain W: I.24 15 PLIP interactions: 14 interactions with chain U, 1 interactions with chain W Hydrophobic interactions: U:I.111, U:I.111, U:T.114, U:F.135, U:F.155, U:V.179, U:V.192, U:W.203, U:W.203, U:N.228, W:I.24 Hydrogen bonds: U:D.112, U:I.113 pi-Stacking: U:F.135, U:F.155

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 2 residues within 4Å: Chain B: G.90 Chain S: L.151 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain F: G.90 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain J: G.90 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain C: L.151 Chain N: G.90 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain O: L.151 Chain R: G.90 Ligand excluded by PLIP CL.22: 1 residues within 4Å: Chain V: G.90 Ligand excluded by PLIP

12 x NA: SODIUM ION(Non-functional Binders)

NA.3: 1 residues within 4Å: Chain C: G.1 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.1, C:G.1 NA.4: 5 residues within 4Å: Chain C: P.23, P.26 Chain D: K.34, D.35 Chain G: D.18 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.35, D:D.35 NA.7: 2 residues within 4Å: Chain C: E.5 Chain G: G.1 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain G Hydrogen bonds: C:E.5, G:G.1 NA.8: 4 residues within 4Å: Chain G: P.23, P.26 Chain H: K.34, D.35 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:D.35, H:D.35 NA.11: 2 residues within 4Å: Chain K: G.1 Chain O: E.5 2 PLIP interactions: 1 interactions with chain K, 1 interactions with chain O Hydrogen bonds: K:G.1, O:E.5 NA.12: 4 residues within 4Å: Chain K: P.23, P.26 Chain L: K.34, D.35 No protein-ligand interaction detected (PLIP) NA.15: 1 residues within 4Å: Chain O: G.1 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:G.1 NA.16: 5 residues within 4Å: Chain K: D.18 Chain O: P.23, P.26 Chain P: K.34, D.35 2 PLIP interactions: 2 interactions with chain P Hydrogen bonds: P:D.35, P:D.35 NA.19: 1 residues within 4Å: Chain S: G.1 1 PLIP interactions: 1 interactions with chain S Hydrogen bonds: S:G.1 NA.20: 5 residues within 4Å: Chain S: P.23, P.26 Chain T: K.34, D.35 Chain W: D.18 1 PLIP interactions: 1 interactions with chain T Hydrogen bonds: T:D.35 NA.23: 2 residues within 4Å: Chain S: E.5 Chain W: G.1 2 PLIP interactions: 2 interactions with chain W Hydrogen bonds: W:G.1, W:G.1 NA.24: 4 residues within 4Å: Chain W: P.23, P.26 Chain X: K.34, D.35 1 PLIP interactions: 1 interactions with chain X Hydrogen bonds: X:D.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

De Colibus, L. et al., More-Powerful Virus Inhibitors from Structure-Based Analysis of Hev71 Capsid-Binding Molecules. Nat.Struct.Mol.Biol. (2014)

Release Date

2014-02-12

Peptides

VP1: AEIMQU
VP2: BFJNRV
VP3: CGKOSW
VP4: DHLPTX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
A

I
A

M
A

Q
A

U
A

B
B

F
B

J
B

N
B

R
B

V
B

C
C

G
C

K
C

O
C

S
C

W
C

D
D

H
D

L
D

P
D

T
D

X
D

VP1

VP2

VP3

VP4

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