SMTL ID : 4cey.2 (3 other biounits)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

hetero-oligomer

Ligands

5 x 906: 1-(2-AMINOPYRIDIN-4-YL)-3-[(3S)-5-{4-[(E)-(ETHOXYIMINO)METHYL]PHENOXY}-3-METHYLPENTYL]IMIDAZOLIDIN-2-ONE(Non-covalent)

906.1: 19 residues within 4Å: Chain A: I.111, D.112, I.113, T.114, F.131, 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, K.274 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:I.111, A:I.111, A:T.114, A:F.131, A:F.135, A:V.179, A:V.192, A:W.203, A:W.203, A:N.228 Hydrogen bonds: A:D.112, A:D.112, A:I.113, A:T.114 pi-Stacking: A:F.135, A:F.155 906.4: 19 residues within 4Å: Chain E: I.111, D.112, I.113, T.114, F.131, 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, K.274 16 PLIP interactions: 16 interactions with chain E Hydrophobic interactions: E:I.111, E:I.111, E:T.114, E:F.131, E:F.135, E:V.179, E:V.192, E:W.203, E:W.203, E:N.228 Hydrogen bonds: E:D.112, E:D.112, E:I.113, E:T.114 pi-Stacking: E:F.135, E:F.155 906.7: 19 residues within 4Å: Chain I: I.111, D.112, I.113, T.114, F.131, 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, K.274 14 PLIP interactions: 14 interactions with chain I Hydrophobic interactions: I:I.111, I:I.111, I:T.114, I:F.131, I:F.135, I:V.179, I:V.192, I:W.203, I:W.203, I:N.228 Hydrogen bonds: I:D.112, I:I.113 pi-Stacking: I:F.135, I:F.155 906.10: 19 residues within 4Å: Chain M: I.111, D.112, I.113, T.114, F.131, 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, K.274 14 PLIP interactions: 14 interactions with chain M Hydrophobic interactions: M:I.111, M:I.111, M:T.114, M:F.131, M:F.135, M:V.179, M:V.192, M:W.203, M:W.203, M:N.228 Hydrogen bonds: M:D.112, M:I.113 pi-Stacking: M:F.135, M:F.155 906.13: 19 residues within 4Å: Chain Q: I.111, D.112, I.113, T.114, F.131, 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, K.274 16 PLIP interactions: 16 interactions with chain Q Hydrophobic interactions: Q:I.111, Q:I.111, Q:T.114, Q:F.131, Q:F.135, Q:V.179, Q:V.192, Q:W.203, Q:W.203, Q:N.228 Hydrogen bonds: Q:D.112, Q:D.112, Q:I.113, Q:T.114 pi-Stacking: Q:F.135, Q:F.155

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

NA.2: 6 residues within 4Å: Chain A: Q.189 Chain C: V.20, S.21 Chain G: P.8 Chain K: E.5 Chain O: G.1 2 PLIP interactions: 2 interactions with chain O Hydrogen bonds: O:G.1, O:G.1 NA.3: 4 residues within 4Å: Chain C: Y.188 Chain Q: Y.205 Chain R: D.204, N.208 1 PLIP interactions: 1 interactions with chain R Hydrogen bonds: R:D.204 NA.5: 6 residues within 4Å: Chain E: Q.189 Chain G: V.20, S.21 Chain K: P.8 Chain O: E.5 Chain S: G.1 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain S Hydrogen bonds: E:Q.189, S:G.1 NA.6: 4 residues within 4Å: Chain A: Y.205 Chain B: D.204, N.208 Chain G: Y.188 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.204 NA.8: 6 residues within 4Å: Chain C: G.1 Chain I: Q.189 Chain K: V.20, S.21 Chain O: P.8 Chain S: E.5 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain S Hydrogen bonds: C:G.1, S:E.5 NA.9: 4 residues within 4Å: Chain E: Y.205 Chain F: D.204, N.208 Chain K: Y.188 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:D.204 NA.11: 6 residues within 4Å: Chain C: E.5 Chain G: G.1 Chain M: Q.189 Chain O: V.20, S.21 Chain S: P.8 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain G Hydrogen bonds: C:E.5, G:G.1 NA.12: 4 residues within 4Å: Chain I: Y.205 Chain J: D.204, N.208 Chain O: Y.188 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain J Hydrogen bonds: I:Y.205, J:D.204 NA.14: 6 residues within 4Å: Chain C: P.8 Chain G: E.5 Chain K: G.1 Chain Q: Q.189 Chain S: V.20, S.21 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain K Hydrogen bonds: G:E.5, K:G.1 NA.15: 4 residues within 4Å: Chain M: Y.205 Chain N: D.204, N.208 Chain S: Y.188 1 PLIP interactions: 1 interactions with chain N Hydrogen bonds: N:D.204

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: AEIMQ
VP2: BFJNR
VP3: CGKOS
VP4: DHLPT

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
A

I
A

M
A

Q
A

B
B

F
B

J
B

N
B

R
B

C
C

G
C

K
C

O
C

S
C

D
D

H
D

L
D

P
D

T
D

VP1

VP2

VP3

VP4

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