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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

hetero-6-6-6-6-mer

Ligands

6 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 15 PLIP interactions: 15 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 pi-Stacking: Q:F.135, Q:F.155 906.16: 19 residues within 4Å: Chain U: 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 15 PLIP interactions: 15 interactions with chain U Hydrophobic interactions: U:I.111, U:I.111, U:T.114, U:F.131, U:F.135, U:V.179, U:V.192, U:W.203, U:W.203, U:N.228 Hydrogen bonds: U:D.112, U:D.112, U:I.113 pi-Stacking: U:F.135, U:F.155

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

NA.2: 4 residues within 4Å: Chain A: Q.189 Chain C: V.20, S.21 Chain G: P.8 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:P.8 NA.3: 1 residues within 4Å: Chain C: Y.188 No protein-ligand interaction detected (PLIP) NA.5: 3 residues within 4Å: Chain E: Q.189 Chain G: V.20, S.21 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Q.189 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 A Hydrogen bonds: A:Y.205 NA.8: 3 residues within 4Å: Chain I: Q.189 Chain K: V.20, S.21 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:S.21 NA.9: 4 residues within 4Å: Chain K: Y.188 Chain M: Y.205 Chain N: D.204, N.208 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:Y.205, M:Y.205 NA.11: 4 residues within 4Å: Chain K: P.8 Chain M: Q.189 Chain O: V.20, S.21 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:P.8 NA.12: 1 residues within 4Å: Chain O: Y.188 No protein-ligand interaction detected (PLIP) NA.14: 4 residues within 4Å: Chain Q: Q.189 Chain S: V.20, S.21 Chain W: P.8 1 PLIP interactions: 1 interactions with chain S Hydrogen bonds: S:V.20 NA.15: 1 residues within 4Å: Chain S: Y.188 No protein-ligand interaction detected (PLIP) NA.17: 3 residues within 4Å: Chain U: Q.189 Chain W: V.20, S.21 1 PLIP interactions: 1 interactions with chain W Hydrogen bonds: W:V.20 NA.18: 4 residues within 4Å: Chain Q: Y.205 Chain R: D.204, N.208 Chain W: Y.188 1 PLIP interactions: 1 interactions with chain Q Hydrogen bonds: Q:Y.205

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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