SMTL ID : 6lqd.3 (3 other biounits)

Structure of Enterovirus 71 in complex with NLD-22

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-6-6-mer

Ligands

6 x EQ9: 1-(2-azanylpyridin-4-yl)-3-[5-[4-(5-methyl-1,2,4-oxadiazol-3-yl)phenoxy]pentyl]imidazolidin-2-one(Non-covalent)

EQ9.1: 25 residues within 4Å: Chain A: I.111, D.112, I.113, T.114, F.131, F.135, F.137, Y.153, M.154, F.155, P.177, S.178, V.179, V.190, V.192, M.195, Y.201, Q.202, W.203, N.228, M.230, F.233, A.275 Chain C: I.24 Chain G: L.14 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:I.111, A:F.155, A:F.155, A:V.179, A:V.192, A:W.203, C:I.24 Hydrogen bonds: A:I.113, A:T.114, A:W.203 pi-Stacking: A:F.135, A:W.203 EQ9.2: 24 residues within 4Å: Chain E: I.111, D.112, I.113, T.114, F.131, F.135, F.137, Y.153, M.154, F.155, P.177, S.178, V.179, V.190, V.192, M.195, Y.201, Q.202, W.203, N.228, M.230, F.233, A.275 Chain G: I.24 12 PLIP interactions: 11 interactions with chain E, 1 interactions with chain G Hydrophobic interactions: E:I.111, E:F.155, E:F.155, E:V.179, E:V.192, E:W.203, G:I.24 Hydrogen bonds: E:I.113, E:T.114, E:W.203 pi-Stacking: E:F.135, E:W.203 EQ9.3: 24 residues within 4Å: Chain I: I.111, D.112, I.113, T.114, F.131, F.135, F.137, Y.153, M.154, F.155, P.177, S.178, V.179, V.190, V.192, M.195, Y.201, Q.202, W.203, N.228, M.230, F.233, A.275 Chain K: I.24 13 PLIP interactions: 12 interactions with chain I, 1 interactions with chain K Hydrophobic interactions: I:I.111, I:F.155, I:F.155, I:V.179, I:V.192, I:W.203, K:I.24 Hydrogen bonds: I:D.112, I:I.113, I:T.114, I:W.203 pi-Stacking: I:F.135, I:W.203 EQ9.4: 25 residues within 4Å: Chain K: L.14 Chain M: I.111, D.112, I.113, T.114, F.131, F.135, F.137, Y.153, M.154, F.155, P.177, S.178, V.179, V.190, V.192, M.195, Y.201, Q.202, W.203, N.228, M.230, F.233, A.275 Chain O: I.24 12 PLIP interactions: 11 interactions with chain M, 1 interactions with chain O Hydrophobic interactions: M:I.111, M:F.155, M:F.155, M:V.179, M:V.192, M:W.203, O:I.24 Hydrogen bonds: M:I.113, M:T.114, M:W.203 pi-Stacking: M:F.135, M:W.203 EQ9.5: 25 residues within 4Å: Chain Q: I.111, D.112, I.113, T.114, F.131, F.135, F.137, Y.153, M.154, F.155, P.177, S.178, V.179, V.190, V.192, M.195, Y.201, Q.202, W.203, N.228, M.230, F.233, A.275 Chain S: I.24 Chain W: L.14 12 PLIP interactions: 11 interactions with chain Q, 1 interactions with chain S Hydrophobic interactions: Q:I.111, Q:F.155, Q:F.155, Q:V.179, Q:V.192, Q:W.203, S:I.24 Hydrogen bonds: Q:I.113, Q:T.114, Q:W.203 pi-Stacking: Q:F.135, Q:W.203 EQ9.6: 24 residues within 4Å: Chain U: I.111, D.112, I.113, T.114, F.131, F.135, F.137, Y.153, M.154, F.155, P.177, S.178, V.179, V.190, V.192, M.195, Y.201, Q.202, W.203, N.228, M.230, F.233, A.275 Chain W: I.24 12 PLIP interactions: 11 interactions with chain U, 1 interactions with chain W Hydrophobic interactions: U:I.111, U:F.155, U:F.155, U:V.179, U:V.192, U:W.203, W:I.24 Hydrogen bonds: U:I.113, U:T.114, U:W.203 pi-Stacking: U:F.135, U:W.203

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, M. et al., Design, Synthesis, and Evaluation of Novel Enterovirus 71 Inhibitors as Therapeutic Drug Leads for the Treatment of Human Hand, Foot, and Mouth Disease. J.Med.Chem. (2020)

Release Date

2020-03-11

Peptides

Capsid protein VP1: AEIMQU
Capsid protein VP2: BFJNRV
Capsid protein VP3: CGKOSW
Capsid protein 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

Capsid protein VP1

Capsid protein VP2

Capsid protein VP3

Capsid protein VP4

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