SMTL ID : 9b18.2 (3 other biounits)

EV-D68 in complex with inhibitor Jun11-53-7

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-5-5-5-5-mer

Ligands

5 x 01: (4M)-4-[1-(2-methoxyethyl)-1H-pyrazol-4-yl]-N-({4-[(propan-2-yl)oxy]phenyl}methyl)quinolin-8-amine

01.1: 20 residues within 4Å: Chain A: I.107, N.108, T.109, L.119, L.125, F.127, I.131, A.157, M.158, F.159, A.181, S.182, V.183, I.194, I.196, Y.205, I.229, L.232, M.253 Chain F: L.14 14 PLIP interactions: 1 interactions with chain F, 13 interactions with chain A Hydrophobic interactions: F:L.14, A:I.107, A:T.109, A:I.131, A:A.157, A:F.159, A:A.181, A:I.194, A:I.196, A:I.229, A:I.229, A:L.232 Hydrogen bonds: A:T.109 pi-Stacking: A:Y.205 01.2: 20 residues within 4Å: Chain E: I.107, N.108, T.109, L.119, L.125, F.127, I.131, A.157, M.158, F.159, A.181, S.182, V.183, I.194, I.196, Y.205, I.229, L.232, M.253 Chain J: L.14 14 PLIP interactions: 13 interactions with chain E, 1 interactions with chain J Hydrophobic interactions: E:I.107, E:T.109, E:I.131, E:A.157, E:F.159, E:A.181, E:I.194, E:I.196, E:I.229, E:I.229, E:L.232, J:L.14 Hydrogen bonds: E:T.109 pi-Stacking: E:Y.205 01.3: 20 residues within 4Å: Chain I: I.107, N.108, T.109, L.119, L.125, F.127, I.131, A.157, M.158, F.159, A.181, S.182, V.183, I.194, I.196, Y.205, I.229, L.232, M.253 Chain N: L.14 14 PLIP interactions: 13 interactions with chain I, 1 interactions with chain N Hydrophobic interactions: I:I.107, I:T.109, I:I.131, I:A.157, I:F.159, I:A.181, I:I.194, I:I.196, I:I.229, I:I.229, I:L.232, N:L.14 Hydrogen bonds: I:T.109 pi-Stacking: I:Y.205 01.4: 20 residues within 4Å: Chain M: I.107, N.108, T.109, L.119, L.125, F.127, I.131, A.157, M.158, F.159, A.181, S.182, V.183, I.194, I.196, Y.205, I.229, L.232, M.253 Chain R: L.14 14 PLIP interactions: 13 interactions with chain M, 1 interactions with chain R Hydrophobic interactions: M:I.107, M:T.109, M:I.131, M:A.157, M:F.159, M:A.181, M:I.194, M:I.196, M:I.229, M:I.229, M:L.232, R:L.14 Hydrogen bonds: M:T.109 pi-Stacking: M:Y.205 01.5: 20 residues within 4Å: Chain B: L.14 Chain Q: I.107, N.108, T.109, L.119, L.125, F.127, I.131, A.157, M.158, F.159, A.181, S.182, V.183, I.194, I.196, Y.205, I.229, L.232, M.253 14 PLIP interactions: 13 interactions with chain Q, 1 interactions with chain B Hydrophobic interactions: Q:I.107, Q:T.109, Q:I.131, Q:A.157, Q:F.159, Q:A.181, Q:I.194, Q:I.196, Q:I.229, Q:I.229, Q:L.232, B:L.14 Hydrogen bonds: Q:T.109 pi-Stacking: Q:Y.205

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, K. et al., Design of enterovirus D68 capsid inhibitors with in vivo antiviral efficacy. To Be Published

Release Date

2025-03-19

Peptides

Capsid protein VP1: AEIMQ
viral protein 3: BFJNR
viral protein 2: CGKOS
Capsid protein 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

Capsid protein VP1

viral protein 3

viral protein 2

Capsid protein VP4

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