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

A benzonitrile analogue inhibits rhinovirus replication

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-6-6-6-6-mer

Ligands

24 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: A.196, Y.197, N.198, L.218, N.219, M.221 Ligands: 2XK.3 Ligand excluded by PLIP GOL.2: 3 residues within 4Å: Chain A: V.79, L.109 Chain C: Q.230 Ligand excluded by PLIP GOL.4: 4 residues within 4Å: Chain B: D.88, F.97, K.257, S.258 Ligand excluded by PLIP GOL.5: 9 residues within 4Å: Chain C: L.71, N.72, A.73, L.195, L.197, T.202, G.203, Q.204, V.205 Ligand excluded by PLIP GOL.6: 7 residues within 4Å: Chain E: A.196, Y.197, N.198, L.218, N.219, M.221 Ligands: 2XK.8 Ligand excluded by PLIP GOL.7: 6 residues within 4Å: Chain A: D.165, Y.166, Q.169 Chain E: V.79, L.109 Chain G: Q.230 Ligand excluded by PLIP GOL.9: 4 residues within 4Å: Chain F: D.88, F.97, K.257, S.258 Ligand excluded by PLIP GOL.10: 9 residues within 4Å: Chain G: L.71, N.72, A.73, L.195, L.197, T.202, G.203, Q.204, V.205 Ligand excluded by PLIP GOL.11: 7 residues within 4Å: Chain I: A.196, Y.197, N.198, L.218, N.219, M.221 Ligands: 2XK.13 Ligand excluded by PLIP GOL.12: 6 residues within 4Å: Chain I: V.79, L.109 Chain K: Q.230 Chain M: D.165, Y.166, Q.169 Ligand excluded by PLIP GOL.14: 4 residues within 4Å: Chain J: D.88, F.97, K.257, S.258 Ligand excluded by PLIP GOL.15: 9 residues within 4Å: Chain K: L.71, N.72, A.73, L.195, L.197, T.202, G.203, Q.204, V.205 Ligand excluded by PLIP GOL.16: 7 residues within 4Å: Chain M: A.196, Y.197, N.198, L.218, N.219, M.221 Ligands: 2XK.18 Ligand excluded by PLIP GOL.17: 3 residues within 4Å: Chain M: V.79, L.109 Chain O: Q.230 Ligand excluded by PLIP GOL.19: 4 residues within 4Å: Chain N: D.88, F.97, K.257, S.258 Ligand excluded by PLIP GOL.20: 9 residues within 4Å: Chain O: L.71, N.72, A.73, L.195, L.197, T.202, G.203, Q.204, V.205 Ligand excluded by PLIP GOL.21: 7 residues within 4Å: Chain Q: A.196, Y.197, N.198, L.218, N.219, M.221 Ligands: 2XK.23 Ligand excluded by PLIP GOL.22: 3 residues within 4Å: Chain Q: V.79, L.109 Chain S: Q.230 Ligand excluded by PLIP GOL.24: 4 residues within 4Å: Chain R: D.88, F.97, K.257, S.258 Ligand excluded by PLIP GOL.25: 9 residues within 4Å: Chain S: L.71, N.72, A.73, L.195, L.197, T.202, G.203, Q.204, V.205 Ligand excluded by PLIP GOL.26: 7 residues within 4Å: Chain U: A.196, Y.197, N.198, L.218, N.219, M.221 Ligands: 2XK.28 Ligand excluded by PLIP GOL.27: 6 residues within 4Å: Chain Q: D.165, Y.166, Q.169 Chain U: V.79, L.109 Chain W: Q.230 Ligand excluded by PLIP GOL.29: 4 residues within 4Å: Chain V: D.88, F.97, K.257, S.258 Ligand excluded by PLIP GOL.30: 9 residues within 4Å: Chain W: L.71, N.72, A.73, L.195, L.197, T.202, G.203, Q.204, V.205 Ligand excluded by PLIP

6 x 2XK: 4-[(4,5-dimethoxy-2-nitrophenyl)acetyl]benzonitrile(Non-covalent)

2XK.3: 14 residues within 4Å: Chain A: I.104, L.106, S.126, Y.128, Y.152, F.186, V.188, V.191, Y.197, M.221, M.224 Chain C: L.25 Chain G: L.221 Ligands: GOL.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.104, A:L.106, A:Y.128, A:Y.197, A:Y.197 Hydrogen bonds: A:S.126 pi-Stacking: A:Y.152 2XK.8: 13 residues within 4Å: Chain E: I.104, L.106, S.126, Y.128, Y.152, F.186, V.188, V.191, Y.197, M.221, M.224 Chain G: L.25 Ligands: GOL.6 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:I.104, E:L.106, E:Y.128, E:Y.197, E:Y.197 Hydrogen bonds: E:S.126, E:Y.128 pi-Stacking: E:Y.152 2XK.13: 13 residues within 4Å: Chain I: I.104, L.106, S.126, Y.128, Y.152, F.186, V.188, V.191, Y.197, M.221, M.224 Chain K: L.25 Ligands: GOL.11 7 PLIP interactions: 7 interactions with chain I Hydrophobic interactions: I:I.104, I:L.106, I:Y.128, I:Y.197, I:Y.197 Hydrogen bonds: I:S.126 pi-Stacking: I:Y.152 2XK.18: 14 residues within 4Å: Chain K: L.221 Chain M: I.104, L.106, S.126, Y.128, Y.152, F.186, V.188, V.191, Y.197, M.221, M.224 Chain O: L.25 Ligands: GOL.16 8 PLIP interactions: 8 interactions with chain M Hydrophobic interactions: M:I.104, M:L.106, M:Y.128, M:Y.197, M:Y.197 Hydrogen bonds: M:S.126, M:Y.128 pi-Stacking: M:Y.152 2XK.23: 14 residues within 4Å: Chain Q: I.104, L.106, S.126, Y.128, Y.152, F.186, V.188, V.191, Y.197, M.221, M.224 Chain S: L.25 Chain W: L.221 Ligands: GOL.21 7 PLIP interactions: 7 interactions with chain Q Hydrophobic interactions: Q:I.104, Q:L.106, Q:Y.128, Q:Y.197, Q:Y.197 Hydrogen bonds: Q:S.126 pi-Stacking: Q:Y.152 2XK.28: 13 residues within 4Å: Chain U: I.104, L.106, S.126, Y.128, Y.152, F.186, V.188, V.191, Y.197, M.221, M.224 Chain W: L.25 Ligands: GOL.26 8 PLIP interactions: 8 interactions with chain U Hydrophobic interactions: U:I.104, U:L.106, U:Y.128, U:Y.197, U:Y.197 Hydrogen bonds: U:S.126, U:Y.128 pi-Stacking: U:Y.152

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lacroix, C. et al., A novel benzonitrile analogue inhibits rhinovirus replication. J.Antimicrob.Chemother. (2014)

Release Date

2014-07-02

Peptides

Genome polyprotein: AEIMQU
Genome polyprotein: BFJNRV
Genome polyprotein: CGKOSW
Capsid protein VP4/VP2: 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

Genome polyprotein

Genome polyprotein

Genome polyprotein

Capsid protein VP4/VP2

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