SMTL ID : 6ue3.1

Crystal structure of HCV NS3/4A D168A protease in complex with PC (JZ01-15)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

monomer

Ligands

1 x 9H4: tert-butyl [(2R,6S,12Z,13aS,14aR,16aS)-2-[(7-methoxy-3-methylquinoxalin-2-yl)oxy]-14a-{[(1-methylcyclopropyl)sulfonyl]carbamoyl}-5,16-dioxo-1,2,3,5,6,7,8,9,10,11,13a,14,14a,15,16,16a-hexadecahydrocyclopropa[e]pyrrolo[1,2-a][1,4]diazacyclopentadecin-6-yl]carbamate(Non-covalent)

9H4.1: 24 residues within 4Å: Chain A: Q.60, T.61, F.62, V.74, Y.75, H.76, G.77, V.97, D.100, R.142, I.151, L.154, K.155, G.156, S.157, S.158, F.173, R.174, A.175, A.176, V.177, S.178 Ligands: EDO.3, SO4.9 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Q.60, A:F.62, A:H.76, A:V.97, A:D.100, A:I.151, A:L.154, A:F.173, A:R.174, A:A.176 Hydrogen bonds: A:H.76, A:G.156, A:S.157, A:S.158, A:R.174, A:A.176, A:A.176

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: C.116, T.117, C.118, C.164, A.166, H.168 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.116, A:C.118, A:C.164, A:H.168

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 6 residues within 4Å: Chain A: S.141, R.142, R.174, A.187 Ligands: 9H4.1, EDO.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.141, A:R.142, A:R.142 Water bridges: A:R.174 EDO.4: 3 residues within 4Å: Chain A: M.2, A.3, S.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.2, A:A.3, A:S.4 EDO.5: 7 residues within 4Å: Chain A: K.99, S.141, R.174, I.189, P.190, S.193 Ligands: EDO.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.141, A:R.174, A:S.193 Water bridges: A:S.141 EDO.6: 5 residues within 4Å: Chain A: V.14, G.15, Q.28, I.54, R.128 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.56, A:R.128

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 8 residues within 4Å: Chain A: C.116, T.117, C.118, G.119, R.137, V.170, V.191, E.192 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.117, A:G.119, A:R.137 Water bridges: A:S.120 GOL.8: 6 residues within 4Å: Chain A: K.8, T.57, T.59, Q.60, H.76, R.81 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.8, A:Q.60, A:R.81 Water bridges: A:T.57, A:H.76, A:G.77, A:R.81

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.9: 3 residues within 4Å: Chain A: Y.75, G.79 Ligands: 9H4.1 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Y.75, A:Y.75, A:G.79 SO4.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Matthew, A.N. et al., Avoiding Drug Resistance by Substrate Envelope-Guided Design: Toward Potent and Robust HCV NS3/4A Protease Inhibitors. Mbio (2020)

Release Date

2020-03-04

Peptides

NS3 protease: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

NS3 protease

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