SMTL ID : 7mme.1

Crystal structure of HCV NS3/4A D168A protease in complex with 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

Zephyr, J. et al., Deciphering the Molecular Mechanism and Role of Fluorination in HCV Protease Inhibitor Potency and Drug Resistance. To Be Published

Release Date

2022-08-31

Peptides

NS3/4A protease: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

NS3/4A protease

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