SMTL ID : 7mmk.1

Crystal structure of HCV NS3/4A D168A protease in complex with NR01-149

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 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

1 x ZJJ: 3,3-difluorocyclobutyl {(2R,4S,6S,12Z,13aS,14aR,16aS)-2-[(7-methoxy-3-methylquinoxalin-2-yl)oxy]-14a-[(1-methylcyclopropane-1-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)

ZJJ.2: 26 residues within 4Å: Chain A: Q.60, T.61, F.62, V.74, Y.75, H.76, G.77, V.97, D.100, I.151, L.154, K.155, G.156, S.157, S.158, F.173, R.174, A.175, A.176, V.177, A.187 Ligands: EDO.5, EDO.8, EDO.10, EDO.13, SO4.14 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Q.60, A:H.76, A:V.97, A:D.100, A:I.151, A:L.154, A:F.173, A:A.176 Hydrogen bonds: A:H.76, A:G.156, A:S.157, A:S.158, A:S.158, A:R.174, A:A.176, A:A.176 Water bridges: A:K.155

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

EDO.3: 4 residues within 4Å: Chain A: I.54, R.128, H.129 Ligands: EDO.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.128, A:R.128 EDO.4: 3 residues within 4Å: Chain A: N.68, E.195, M.198 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.68, A:M.198 EDO.5: 4 residues within 4Å: Chain A: Q.60, K.155 Ligands: ZJJ.2, EDO.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.60 Water bridges: A:K.155, A:K.155 EDO.6: 4 residues within 4Å: Chain A: K.8, T.59, Q.60, R.81 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.8, A:K.8, A:T.59, A:R.81 Water bridges: A:Q.60 EDO.7: 3 residues within 4Å: Chain A: C.118, G.119, S.120 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:C.118 Water bridges: A:S.120, A:S.120, A:S.120, A:S.120 EDO.8: 7 residues within 4Å: Chain A: V.97, D.98, K.99, D.100, R.174 Ligands: ZJJ.2, EDO.9 No protein-ligand interaction detected (PLIP) EDO.9: 9 residues within 4Å: Chain A: D.98, K.99, S.141, R.174, F.188, I.189, P.190, S.193 Ligands: EDO.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.193 EDO.10: 8 residues within 4Å: Chain A: T.59, Q.60, T.61, K.155 Ligands: ZJJ.2, EDO.5, EDO.11, EDO.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.61, A:K.155 EDO.11: 7 residues within 4Å: Chain A: S.56, T.57, A.58, T.59, Q.60, T.61 Ligands: EDO.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.57 EDO.12: 8 residues within 4Å: Chain A: T.61, R.128, H.129, S.152, K.155, G.156 Ligands: EDO.3, EDO.10 3 PLIP interactions: 3 interactions with chain A Water bridges: A:S.152, A:K.155, A:K.155 EDO.13: 6 residues within 4Å: Chain A: S.141, R.142, R.174, A.187, F.188 Ligands: ZJJ.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.141, A:S.141, A:R.174

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

SO4.14: 3 residues within 4Å: Chain A: Y.75, G.79 Ligands: ZJJ.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.75 Water bridges: A:G.79

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zephyr, J. et al., Deciphering the Molecular Mechanism of HCV Protease Inhibitor Fluorination as a General Approach to Avoid Drug Resistance. J.Mol.Biol. (2022)

Release Date

2022-03-16

Peptides

NS3 protease: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

NS3 protease