SMTL ID : 7mmc.1

Crystal structure of HCV NS3/4A D168A protease in complex with NR01-115

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: C.117, T.118, C.119, C.165, A.167, H.169 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.117, A:C.119, A:C.165, A:H.169

1 x ZKA: (1-methylcyclopropyl)methyl {(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)

ZKA.2: 24 residues within 4Å: Chain A: Q.61, T.62, F.63, V.75, Y.76, H.77, G.78, V.98, D.101, R.143, I.152, L.155, K.156, G.157, S.158, S.159, F.174, R.175, A.176, A.177, V.178, A.188 Ligands: EDO.11, SO4.13 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:Q.61, A:F.63, A:Y.76, A:H.77, A:V.98, A:D.101, A:I.152, A:I.152, A:L.155, A:F.174, A:A.176, A:A.177, A:V.178, A:A.188 Hydrogen bonds: A:H.77, A:G.157, A:S.158, A:S.159, A:S.159, A:R.175, A:A.177, A:A.177 pi-Cation interactions: A:H.77

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

EDO.3: 5 residues within 4Å: Chain A: A.25, Y.26, A.27, H.130, A.131 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.27, A:H.130 EDO.4: 12 residues within 4Å: Chain A: I.14, D.45, V.49, I.84, A.85, S.86, P.87, V.91, Q.106, A.107, P.108, Q.109 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.85, A:Q.106 Water bridges: A:Q.109, A:Q.109 EDO.5: 10 residues within 4Å: Chain A: K.8, K.9, G.10, S.11, S.40, Q.41, T.42, G.43, T.83, P.90 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.11 Water bridges: A:T.83 EDO.6: 8 residues within 4Å: Chain A: E.33, C.36, S.57, T.58, A.59, T.60, Q.61, T.62 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.33, A:Q.61 Water bridges: A:S.57 EDO.7: 6 residues within 4Å: Chain A: K.9, T.58, T.60, Q.61, R.82 Ligands: EDO.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.9, A:R.82 EDO.8: 7 residues within 4Å: Chain A: K.9, G.10, Q.41, A.59, T.60, R.82 Ligands: EDO.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.10, A:R.82 Water bridges: A:Q.41 EDO.9: 5 residues within 4Å: Chain A: V.15, G.16, Q.29, I.55, R.129 3 PLIP interactions: 3 interactions with chain A Water bridges: A:S.57, A:S.57, A:R.129 EDO.10: 5 residues within 4Å: Chain A: S.86, K.88, G.89, P.90, V.91 No protein-ligand interaction detected (PLIP) EDO.11: 3 residues within 4Å: Chain A: R.143, R.175 Ligands: ZKA.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.175 EDO.12: 2 residues within 4Å: Chain A: T.30, N.47 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.30

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

SO4.13: 3 residues within 4Å: Chain A: Y.76, G.80 Ligands: ZKA.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.76 Water bridges: A:G.80 SO4.14: 4 residues within 4Å: Chain A: G.140, D.141, S.142, R.143 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.141, A:S.142

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