SMTL ID : 7l7o.1

Crystal structure of HCV NS3/4A D168A protease in complex with NR04-49

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.72 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 XSY: (1R,3r,5S)-bicyclo[3.1.0]hexan-3-yl [(2R,6S,12Z,13aS,14aR,16aS)-2-{[6-methoxy-3-(trifluoromethyl)quinoxalin-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)

XSY.2: 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, A.187 Ligands: EDO.5 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:Q.60, A:F.62, A:F.62, A:H.76, A:I.151, A:L.154, A:F.173, A:A.175, A:A.176, A:V.177, A:A.187 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 pi-Stacking: A:H.76 Halogen bonds: A:R.174

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

EDO.3: 5 residues within 4Å: Chain A: K.8, G.9, Q.40, A.58, R.81 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.9, A:R.81, A:R.81 EDO.4: 5 residues within 4Å: Chain A: K.8, T.57, T.59, Q.60, R.81 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.8, A:T.59, A:R.81 Water bridges: A:T.57 EDO.5: 4 residues within 4Å: Chain A: S.141, R.142, R.174 Ligands: XSY.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.141, A:S.141, A:R.142, A:R.142, A:R.174, A:R.174 EDO.7: 2 residues within 4Å: Chain A: R.128, H.129 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.128, A:R.128 Water bridges: A:H.129

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

SO4.6: 3 residues within 4Å: Chain A: Y.25, Q.27, Q.28 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.25, A:Q.27 Water bridges: A:Q.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nageswara Rao, D. et al., Discovery of Quinoxaline-Based P1-P3 Macrocyclic NS3/4A Protease Inhibitors with Potent Activity against Drug-Resistant Hepatitis C Virus Variants. J.Med.Chem. (2021)

Release Date

2021-09-01

Peptides

NS3/4A protease: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

NS3/4A protease

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