SMTL ID : 6p6r.1

HCV NS3/4A protease domain of genotype 1a3a chimera in complex with glecaprevir

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: K.10, T.59, T.61, Q.62, R.83 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.10, A:T.61, A:R.83 Water bridges: A:T.59, A:T.61, A:R.83 EDO.2: 4 residues within 4Å: Chain A: I.56, T.63, R.130, H.131 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.130, A:R.130 Water bridges: A:H.131

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain A: C.118, T.119, C.120, C.166, A.168, H.170 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.118, A:C.120, A:C.166, A:H.170

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

SO4.4: 3 residues within 4Å: Chain A: Y.77, G.81 Ligands: O31.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.77 SO4.5: 3 residues within 4Å: Chain A: S.22, E.53, R.113 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.113

1 x O31: (3aR,7S,10S,12R,21E,24aR)-7-tert-butyl-N-[(1R,2R)-2-(difluoromethyl)-1-{[(1-methylcyclopropyl)sulfonyl]carbamoyl}cyclop ropyl]-20,20-difluoro-5,8-dioxo-2,3,3a,5,6,7,8,11,12,20,23,24a-dodecahydro-1H,10H-9,12-methanocyclopenta[18,19][1,10,17, 3,6]trioxadiazacyclononadecino[11,12-b]quinoxaline-10-carboxamide(Non-covalent)

O31.6: 23 residues within 4Å: Chain A: Q.62, T.63, F.64, V.76, Y.77, H.78, G.79, V.99, D.102, L.153, L.156, K.157, G.158, S.159, S.160, F.175, R.176, A.177, A.178, V.179, S.180, Q.189 Ligands: SO4.4 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Q.62, A:F.64, A:Y.77, A:H.78, A:V.99, A:L.153, A:F.175, A:A.178, A:Q.189 Hydrogen bonds: A:H.78, A:G.158, A:S.159, A:S.160, A:S.160, A:R.176, A:A.178, A:A.178 pi-Stacking: A:H.78 Halogen bonds: A:R.176

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 5 residues within 4Å: Chain A: K.101, R.176, I.191, P.192, S.195 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Timm, J. et al., Molecular mechanism of pan-genotypic HCV NS3/4A protease inhibition by glecaprevir and characterization of genotype-specific structural differences. To Be Published

Release Date

2020-06-10

Peptides

Non-structural protein 4A,Serine protease NS3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Non-structural protein 4A,Serine protease NS3

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