SMTL ID : 6diw.1

Crystal structure of HCV NS3/4A D168A protease in complex with P4-1 (AJ-71)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x GKG: 1,1,1-trifluoro-2-methylpropan-2-yl [(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)

GKG.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, A.187 Ligands: SO4.2 21 PLIP interactions: 21 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.175, 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:R.174 pi-Cation interactions: A:H.76

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

SO4.2: 3 residues within 4Å: Chain A: Y.75, G.79 Ligands: GKG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.75 Water bridges: A:G.79 SO4.3: 4 residues within 4Å: Chain A: K.8, T.59, Q.60, R.81 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:T.59, A:T.59, A:Q.60 Water bridges: A:K.8, A:T.57, A:R.81, A:R.81, A:R.81, A:R.81 Salt bridges: A:K.8, A:R.81 SO4.4: 2 residues within 4Å: Chain A: T.91, Q.92 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.92 SO4.5: 4 residues within 4Å: Chain A: S.141, R.142, R.174, A.187 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.141 Salt bridges: A:R.142, A:R.174

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 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

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain A: V.14, G.15, A.26, Q.27, Q.28, I.54, R.128 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.14, A:Q.28 GOL.8: 3 residues within 4Å: Chain A: N.68, G.69, M.198 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.68, A:N.68 Water bridges: A:N.68, A:G.69, A:G.69 GOL.9: 8 residues within 4Å: Chain A: K.8, G.9, S.39, Q.40, T.57, A.58, T.59, R.81 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.9, A:S.39, A:A.58, A:R.81, A:R.81 Water bridges: A:K.7, A:G.9, A:Q.40 GOL.10: 5 residues within 4Å: Chain A: R.30, R.43, D.44, K.45, N.46 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.30, A:R.30, A:K.45 GOL.11: 5 residues within 4Å: Chain A: I.151, S.178, T.179, R.180, G.181 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.178, A:G.181 Water bridges: A:R.180, A:R.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Matthew, A.N. et al., Design of Hepatitis C NS3/4A Protease Inhibitors Leveraging Untapped Regions of the Substrate Envelope. To Be Published

Release Date

2019-07-31

Peptides

NS3 protease: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

NS3 protease

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