SMTL ID : 6mcr.1

X-ray crystal structure of wild type HIV-1 protease in complex with GRL-001

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 8 residues within 4Å: Chain A: P.79, P.81 Chain B: G.48, G.49, I.50, G.51, G.52, F.53 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.49, B:G.52 EDO.2: 6 residues within 4Å: Chain A: L.10, E.21, A.22, L.23, V.82, N.83 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.21, A:E.21, A:N.83 EDO.3: 3 residues within 4Å: Chain A: Q.18, L.19, K.20 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.18, A:L.19, A:L.19 EDO.5: 8 residues within 4Å: Chain A: G.48, G.49, I.50, G.51, G.52, F.53 Chain B: P.79, P.81 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.49, A:G.52 EDO.6: 6 residues within 4Å: Chain B: L.10, E.21, A.22, L.23, V.82, N.83 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.21, B:N.83 EDO.7: 3 residues within 4Å: Chain B: Q.18, L.19, K.20 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.18, B:L.19, B:L.19

2 x JDY: (3S,3aR,5R,7aS,8S)-hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-yl [(2S,3R)-4-[{[2-(cyclopropylamino)-1,3-benzothiazol-6-yl]sulfonyl}(2-methylpropyl)amino]-1-(3-fluorophenyl)-3-hydroxybutan-2-yl]carbamate(Non-covalent)

JDY.4: 32 residues within 4Å: Chain A: R.8, L.23, D.25, G.27, A.28, D.29, D.30, V.32, K.45, I.47, G.48, G.49, I.50, P.81, V.82, I.84 Chain B: R.8, L.23, D.25, G.27, A.28, D.29, D.30, V.32, I.47, G.48, G.49, I.50, P.81, V.82, I.84 Ligands: JDY.8 23 PLIP interactions: 11 interactions with chain B, 12 interactions with chain A Hydrophobic interactions: B:L.23, B:I.47, B:I.47, B:I.84, A:A.28, A:D.29, A:V.32, A:P.81, A:V.82, A:I.84 Hydrogen bonds: B:D.25, B:G.27, B:D.29, B:D.30, A:D.29, A:D.30, A:D.30, A:D.30, A:I.50 Water bridges: B:I.50, B:I.50 Salt bridges: B:D.25, A:D.25 JDY.8: 32 residues within 4Å: Chain A: R.8, L.23, D.25, G.27, A.28, D.29, D.30, V.32, I.47, G.48, G.49, I.50, P.81, V.82, I.84 Chain B: R.8, L.23, D.25, G.27, A.28, D.29, D.30, V.32, K.45, I.47, G.48, G.49, I.50, P.81, V.82, I.84 Ligands: JDY.4 24 PLIP interactions: 12 interactions with chain B, 12 interactions with chain A Hydrophobic interactions: B:A.28, B:D.29, B:V.32, B:P.81, B:V.82, B:I.84, A:L.23, A:I.47, A:I.47, A:I.84 Hydrogen bonds: B:D.29, B:D.29, B:D.30, B:D.30, B:I.50, A:D.25, A:G.27, A:D.29, A:D.30, A:D.30 Salt bridges: B:D.25, A:D.25 Water bridges: A:I.50, A:I.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hattori, S.I. et al., Halogen Bond Interactions of Novel HIV-1 Protease Inhibitors (PI) (GRL-001-15 and GRL-003-15) with the Flap of Protease Are Critical for Their Potent Activity against Wild-Type HIV-1 and Multi-PI-Resistant Variants. Antimicrob.Agents Chemother. (2019)

Release Date

2019-04-24

Peptides

Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Protease

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