SMTL ID : 6mcs.1

X-ray crystal structure of wild type HIV-1 protease in complex with GRL-003

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

homo-dimer

Ligands

2 x JDV: (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-(4-fluorophenyl)-3-hydroxybutan-2-yl]carbamate(Non-covalent)

JDV.1: 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: JDV.2 22 PLIP interactions: 11 interactions with chain A, 11 interactions with chain B Hydrophobic interactions: A:A.28, A:V.32, A:P.81, A:V.82, A:I.84, B:I.47, B:I.84 Hydrogen bonds: A:D.29, A:D.30, A:D.30, A:D.30, A:I.50, B:G.27, B:G.27, B:D.29, B:D.30 Salt bridges: A:D.25, B:D.25 Water bridges: B:I.50, B:I.50, B:I.50, B:I.50 JDV.2: 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: JDV.1 23 PLIP interactions: 11 interactions with chain B, 12 interactions with chain A Hydrophobic interactions: B:A.28, B:V.32, B:P.81, B:V.82, B:I.84, A:I.47, A:I.84 Hydrogen bonds: B:G.27, B:D.29, B:D.30, B:D.30, B:I.50, A:G.27, 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, 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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