SMTL ID : 6um8.1

HIV Integrase in complex with Compound-14

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

homo-dimer

Ligands

4 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.1: 4 residues within 4Å: Chain A: D.121, Q.122, E.124 Ligands: QCG.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.124, A:E.124 1PE.2: 12 residues within 4Å: Chain A: E.41, Y.53, K.57, H.125, K.127 Chain B: E.41, Q.49, E.50, Y.53, K.57 Ligands: QCG.5, 1PE.10 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:K.57, A:K.127, B:E.41, B:Y.53 Water bridges: B:E.50 1PE.9: 5 residues within 4Å: Chain B: D.121, Q.122, A.123, E.124 Ligands: QCG.11 No protein-ligand interaction detected (PLIP) 1PE.10: 9 residues within 4Å: Chain A: Q.49, E.50, Y.53 Chain B: E.41, V.42, H.125, K.127 Ligands: 1PE.2, QCG.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.42, B:K.127 Water bridges: B:K.127

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 3 residues within 4Å: Chain A: W.86 Chain B: F.135, I.136 No protein-ligand interaction detected (PLIP) PEG.4: 4 residues within 4Å: Chain A: F.135, I.136, K.139 Chain B: W.86 No protein-ligand interaction detected (PLIP)

2 x QCG: (2S)-tert-butoxy[7-(8-fluoro-5-methyl-3,4-dihydro-2H-1-benzopyran-6-yl)-5-methyl-2-phenylpyrazolo[1,5-a]pyrimidin-6-yl]acetic acid(Non-covalent)

QCG.5: 18 residues within 4Å: Chain A: Q.122, A.123, E.124, H.125, K.127, T.128, M.132 Chain B: Q.49, A.52, Y.53, L.56, T.78, T.79, A.82, A.83, W.86 Ligands: 1PE.1, 1PE.2 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Q.49, B:Y.53, B:T.79, B:A.82, B:W.86 Hydrogen bonds: A:E.124, A:H.125, A:H.125 Salt bridges: A:H.125 QCG.11: 18 residues within 4Å: Chain A: Q.49, A.52, Y.53, L.56, T.78, T.79, A.82, A.83, W.86 Chain B: Q.122, A.123, E.124, H.125, K.127, T.128, M.132 Ligands: 1PE.9, 1PE.10 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:Q.49, A:A.82, A:W.86, B:T.128 Water bridges: A:Q.49 Hydrogen bonds: B:E.124, B:H.125, B:H.125 Salt bridges: B:H.125

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

SO4.6: 5 residues within 4Å: Chain A: K.25, R.120, E.124, H.125, L.126 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.120, A:L.126 Water bridges: A:K.127 Salt bridges: A:K.25, A:H.125 SO4.7: 3 residues within 4Å: Chain A: T.20, H.21, K.113 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.20, A:T.20, A:H.21, A:N.109 Salt bridges: A:H.21, A:K.113 SO4.8: 5 residues within 4Å: Chain A: T.47, G.48, Q.49, S.77, T.79 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.48, A:Q.49, A:S.77, A:T.79, A:T.79 Water bridges: A:Q.49 SO4.12: 5 residues within 4Å: Chain B: T.47, G.48, Q.49, S.77, T.79 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.48, B:Q.49, B:Q.49, B:S.77, B:T.79, B:T.79 Water bridges: B:T.47, B:T.79 SO4.13: 3 residues within 4Å: Chain B: D.70, N.71, G.94 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.71, B:N.71 SO4.14: 5 residues within 4Å: Chain B: K.25, R.120, E.124, H.125, L.126 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.120, B:L.126 Water bridges: B:K.127, B:K.127 Salt bridges: B:K.25, B:H.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, G. et al., Discovery and Optimization of Novel Pyrazolopyrimidines as Potent and Orally Bioavailable Allosteric HIV-1 Integrase Inhibitors. J.Med.Chem. (2020)

Release Date

2020-03-04

Peptides

Integrase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Integrase

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