SMTL ID : 7l2y.1

HIV Integrase core domain in complex with inhibitor 2-(5-(3-fluorophenyl)-2-(2-(thiophen-2-yl)ethynyl)-1- benzofuran-3-yl)ethanoic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: G.45, S.74, T.75, T.76 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.45, A:S.74, A:T.75, A:T.76, A:T.76, A:T.76 SO4.2: 3 residues within 4Å: Chain A: T.17, H.18, K.109 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.17, A:T.17, A:H.18 Salt bridges: A:H.18, A:K.109 SO4.3: 7 residues within 4Å: Chain A: S.32, G.33, H.133, K.136, K.138, A.146, R.149 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.32 Water bridges: A:K.138, A:A.146, A:R.149, A:R.149 Salt bridges: A:H.133, A:K.136, A:K.138, A:R.149 SO4.10: 3 residues within 4Å: Chain A: F.90, G.91, I.92 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.92 SO4.11: 4 residues within 4Å: Chain B: G.45, S.74, T.75, T.76 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.45, B:S.74, B:T.75, B:T.75, B:T.76, B:T.76, B:T.76 SO4.12: 3 residues within 4Å: Chain B: T.17, H.18, K.109 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.17, B:H.18 Salt bridges: B:H.18, B:K.109 SO4.13: 7 residues within 4Å: Chain B: S.32, G.33, H.133, K.136, K.138, A.146, R.149 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.32 Water bridges: B:K.138, B:A.146, B:R.149, B:R.149 Salt bridges: B:H.133, B:K.136, B:K.138, B:R.149 SO4.20: 3 residues within 4Å: Chain B: F.90, G.91, I.92 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.92

10 x IOD: IODIDE ION(Non-functional Binders)

IOD.4: 2 residues within 4Å: Chain A: Q.13, H.65 Ligand excluded by PLIP IOD.5: 2 residues within 4Å: Chain A: H.18, G.21 Ligand excluded by PLIP IOD.6: 5 residues within 4Å: Chain A: L.52, V.64, N.71, C.81, Q.88 Ligand excluded by PLIP IOD.7: 3 residues within 4Å: Chain A: K.22, L.122, K.123 Ligand excluded by PLIP IOD.8: 5 residues within 4Å: Chain A: S.8, P.9, G.10, I.11, K.62 Ligand excluded by PLIP IOD.14: 2 residues within 4Å: Chain B: Q.13, H.65 Ligand excluded by PLIP IOD.15: 2 residues within 4Å: Chain B: H.18, G.21 Ligand excluded by PLIP IOD.16: 5 residues within 4Å: Chain B: L.52, V.64, N.71, C.81, Q.88 Ligand excluded by PLIP IOD.17: 3 residues within 4Å: Chain B: K.22, L.122, K.123 Ligand excluded by PLIP IOD.18: 5 residues within 4Å: Chain B: S.8, P.9, G.10, I.11, K.62 Ligand excluded by PLIP

2 x XHY: 4-{[3-(carboxymethyl)-5-methyl-1-benzofuran-2-yl]ethynyl}benzoic acid(Non-covalent)

XHY.9: 14 residues within 4Å: Chain A: Q.46, E.47, A.49, Y.50, L.53, T.76, A.79, A.80 Chain B: A.119, E.120, H.121, K.123, T.124, M.128 14 PLIP interactions: 7 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:Q.46, A:A.49, A:Y.50, A:L.53, A:T.76, A:A.79, A:A.80, B:T.124 Hydrogen bonds: B:E.120, B:H.121, B:T.124 Salt bridges: B:H.121, B:K.123 pi-Stacking: B:H.121 XHY.19: 14 residues within 4Å: Chain A: A.119, E.120, H.121, K.123, T.124, M.128 Chain B: Q.46, E.47, A.49, Y.50, L.53, T.76, A.79, A.80 13 PLIP interactions: 7 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:Q.46, B:A.49, B:Y.50, B:L.53, B:T.76, B:A.79, B:A.80, A:T.124 Hydrogen bonds: A:E.120, A:H.121 Salt bridges: A:H.121, A:K.123 pi-Stacking: A:H.121

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gorman, M.A. et al., HIV Integrase core domain in complex with inhibitor. To Be Published

Release Date

2021-12-22

Peptides

Integrase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
AAA

Integrase