SMTL ID : 6w42.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: G.47, S.76, T.77, T.78 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.47, A:S.76, A:T.77, A:T.78, A:T.78 SO4.2: 3 residues within 4Å: Chain A: T.19, H.20, K.112 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.19, A:H.20 Salt bridges: A:H.20, A:K.112 SO4.8: 4 residues within 4Å: Chain B: G.47, S.76, T.77, T.78 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.47, B:S.76, B:T.77, B:T.78 SO4.9: 3 residues within 4Å: Chain B: T.19, H.20, K.112 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.20 Salt bridges: B:H.20, B:K.112

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

IOD.3: 2 residues within 4Å: Chain A: Q.15, H.67 Ligand excluded by PLIP IOD.4: 3 residues within 4Å: Chain A: H.20, L.21, G.23 Ligand excluded by PLIP IOD.5: 4 residues within 4Å: Chain A: L.54, V.66, C.83, Q.90 Ligand excluded by PLIP IOD.6: 2 residues within 4Å: Chain A: L.125, K.126 Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain B: Q.15, H.67 Ligand excluded by PLIP IOD.11: 3 residues within 4Å: Chain B: H.20, L.21, G.23 Ligand excluded by PLIP IOD.12: 4 residues within 4Å: Chain B: L.54, V.66, C.83, Q.90 Ligand excluded by PLIP IOD.13: 2 residues within 4Å: Chain B: L.125, K.126 Ligand excluded by PLIP

2 x SJY: 2-[5-methyl-2-(2-thiophen-2-ylethynyl)-1-benzofuran-3-yl]ethanoic acid(Non-covalent)

SJY.7: 15 residues within 4Å: Chain A: Q.48, E.49, A.51, Y.52, L.55, T.78, A.81, A.82, W.85 Chain B: A.122, E.123, H.124, K.126, T.127, M.131 13 PLIP interactions: 7 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:T.127, A:Q.48, A:Y.52, A:L.55, A:T.78, A:A.82, A:W.85 Hydrogen bonds: B:E.123, B:H.124, B:T.127, B:T.127 Salt bridges: B:H.124 pi-Stacking: B:H.124 SJY.14: 15 residues within 4Å: Chain A: A.122, E.123, H.124, K.126, T.127, M.131 Chain B: Q.48, E.49, A.51, Y.52, L.55, T.78, A.81, A.82, W.85 12 PLIP interactions: 6 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:Q.48, B:Y.52, B:L.55, B:T.78, B:A.82, B:W.85, A:T.127 Hydrogen bonds: A:E.123, A:H.124, A:T.127 Salt bridges: A:H.124 pi-Stacking: A:H.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gorman, M.A. et al., HIV Integrase core domain in complex with inhibitor (5-methyl-1-benzofuran-3-yl)acetic acid. To Be Published

Release Date

2021-03-10

Peptides

HIV Integrase catalytic domain: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

HIV Integrase catalytic domain