SMTL ID : 7l23.1

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 Compare

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: G.38, T.66, S.67, T.68, T.69 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.38, A:S.67, A:T.68, A:T.69 SO4.2: 3 residues within 4Å: Chain A: T.10, H.11, K.103 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.10, A:H.11 Salt bridges: A:H.11, A:K.103 SO4.9: 5 residues within 4Å: Chain B: G.38, T.66, S.67, T.68, T.69 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.38, B:S.67, B:T.68, B:T.69 SO4.10: 3 residues within 4Å: Chain B: T.10, H.11, K.103 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.11 Salt bridges: B:H.11, B:K.103

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

IOD.3: 3 residues within 4Å: Chain A: H.11, L.12, G.14 Ligand excluded by PLIP IOD.4: 2 residues within 4Å: Chain A: V.57, Q.81 Ligand excluded by PLIP IOD.5: 3 residues within 4Å: Chain A: K.15, L.116, K.117 Ligand excluded by PLIP IOD.6: 1 residues within 4Å: Chain A: H.58 Ligand excluded by PLIP IOD.7: 4 residues within 4Å: Chain A: Q.6, T.59, D.60, G.84 Ligand excluded by PLIP IOD.11: 3 residues within 4Å: Chain B: H.11, L.12, G.14 Ligand excluded by PLIP IOD.12: 2 residues within 4Å: Chain B: V.57, Q.81 Ligand excluded by PLIP IOD.13: 3 residues within 4Å: Chain B: K.15, L.116, K.117 Ligand excluded by PLIP IOD.14: 1 residues within 4Å: Chain B: H.58 Ligand excluded by PLIP IOD.15: 4 residues within 4Å: Chain B: Q.6, T.59, D.60, G.84 Ligand excluded by PLIP

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

XFS.8: 14 residues within 4Å: Chain A: Q.39, E.40, A.42, Y.43, L.46, T.69, A.72, A.73 Chain B: A.113, E.114, H.115, K.117, T.118, M.122 13 PLIP interactions: 5 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:Q.39, A:Y.43, A:L.46, A:A.72, A:A.73, B:T.118 Hydrogen bonds: B:E.114, B:H.115, B:T.118, B:T.118 Salt bridges: B:H.115, B:H.115 pi-Stacking: B:H.115 XFS.16: 14 residues within 4Å: Chain A: A.113, E.114, H.115, K.117, T.118, M.122 Chain B: Q.39, E.40, A.42, Y.43, L.46, T.69, A.72, A.73 12 PLIP interactions: 5 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:Q.39, B:Y.43, B:L.46, B:A.72, B:A.73, A:T.118 Hydrogen bonds: A:E.114, A:H.115, A:T.118 Salt bridges: A:H.115, A:H.115 pi-Stacking: A:H.115

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chiew, B. et al., Rapid development of potent inhibitors of the HIV integrase-LEDGF interaction by fragment-linking using off-rate screening. To Be Published

Release Date

2021-12-22

Peptides

Integrase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Integrase