SMTL ID : 6wc8.1

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 1.88 Å

Oligo State

homo-dimer

Ligands

2 x TQM: {5-(3-fluorophenyl)-2-[(thiophen-2-yl)ethynyl]-1-benzofuran-3-yl}acetic acid(Non-covalent)

TQM.1: 14 residues within 4Å: Chain A: Q.48, E.49, A.51, Y.52, L.55, A.81, A.82, W.85 Chain B: Q.121, A.122, E.123, H.124, K.126, T.127 12 PLIP interactions: 5 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:T.127, A:Q.48, A:E.49, A:A.51, A:Y.52, A:L.55, A:A.81, A:A.82 Hydrogen bonds: B:E.123, B:H.124 Salt bridges: B:H.124 pi-Cation interactions: B:K.126 TQM.10: 14 residues within 4Å: Chain A: Q.121, A.122, E.123, H.124, K.126, T.127 Chain B: Q.48, E.49, A.51, Y.52, L.55, A.81, A.82, W.85 13 PLIP interactions: 6 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:T.127, B:Q.48, B:E.49, B:A.51, B:Y.52, B:L.55, B:A.81, B:A.82 Hydrogen bonds: A:E.123, A:H.124, A:T.127 Salt bridges: A:H.124 pi-Cation interactions: A:K.126

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

IOD.2: 2 residues within 4Å: Chain A: H.20, G.23 Ligand excluded by PLIP IOD.3: 4 residues within 4Å: Chain A: K.24, L.125, K.126 Ligands: IOD.5 Ligand excluded by PLIP IOD.4: 1 residues within 4Å: Chain A: R.140 Ligand excluded by PLIP IOD.5: 4 residues within 4Å: Chain A: K.24, V.41, P.43 Ligands: IOD.3 Ligand excluded by PLIP IOD.11: 2 residues within 4Å: Chain B: H.20, G.23 Ligand excluded by PLIP IOD.12: 4 residues within 4Å: Chain B: K.24, L.125, K.126 Ligands: IOD.14 Ligand excluded by PLIP IOD.13: 1 residues within 4Å: Chain B: R.140 Ligand excluded by PLIP IOD.14: 4 residues within 4Å: Chain B: K.24, V.41, P.43 Ligands: IOD.12 Ligand excluded by PLIP

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

SO4.6: 6 residues within 4Å: Chain A: S.34, G.35, M.107, H.136, A.149, R.152 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.136, A:R.152 SO4.7: 3 residues within 4Å: Chain A: F.74, T.75, K.80 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.75 Salt bridges: A:K.80 SO4.8: 4 residues within 4Å: Chain A: C.18, T.19, H.20, K.112 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:C.18, A:H.20 Salt bridges: A:H.20, A:K.112 SO4.9: 5 residues within 4Å: Chain A: G.47, T.75, S.76, T.77, T.78 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.47, A:T.77, A:T.77, A:T.78, A:T.78 SO4.15: 6 residues within 4Å: Chain B: S.34, G.35, M.107, H.136, A.149, R.152 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.136, B:R.152 SO4.16: 3 residues within 4Å: Chain B: F.74, T.75, K.80 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.75 Salt bridges: B:K.80 SO4.17: 4 residues within 4Å: Chain B: C.18, T.19, H.20, K.112 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:C.18, B:T.19, B:H.20 Salt bridges: B:H.20, B:K.112 SO4.18: 5 residues within 4Å: Chain B: G.47, T.75, S.76, T.77, T.78 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.47, B:T.77, B:T.78, B:T.78

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

2021-03-31

Peptides

Integrase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Integrase

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