SMTL ID : 6we7.1

HIV Integrase core domain in complex with inhibitor 3-methyl-2-{5-methyl-2-[2-(thiophen-2-yl)ethynyl]-1- benzofuran-3-yl}butanoic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: G.47, S.76, T.77, T.78, V.79 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.76, A:T.77, A:T.78 SO4.2: 4 residues within 4Å: Chain A: C.18, T.19, H.20, K.112 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.20 Salt bridges: A:H.20, A:K.112 SO4.3: 3 residues within 4Å: Chain A: K.138, K.139, R.140 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.140 SO4.4: 7 residues within 4Å: Chain A: S.34, G.35, H.136, K.139, K.141, A.149, R.152 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.34 Water bridges: A:R.152, A:R.152 Salt bridges: A:H.136, A:K.141, A:R.152 SO4.5: 5 residues within 4Å: Chain A: S.10, P.11, G.12, I.13, K.64 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.10, A:G.12, A:G.12 Salt bridges: A:K.64 SO4.9: 5 residues within 4Å: Chain B: G.47, S.76, T.77, T.78, V.79 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.76, B:T.77, B:T.78 SO4.10: 4 residues within 4Å: Chain B: C.18, 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 SO4.11: 3 residues within 4Å: Chain B: K.138, K.139, R.140 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.140 SO4.12: 7 residues within 4Å: Chain B: S.34, G.35, H.136, K.139, K.141, A.149, R.152 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.34 Water bridges: B:R.152, B:R.152 Salt bridges: B:H.136, B:K.141, B:R.152 SO4.13: 5 residues within 4Å: Chain B: S.10, P.11, G.12, I.13, K.64 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.10, B:G.12, B:G.12 Salt bridges: B:K.64

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

IOD.6: 4 residues within 4Å: Chain A: H.20, L.21, E.22, G.23 Ligand excluded by PLIP IOD.7: 5 residues within 4Å: Chain A: K.24, V.41, H.124, L.125, K.126 Ligand excluded by PLIP IOD.14: 4 residues within 4Å: Chain B: H.20, L.21, E.22, G.23 Ligand excluded by PLIP IOD.15: 5 residues within 4Å: Chain B: K.24, V.41, H.124, L.125, K.126 Ligand excluded by PLIP

2 x TXM: (2S)-3-methyl-2-{5-methyl-2-[(thiophen-2-yl)ethynyl]-1-benzofuran-3-yl}butanoic acid(Non-covalent)

TXM.8: 16 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: Q.121, A.122, E.123, H.124, K.126, T.127, M.131 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:T.127, A:Q.48, A:Y.52, A:L.55, A:A.82 Hydrogen bonds: B:E.123, B:H.124, B:T.127 Salt bridges: B:H.124 pi-Stacking: B:H.124 TXM.16: 16 residues within 4Å: Chain A: Q.121, 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 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:Q.48, B:Y.52, B:L.55, B:A.82, 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. To Be Published

Release Date

2021-04-07

Peptides

Integrase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Integrase