SMTL ID : 7sia.1

HIV Integrase core domain in complex with inhibitor 2-[2-(2-{3-[(4-{2-[(3-{2-[3-(carboxymethyl)-5-methyl-1-benzofuran-2-yl]ethynyl}phenyl)formamido]ethyl}piperazin-1-yl)methyl]phenyl}ethynyl)-5-methyl-1-benzofuran-3-yl]acetic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

1 x 9I4: (2-{[3-({4-[2-(3-{[3-(carboxymethyl)-5-methyl-1-benzofuran-2-yl]ethynyl}benzamido)ethyl]piperazin-1-yl}methyl)phenyl]ethynyl}-5-methyl-1-benzofuran-3-yl)acetic acid(Non-covalent)

9I4.1: 31 residues within 4Å: Chain A: P.41, Q.46, E.47, A.49, Y.50, L.53, T.76, A.79, A.80, W.83, A.120, E.121, H.122, K.124, T.125, M.129 Chain B: Q.46, E.47, A.49, Y.50, L.53, T.76, A.79, A.80, W.83, A.120, E.121, H.122, K.124, T.125, M.129 26 PLIP interactions: 12 interactions with chain B, 14 interactions with chain A Hydrophobic interactions: B:Q.46, B:Y.50, B:L.53, B:T.76, B:A.79, B:A.80, B:T.125, A:Q.46, A:A.49, A:Y.50, A:L.53, A:T.76, A:A.80, A:T.125 Hydrogen bonds: B:E.121, B:H.122, B:T.125, A:E.121, A:H.122, A:K.124, A:T.125, A:T.125 Salt bridges: B:H.122, A:E.47, A:H.122 pi-Stacking: B:H.122

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

IOD.2: 5 residues within 4Å: Chain A: K.22, V.39, H.122, L.123, K.124 Ligand excluded by PLIP IOD.3: 3 residues within 4Å: Chain A: H.18, L.19, G.21 Ligand excluded by PLIP IOD.6: 6 residues within 4Å: Chain B: L.52, V.64, N.71, V.77, C.81, Q.88 Ligand excluded by PLIP IOD.7: 4 residues within 4Å: Chain B: H.18, L.19, E.20, G.21 Ligand excluded by PLIP

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

SO4.4: 5 residues within 4Å: Chain A: G.45, Q.46, S.74, T.75, T.76 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.74, A:T.75, A:T.76, A:T.76 SO4.5: 7 residues within 4Å: Chain A: I.11, Q.13, V.30, H.65, G.91, I.92, P.93 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.65 SO4.8: 7 residues within 4Å: Chain B: C.16, T.17, H.18, E.103, N.106, K.107, K.110 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.18, B:E.103 Salt bridges: B:H.18, B:K.107, B:K.110 SO4.9: 6 residues within 4Å: Chain B: L.19, E.20, K.110, I.113, G.114, R.117 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.20 SO4.10: 6 residues within 4Å: Chain B: G.45, Q.46, S.74, T.75, T.76, V.77 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.45, B:S.74, B:T.75, B:T.75, B:T.76, B:T.76

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

2022-10-19

Peptides

Integrase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Integrase