SMTL ID : 7rq0.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: T.17, H.18, N.106, K.107, K.110 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.18, A:N.106 Water bridges: A:C.16 Salt bridges: A:H.18, A:K.107, A:K.110 SO4.2: 4 residues within 4Å: Chain A: G.45, 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 SO4.6: 5 residues within 4Å: Chain B: T.17, H.18, E.103, N.106, K.110 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.17, B:H.18, B:H.18, B:E.103 Salt bridges: B:H.18, B:K.110 SO4.7: 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 SO4.8: 5 residues within 4Å: Chain B: S.8, P.9, G.10, I.11, K.62 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.8, B:G.10 Salt bridges: B:K.62 SO4.9: 6 residues within 4Å: Chain B: G.45, Q.46, S.74, T.75, T.76, V.77 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.74, B:T.75, B:T.76

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

IOD.3: 4 residues within 4Å: Chain A: K.22, V.39, L.123, K.124 Ligand excluded by PLIP IOD.4: 4 residues within 4Å: Chain A: H.18, L.19, E.20, G.21 Ligand excluded by PLIP IOD.5: 5 residues within 4Å: Chain A: E.38, Y.50, F.51, K.54 Chain B: K.54 Ligand excluded by PLIP IOD.11: 4 residues within 4Å: Chain B: H.18, L.19, E.20, G.21 Ligand excluded by PLIP IOD.12: 4 residues within 4Å: Chain B: K.22, H.122, L.123, K.124 Ligand excluded by PLIP

1 x 6I2: {2-[(3-{[4-(2-{[(3-{[3-(carboxymethyl)-5-methyl-1-benzofuran-2-yl]ethynyl}phenyl)methyl]amino}ethyl)piperazin-1-yl]methyl}phenyl)ethynyl]-5-methyl-1-benzofuran-3-yl}acetic acid(Non-covalent)

6I2.10: 30 residues within 4Å: Chain A: 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 27 PLIP interactions: 13 interactions with chain A, 14 interactions with chain B Hydrophobic interactions: A:Q.46, A:Y.50, A:Y.50, A:L.53, A:T.76, A:A.79, A:A.80, A:T.125, B:Q.46, B:Y.50, B:L.53, B:T.76, B:A.79, B:A.80, B:K.124, B:T.125 Hydrogen bonds: A:E.121, A:H.122, A:T.125, B:E.121, B:H.122 Salt bridges: A:H.122, B:E.38, B:E.47, B:H.122 pi-Cation interactions: A:K.124 pi-Stacking: B:Y.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gorman, M.A. et al., HIV integrase-LEDGF interaction screening by fragment linking using off-rate screening. To Be Published

Release Date

2022-08-10

Peptides

Integrase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Integrase

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