SMTL ID : 6w0u.1

HIV Integrase core domain in complex with inhibitor 2-(2-ethynyl-5-methyl-1-benzofuran-3-yl)acetic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

homo-dimer

Ligands

2 x S0Y: 2-(2-ethynyl-5-methyl-1-benzofuran-3-yl)ethanoic acid(Non-covalent)

S0Y.1: 12 residues within 4Å: Chain A: Q.48, A.51, Y.52, L.55, T.78, A.81, A.82 Chain B: A.122, E.123, H.124, T.127, M.131 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:Q.48, A:Y.52, A:L.55, A:A.82, B:T.127 Hydrogen bonds: B:E.123, B:H.124, B:T.127, B:T.127 Salt bridges: B:H.124 S0Y.8: 12 residues within 4Å: Chain A: A.122, E.123, H.124, T.127, M.131 Chain B: Q.48, A.51, Y.52, L.55, T.78, A.81, A.82 9 PLIP interactions: 4 interactions with chain B, 5 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

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

SO4.2: 4 residues within 4Å: Chain A: T.19, H.20, N.108, K.112 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.19, A:H.20, A:N.108 Salt bridges: A:K.109, A:K.112 SO4.9: 4 residues within 4Å: Chain B: T.19, H.20, N.108, K.112 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.20, B:N.108 Salt bridges: B:K.109, B:K.112

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

IOD.3: 4 residues within 4Å: Chain A: L.54, V.66, C.83, Q.90 Ligand excluded by PLIP IOD.4: 3 residues within 4Å: Chain A: H.20, L.21, G.23 Ligand excluded by PLIP IOD.5: 2 residues within 4Å: Chain A: K.24, K.126 Ligand excluded by PLIP IOD.6: 3 residues within 4Å: Chain A: S.76, T.77, T.78 Ligand excluded by PLIP IOD.7: 3 residues within 4Å: Chain A: Q.15, H.67, P.95 Ligand excluded by PLIP IOD.10: 4 residues within 4Å: Chain B: L.54, V.66, C.83, Q.90 Ligand excluded by PLIP IOD.11: 3 residues within 4Å: Chain B: H.20, L.21, G.23 Ligand excluded by PLIP IOD.12: 2 residues within 4Å: Chain B: K.24, K.126 Ligand excluded by PLIP IOD.13: 3 residues within 4Å: Chain B: S.76, T.77, T.78 Ligand excluded by PLIP IOD.14: 3 residues within 4Å: Chain B: Q.15, H.67, P.95 Ligand excluded by PLIP

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

2021-03-03

Peptides

Integrase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Integrase

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