SMTL ID : 6vlh.1

HIV Integrase Core domain (IN) in complex with dimer-spanning ligand

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

homo-dimer

Ligands

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

IOD.1: 5 residues within 4Å: Chain A: K.24, V.41, H.124, L.125, K.126 Ligand excluded by PLIP IOD.2: 3 residues within 4Å: Chain A: H.20, G.23, K.24 Ligand excluded by PLIP IOD.3: 2 residues within 4Å: Chain A: K.139, R.140 Ligand excluded by PLIP IOD.4: 5 residues within 4Å: Chain A: G.35, M.107, H.136, A.149, R.152 Ligand excluded by PLIP IOD.9: 4 residues within 4Å: Chain B: K.24, H.124, L.125, K.126 Ligand excluded by PLIP IOD.10: 4 residues within 4Å: Chain B: H.20, L.21, E.22, G.23 Ligand excluded by PLIP

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

SO4.5: 5 residues within 4Å: Chain A: C.18, T.19, H.20, N.108, K.112 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.20 Salt bridges: A:H.20, A:K.112 SO4.6: 2 residues within 4Å: Chain A: D.69, N.70 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.69, A:N.70 SO4.7: 6 residues within 4Å: Chain A: G.47, T.75, S.76, T.77, T.78, V.79 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.47, A:T.75, A:S.76, A:T.77, A:T.78, A:T.78, A:T.78 SO4.8: 3 residues within 4Å: Chain A: P.62, K.64 Chain B: K.138 3 PLIP interactions: 3 interactions with chain B Water bridges: B:E.151, B:E.151 Salt bridges: B:K.138 SO4.11: 3 residues within 4Å: Chain B: T.19, H.20, K.112 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.19, B:H.20 Salt bridges: B:H.20, B:K.112 SO4.12: 5 residues within 4Å: Chain B: L.21, K.112, I.115, G.116, R.119 No protein-ligand interaction detected (PLIP) SO4.13: 5 residues within 4Å: Chain B: S.10, P.11, G.12, I.13, K.64 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.10, B:G.12 Water bridges: B:K.64 SO4.14: 6 residues within 4Å: Chain B: G.47, Q.48, S.76, T.77, T.78, V.79 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.76, B:T.77, B:T.78, B:T.78 Water bridges: B:T.77 SO4.15: 4 residues within 4Å: Chain B: I.13, Q.15, V.32, H.67 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.15 Salt bridges: B:H.67

1 x R2A: (2-{[3-(4-{2-[(3-{[3-(carboxymethyl)-5-methyl-1-benzofuran-2-yl]ethynyl}benzene-1-carbonyl)amino]ethyl}piperazine-1-carbonyl)phenyl]ethynyl}-5-methyl-1-benzofuran-3-yl)acetic acid(Non-covalent)

R2A.16: 37 residues within 4Å: Chain A: E.40, V.41, I.42, P.43, Q.48, E.49, A.51, Y.52, L.55, K.56, T.78, A.81, A.82, W.85, A.122, E.123, H.124, K.126, T.127, M.131 Chain B: E.40, Q.48, E.49, A.51, Y.52, L.55, K.56, T.78, A.81, A.82, W.85, A.122, E.123, H.124, K.126, T.127, M.131 28 PLIP interactions: 15 interactions with chain A, 13 interactions with chain B Hydrophobic interactions: A:Q.48, A:E.49, A:A.51, A:L.55, A:T.78, A:A.81, A:A.82, A:K.126, A:T.127, B:Y.52, B:Y.52, B:L.55, B:T.78, B:A.82, B:T.127 Hydrogen bonds: A:E.123, A:E.123, A:H.124, A:T.127, B:Q.48, B:E.123, B:H.124, B:K.126, B:T.127 Salt bridges: A:E.40, A:H.124, B:H.124 pi-Cation interactions: B:K.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Scanlon, M. et al., HIV Integrase core domain (IN) in complex with dimeric spanning inhibitor. To Be Published

Release Date

2021-01-27

Peptides

Integrase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Integrase