SMTL ID : 3lpt.1

HIV integrase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x 723: (6-chloro-2-oxo-4-phenyl-1,2-dihydroquinolin-3-yl)acetic acid(Non-covalent)

723.1: 12 residues within 4Å: Chain A: T.78, T.79, A.82, A.83 Chain B: Q.122, A.123, E.124, H.125, T.128, M.132 Ligands: P03.16, CL.22 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:T.128, A:T.78, A:T.79, A:A.82 Hydrogen bonds: B:E.124, B:H.125, B:T.128, B:T.128 Salt bridges: B:H.125 Water bridges: A:Q.49, A:T.79 723.12: 12 residues within 4Å: Chain A: Q.122, A.123, E.124, H.125, T.128, M.132 Chain B: T.78, T.79, A.82, A.83 Ligands: P03.5, CL.11 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:T.78, B:T.79, B:A.82, A:T.128 Water bridges: B:T.79, B:T.79, A:E.124 Hydrogen bonds: A:E.124, A:H.125, A:T.128 Salt bridges: A:H.125

8 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 4 residues within 4Å: Chain A: T.78, K.81, A.82, W.85 No protein-ligand interaction detected (PLIP) PEG.3: 8 residues within 4Å: Chain A: V.31, H.32, V.33, S.35, G.36, E.106, M.108, R.153 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.36, A:E.106, A:R.153 PEG.4: 4 residues within 4Å: Chain A: Q.49, E.50, Y.53 Chain B: K.127 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.49, A:E.50, B:K.127 Water bridges: B:V.42 PEG.6: 3 residues within 4Å: Chain A: I.157, T.160, D.161 No protein-ligand interaction detected (PLIP) PEG.13: 4 residues within 4Å: Chain B: T.78, K.81, A.82, W.85 No protein-ligand interaction detected (PLIP) PEG.14: 8 residues within 4Å: Chain B: V.31, H.32, V.33, S.35, G.36, E.106, M.108, R.153 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.36, B:E.106, B:R.153 PEG.15: 4 residues within 4Å: Chain A: K.127 Chain B: Q.49, E.50, Y.53 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.127, B:Q.49 Water bridges: A:V.42 PEG.17: 3 residues within 4Å: Chain B: I.157, T.160, D.161 No protein-ligand interaction detected (PLIP)

2 x P03: 2-[3-[3-(2-hydroxyethoxy)propoxy]propoxy]ethanol(Non-covalent)

P03.5: 6 residues within 4Å: Chain A: D.121, Q.122, A.123, E.124 Ligands: CL.11, 723.12 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.124 P03.16: 6 residues within 4Å: Chain B: D.121, Q.122, A.123, E.124 Ligands: 723.1, CL.22 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:E.124

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

SO4.7: 4 residues within 4Å: Chain A: C.19, T.20, H.21, K.113 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.21 Water bridges: A:N.109 Salt bridges: A:H.21, A:K.113 SO4.8: 4 residues within 4Å: Chain A: G.48, S.77, T.78, T.79 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.48, A:Q.49, A:S.77, A:T.78, A:T.79, A:T.79, A:T.79 Water bridges: A:S.77, A:T.78 SO4.9: 6 residues within 4Å: Chain A: E.23, K.25, R.120, E.124, H.125, L.126 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.126 Water bridges: A:K.127 Salt bridges: A:K.25, A:H.125 SO4.18: 4 residues within 4Å: Chain B: C.19, T.20, H.21, K.113 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.21 Water bridges: B:N.109 Salt bridges: B:H.21, B:K.113 SO4.19: 4 residues within 4Å: Chain B: G.48, S.77, T.78, T.79 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.48, B:Q.49, B:S.77, B:T.78, B:T.79, B:T.79 Water bridges: B:S.77 SO4.20: 6 residues within 4Å: Chain B: E.23, K.25, R.120, E.124, H.125, L.126 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.126 Water bridges: B:K.127 Salt bridges: B:K.25, B:H.125

2 x CA: CALCIUM ION(Non-covalent)

CA.10: 1 residues within 4Å: Chain A: T.78 No protein-ligand interaction detected (PLIP) CA.21: 1 residues within 4Å: Chain B: T.78 No protein-ligand interaction detected (PLIP)

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.11: 3 residues within 4Å: Chain A: E.124 Ligands: P03.5, 723.12 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain B: E.124 Ligands: 723.1, P03.16 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Christ, F. et al., Rational design of small-molecule inhibitors of the LEDGF/p75-integrase interaction and HIV replication. Nat.Chem.Biol. (2010)

Release Date

2010-05-12

Peptides

Integrase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Integrase

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