SMTL ID : 3lpu.1

HIV integrase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x 976: (2S)-2-(6-chloro-2-methyl-4-phenylquinolin-3-yl)pentanoic acid(Non-covalent)

976.1: 12 residues within 4Å: Chain A: Q.49, Y.53, T.78, T.79, A.82, A.83 Chain B: Q.122, A.123, E.124, H.125, T.128, M.132 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:T.128, 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.49 976.9: 12 residues within 4Å: Chain A: Q.122, A.123, E.124, H.125, T.128, M.132 Chain B: Q.49, Y.53, T.78, T.79, A.82, A.83 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:T.128, B:A.82 Hydrogen bonds: A:E.124, A:H.125, A:T.128 Salt bridges: A:H.125 Water bridges: B:Q.49

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

P03.2: 6 residues within 4Å: Chain A: Q.49, E.50, Y.53 Chain B: H.125, K.127 Ligands: SO4.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.127 P03.10: 6 residues within 4Å: Chain A: H.125, K.127 Chain B: Q.49, E.50, Y.53 Ligands: SO4.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.127

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

PEG.3: 1 residues within 4Å: Chain A: W.85 No protein-ligand interaction detected (PLIP) PEG.4: 6 residues within 4Å: Chain A: V.33, A.34, S.35, G.36, M.108, R.153 No protein-ligand interaction detected (PLIP) PEG.11: 1 residues within 4Å: Chain B: W.85 No protein-ligand interaction detected (PLIP) PEG.12: 6 residues within 4Å: Chain B: V.33, A.34, S.35, G.36, M.108, R.153 No protein-ligand interaction detected (PLIP)

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

SO4.5: 3 residues within 4Å: Chain A: T.20, H.21, K.113 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.21 Water bridges: A:H.21 Salt bridges: A:H.21, A:K.113 SO4.6: 5 residues within 4Å: Chain A: G.48, Q.49, S.77, T.78, T.79 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.48, A:Q.49, A:S.77, A:T.78, A:T.79, A:T.79 SO4.7: 6 residues within 4Å: Chain A: K.25, R.120, E.124, H.125, L.126 Ligands: P03.10 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.120, A:L.126 Water bridges: A:K.25, A:K.25, A:K.25, A:K.25, A:K.127 Salt bridges: A:K.25, A:H.125 SO4.13: 3 residues within 4Å: Chain B: T.20, H.21, K.113 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.21 Salt bridges: B:H.21, B:K.113 SO4.14: 5 residues within 4Å: Chain B: G.48, Q.49, S.77, T.78, T.79 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.48, B:Q.49, B:S.77, B:T.78, B:T.79, B:T.79 SO4.15: 6 residues within 4Å: Chain B: K.25, R.120, E.124, H.125, L.126 Ligands: P03.2 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:R.120, B:L.126 Water bridges: B:K.25, B:K.25, B:K.25, B:K.25, B:K.127 Salt bridges: B:K.25, B:H.125

2 x CA: CALCIUM ION(Non-covalent)

CA.8: 1 residues within 4Å: Chain A: T.78 No protein-ligand interaction detected (PLIP) CA.16: 1 residues within 4Å: Chain B: T.78 No protein-ligand interaction detected (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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