SMTL ID : 3zcm.1

Small molecule inhibitors of the LEDGF site of HIV integrase identified by fragment screening and structure based design.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: T.21, H.22, K.114 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.22 Water bridges: A:N.110 Salt bridges: A:H.22, A:K.114 SO4.2: 5 residues within 4Å: Chain A: K.26, R.121, E.125, H.126, L.127 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.121, A:E.125, A:L.127 Water bridges: A:K.26, A:K.128 Salt bridges: A:K.26, A:H.126 SO4.3: 8 residues within 4Å: Chain A: E.40, A.41, F.55, K.58, L.59, R.62 Chain B: R.62 Ligands: SO4.8 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Salt bridges: B:R.62, A:K.58 Hydrogen bonds: A:E.40, A:E.40, A:A.41 SO4.6: 3 residues within 4Å: Chain B: T.21, H.22, K.114 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.21, B:H.22 Water bridges: B:N.110, B:N.110 Salt bridges: B:H.22, B:K.114 SO4.7: 5 residues within 4Å: Chain B: K.26, R.121, E.125, H.126, L.127 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.121, B:L.127 Water bridges: B:K.26, B:K.128 Salt bridges: B:K.26, B:H.126 SO4.8: 8 residues within 4Å: Chain A: R.62 Chain B: E.40, A.41, F.55, K.58, L.59, R.62 Ligands: SO4.3 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.40, B:A.41, B:A.41, B:R.62 Salt bridges: B:K.58, A:R.62

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: G.49, Q.50, S.78, T.79, T.80 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.49, A:Q.50, A:T.79, A:T.80 GOL.11: 5 residues within 4Å: Chain B: G.49, Q.50, S.78, T.79, T.80 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.49, B:Q.50, B:S.78, B:T.79

2 x PX3: 5-[[[2-[(4-methoxyphenyl)methylcarbamoyl]phenyl]methyl-prop-2-enyl-amino]methyl]-1,3-benzodioxole-4-carboxylic acid(Non-covalent)

PX3.5: 15 residues within 4Å: Chain A: D.122, Q.123, A.124, E.125, H.126, K.128, T.129, M.133 Chain B: Q.50, A.53, Y.54, L.57, T.80, A.83, A.84 10 PLIP interactions: 3 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:Q.50, B:T.80, B:A.83, A:T.129 Hydrogen bonds: A:Q.123, A:E.125, A:H.126, A:T.129, A:T.129 Salt bridges: A:H.126 PX3.12: 15 residues within 4Å: Chain A: Q.50, A.53, Y.54, L.57, T.80, A.83, A.84 Chain B: D.122, Q.123, A.124, E.125, H.126, K.128, T.129, M.133 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:T.129, A:Q.50, A:T.80, A:A.83 Hydrogen bonds: B:Q.123, B:E.125, B:H.126, B:H.126, B:T.129 Water bridges: B:E.125 Salt bridges: B:H.126

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.9: 3 residues within 4Å: Chain B: Y.54, K.58 Ligands: ACT.10 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Y.54 Hydrogen bonds: B:Y.54 Salt bridges: B:K.58, A:K.58, A:K.128 Water bridges: A:V.43, A:Q.132 ACT.10: 3 residues within 4Å: Chain A: Y.54, K.58 Ligands: ACT.9 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Water bridges: B:V.43, B:Q.132 Salt bridges: B:K.58, B:K.128, A:K.58 Hydrophobic interactions: A:Y.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Peat, T.S. et al., Small Molecule Inhibitors of the Ledgf Site of Human Immunodeficiency Virus Integrase Identified by Fragment Screening and Structure Based Design. Plos One (2012)

Release Date

2012-12-05

Peptides

HIV INTEGRASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

HIV INTEGRASE

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