SMTL ID : 3zsz.1

Small molecule inhibitors of the LEDGF site of HIV type 1 integrase identified by fragment screening and structure based drug design

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: C.20, 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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.121, A:L.127 Water bridges: A:K.128 Salt bridges: A:K.26, A:H.126 SO4.3: 4 residues within 4Å: Chain A: G.49, S.78, T.79, T.80 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.79, A:T.80, A:T.80 Water bridges: A:Q.50 SO4.7: 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:T.21, B:H.22 Water bridges: B:N.110 Salt bridges: B:H.22, B:K.114 SO4.8: 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:E.125, B:L.127 Water bridges: B:K.128 Salt bridges: B:K.26, B:H.126 SO4.9: 4 residues within 4Å: Chain B: G.49, S.78, T.79, T.80 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.49, B:T.79, B:T.79, B:T.79, B:T.80, B:T.80 Water bridges: B:Q.50

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

ACT.4: 3 residues within 4Å: Chain A: Y.54, K.58 Ligands: ACT.10 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.54, A:K.58 Hydrogen bonds: A:Y.54 Salt bridges: A:K.58, B:K.58, B:K.128 Water bridges: B:V.43, B:Q.132 ACT.5: 6 residues within 4Å: Chain A: E.40, F.55, K.58, L.59, R.62 Chain B: R.62 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.55, A:K.58, A:L.59 Hydrogen bonds: A:E.40 Salt bridges: A:K.58, B:R.62 ACT.10: 3 residues within 4Å: Chain B: Y.54, K.58 Ligands: ACT.4 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Y.54, B:K.58 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.11: 8 residues within 4Å: Chain A: A.60, G.61, R.62, W.63, P.64 Chain B: Y.38, N.139, H.140 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.140 ACT.12: 6 residues within 4Å: Chain A: R.62 Chain B: E.40, A.41, F.55, K.58, L.59 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Salt bridges: A:R.62, B:K.58 Hydrophobic interactions: B:F.55, B:K.58 Hydrogen bonds: B:A.41

2 x OM2: (R)-[2-[[(2S)-BUTAN-2-YL]CARBAMOYL]PHENYL]METHYL-[(4-CARBOXY-1,3-BENZODIOXOL-5-YL)METHYL]-METHYL-AZANIUM(Non-covalent)

OM2.6: 13 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, Y.54, T.80, A.84, W.87 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:Q.50, B:T.80, B:W.87, A:T.129 Hydrogen bonds: A:Q.123, A:E.125, A:H.126, A:T.129 Salt bridges: A:H.126 OM2.13: 10 residues within 4Å: Chain A: Q.50, Y.54, T.80 Chain B: D.122, Q.123, A.124, E.125, H.126, K.128, T.129 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:E.125, B:T.129, A:Q.50, A:T.80 Hydrogen bonds: B:E.125, B:E.125, B:H.126, B:H.126 Salt bridges: B:H.126

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

CL.14: 1 residues within 4Å: Chain B: M.133 Ligand excluded by PLIP

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

2012-07-11

Peptides

INTEGRASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

INTEGRASE

Related Entries With Identical Sequence