SMTL ID : 3zt3.1

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 1.95 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: T.21, H.22, K.114 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.21, 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.121, A:L.127 Water bridges: A:K.26, A:K.128 Salt bridges: A:K.26, A:H.126 SO4.8: 3 residues within 4Å: Chain B: T.21, H.22, K.114 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.21, B:H.22 Water bridges: B:N.110 Salt bridges: B:H.22, B:K.114 SO4.9: 5 residues within 4Å: Chain B: K.26, R.121, E.125, H.126, L.127 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.121, B:E.125, B:L.127 Water bridges: B:K.26, B:K.26, B:K.128 Salt bridges: B:K.26, B:H.126

7 x ACY: ACETIC ACID(Non-functional Binders)

ACY.3: 4 residues within 4Å: Chain A: G.49, S.78, T.79, T.80 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.79, A:T.79, A:T.80, A:T.80 Water bridges: A:Q.50 ACY.4: 7 residues within 4Å: Chain A: E.40, F.55, K.58, L.59, R.62 Chain B: R.62 Ligands: ACY.11 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:K.58 Salt bridges: A:K.58, B:R.62 ACY.5: 7 residues within 4Å: Chain A: G.61, R.62, W.63, P.64 Chain B: Y.38, N.139, H.140 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.38, B:N.139 Salt bridges: B:H.140 ACY.10: 4 residues within 4Å: Chain B: G.49, S.78, T.79, T.80 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.78, B:T.79, B:T.80, B:T.80 Water bridges: B:G.49 ACY.11: 6 residues within 4Å: Chain B: E.40, F.55, K.58, L.59, R.62 Ligands: ACY.4 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Salt bridges: A:R.62, B:K.58, B:R.62 Hydrophobic interactions: B:F.55, B:K.58 ACY.12: 3 residues within 4Å: Chain B: Y.54, K.58 Ligands: ACY.13 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Water bridges: A:V.43, A:Q.132 Salt bridges: A:K.58, A:K.128, B:K.58 Hydrophobic interactions: B:Y.54 ACY.13: 3 residues within 4Å: Chain A: Y.54, K.58 Ligands: ACY.12 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.54 Hydrogen bonds: A:Y.54 Salt bridges: A:K.58, B:K.58, B:K.128 Water bridges: B:V.43, B:Q.132

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 9 residues within 4Å: Chain A: Y.38, N.139, H.140, G.152 Chain B: A.60, G.61, R.62, W.63, P.64 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:N.139, A:S.150 Hydrogen bonds: B:G.61

2 x ZT4: 5-{(E)-[(2R)-2-HYDROXY-2,3-DIHYDRO-1H-INDEN-1-YLIDENE]METHYL}-1,3-BENZODIOXOLE-4-CARBOXYLIC ACID(Non-covalent)

ZT4.7: 13 residues within 4Å: Chain A: Q.123, A.124, E.125, H.126, K.128, T.129, M.133 Chain B: Q.50, Y.54, L.57, T.80, A.84, W.87 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:Q.50, B:L.57, B:T.80, B:A.84, B:W.87, A:T.129 Hydrogen bonds: A:E.125, A:H.126, A:H.126 Salt bridges: A:H.126 ZT4.14: 12 residues within 4Å: Chain A: Q.50, Y.54, L.57, T.80, A.84, W.87 Chain B: Q.123, A.124, E.125, H.126, T.129, M.133 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:T.129, A:Q.50, A:L.57, A:T.80, A:A.84, A:W.87 Hydrogen bonds: B:E.125, B:H.126, B:T.129 Salt bridges: B:H.126

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

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