SMTL ID : 4cfb.1

Interrogating HIV integrase for compounds that bind- a SAMPL challenge

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: T.37, H.38, K.130 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.37, A:H.38 Water bridges: A:N.126 Salt bridges: A:H.38, A:K.130 SO4.2: 5 residues within 4Å: Chain A: K.42, R.137, E.141, H.142, L.143 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.137, A:L.143 Water bridges: A:K.42, A:K.42, A:K.144 Salt bridges: A:K.42, A:H.142 SO4.3: 4 residues within 4Å: Chain A: G.65, S.94, T.95, T.96 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.65, A:T.95, A:T.95, A:T.96, A:T.96, A:T.96 Water bridges: A:Q.66 SO4.9: 3 residues within 4Å: Chain B: T.37, H.38, K.130 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.37, B:H.38 Water bridges: B:N.126 Salt bridges: B:H.38, B:K.130 SO4.10: 5 residues within 4Å: Chain B: K.42, R.137, E.141, H.142, L.143 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.137, B:E.141, B:L.143 Water bridges: B:K.144 Salt bridges: B:K.42, B:H.142 SO4.11: 4 residues within 4Å: Chain B: G.65, S.94, T.95, T.96 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.65, B:S.94, B:T.95, B:T.96, B:T.96 Water bridges: B:Q.66

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

ACT.4: 7 residues within 4Å: Chain A: E.56, F.71, K.74, L.75, R.78 Chain B: R.78 Ligands: ACT.12 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:R.78, A:K.74 Hydrophobic interactions: A:K.74 ACT.5: 3 residues within 4Å: Chain A: Y.70, K.74 Ligands: ACT.7 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Y.70 Salt bridges: A:K.74, B:K.74, B:K.144 Water bridges: B:V.59, B:Q.148 ACT.6: 9 residues within 4Å: Chain A: Y.54, N.155, H.156, G.168 Chain B: A.76, G.77, R.78, W.79, P.80 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.156 ACT.7: 3 residues within 4Å: Chain B: Y.70, K.74 Ligands: ACT.5 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Water bridges: A:V.59, A:Q.148 Salt bridges: A:K.74, A:K.144, B:K.74 Hydrophobic interactions: B:Y.70 Hydrogen bonds: B:Y.70 ACT.12: 6 residues within 4Å: Chain B: E.56, F.71, K.74, L.75, R.78 Ligands: ACT.4 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.71, B:K.74, B:L.75 Hydrogen bonds: B:E.56 Salt bridges: B:K.74, A:R.78

2 x OM3: (R)-(4-CARBOXY-1,3-BENZODIOXOL-5-YL)METHYL-[[2-(CYCLOHEXYLMETHYLCARBAMOYL)PHENYL]METHYL]-METHYL-AZANIUM(Non-covalent)

OM3.8: 14 residues within 4Å: Chain A: D.138, Q.139, A.140, E.141, H.142, K.144, T.145, M.149 Chain B: Q.66, Y.70, T.96, A.99, A.100, W.103 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Q.139, A:E.141, A:H.142, A:H.142, A:T.145 Salt bridges: A:H.142 Hydrophobic interactions: B:T.96, B:A.99, B:A.100, B:W.103 OM3.13: 14 residues within 4Å: Chain A: Q.66, Y.70, T.96, A.99, A.100, W.103 Chain B: D.138, Q.139, A.140, E.141, H.142, K.144, T.145, M.149 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:T.96, A:A.99, A:A.100, A:W.103 Hydrogen bonds: B:Q.139, B:E.141, B:H.142, B:T.145, B:T.145 Salt bridges: B:H.142

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Peat, T.S. et al., Interrogating HIV Integrase for Compounds that Bind- a Sampl Challenge. J.Comput.Aided Mol.Des. (2014)

Release Date

2013-11-27

Peptides

INTEGRASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

INTEGRASE

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