SMTL ID : 4cjr.1

Interrogating HIV integrase for compounds that bind- a SAMPL challenge

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: T.37, H.38, K.130 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.37, A:H.38 Water bridges: A:N.126, A:N.126 Salt bridges: A:H.38, A:K.130 SO4.2: 4 residues within 4Å: Chain A: K.42, R.137, H.142, L.143 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.137, A:E.141, 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 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.65, A:T.95, A:T.95, A:T.95, A:T.96, A:T.96 Water bridges: A:Q.66, A:Q.66 SO4.4: 8 residues within 4Å: Chain A: E.56, A.57, F.71, K.74, L.75, R.78 Chain B: R.78 Ligands: SO4.10 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:A.57, A:A.57, A:E.58, A:F.71 Salt bridges: A:K.74, B:R.78 SO4.7: 3 residues within 4Å: Chain B: T.37, H.38, K.130 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.38 Water bridges: B:N.126, B:N.126 Salt bridges: B:H.38, B:K.130 SO4.8: 5 residues within 4Å: Chain B: K.42, R.137, E.141, H.142, L.143 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.137, B:L.143 Water bridges: B:K.42, B:K.42, B:K.144 Salt bridges: B:K.42, B:H.142 SO4.9: 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:T.95, B:T.96, B:T.96 Water bridges: B:Q.66, B:Q.66 SO4.10: 8 residues within 4Å: Chain A: R.78 Chain B: E.56, A.57, F.71, K.74, L.75, R.78 Ligands: SO4.4 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.56, B:A.57, B:A.57, B:R.78 Salt bridges: B:K.74, A:R.78 SO4.11: 5 residues within 4Å: Chain A: K.74, Q.148 Chain B: Y.70, K.74 Ligands: ACT.12 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Y.70, A:Q.148 Salt bridges: B:K.74, A:K.74 Water bridges: A:V.59

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

CL.5: 3 residues within 4Å: Chain A: W.79, P.80 Chain B: H.156 Ligand excluded by PLIP

2 x FYM: 2-methoxy-6-[[[6-[(4-methoxyphenyl)methylcarbamoyl]-1,3-benzodioxol-5-yl]methyl-methyl-amino]methyl]benzoic acid(Non-covalent)

FYM.6: 12 residues within 4Å: Chain A: D.138, Q.139, A.140, E.141, H.142, K.144, T.145 Chain B: Q.66, A.69, T.96, A.99, A.100 10 PLIP interactions: 3 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:Q.66, B:T.96, B:A.99, A:E.141 Hydrogen bonds: A:Q.139, A:E.141, A:H.142, A:H.142 Water bridges: A:E.141 Salt bridges: A:H.142 FYM.13: 13 residues within 4Å: Chain A: Q.66, A.69, L.73, T.96, A.99, A.100 Chain B: D.138, Q.139, A.140, E.141, H.142, K.144, T.145 10 PLIP interactions: 3 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:Q.66, A:T.96, A:A.99, B:E.141 Hydrogen bonds: B:Q.139, B:E.141, B:H.142, B:T.145, B:T.145 Salt bridges: B:H.142

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

ACT.12: 3 residues within 4Å: Chain A: Y.70, K.74 Ligands: SO4.11 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Water bridges: B:Q.148 Salt bridges: B:K.74, B:K.144, A:K.74 Hydrogen bonds: A:Y.70

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

2014-01-08

Peptides

INTEGRASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

INTEGRASE

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