SMTL ID : 4chq.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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.137, A:L.143 Water bridges: A:K.144 Salt bridges: A:K.42, A:H.142 SO4.3: 5 residues within 4Å: Chain A: G.65, S.94, T.95, T.96 Ligands: EDO.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.95, A:T.95, A:T.95, A:T.96, A:T.96 SO4.9: 3 residues within 4Å: Chain B: T.37, H.38, K.130 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: 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 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.137, B:L.143 Water bridges: B:K.144 Salt bridges: B:K.42, B:H.142 SO4.11: 5 residues within 4Å: Chain B: G.65, S.94, T.95, T.96 Ligands: EDO.13 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.65, B:S.94, B:T.95, B:T.96, B:T.96

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

CL.4: 1 residues within 4Å: Chain A: H.156 Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain B: H.156 Ligand excluded by PLIP

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

EDO.5: 4 residues within 4Å: Chain A: T.64, G.65, Q.66 Ligands: SO4.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.65, A:Q.66, A:Q.66 EDO.6: 4 residues within 4Å: Chain A: E.67, Y.70 Chain B: K.144 Ligands: CWU.15 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:E.67, A:E.67 Hydrogen bonds: B:K.144 EDO.13: 4 residues within 4Å: Chain B: T.64, G.65, Q.66 Ligands: SO4.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.65, B:Q.66

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

ACT.7: 6 residues within 4Å: Chain A: E.56, F.71, K.74, L.75, R.78 Chain B: R.78 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:K.74 Hydrogen bonds: A:F.71 Salt bridges: A:K.74, B:R.78 ACT.14: 6 residues within 4Å: Chain A: R.78 Chain B: E.56, F.71, K.74, L.75, R.78 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.71, B:K.74 Hydrogen bonds: B:E.56, B:A.57 Salt bridges: B:K.74, A:R.78

2 x CWU: 5-[[(1S,2R)-2-oxidanyl-2,3-dihydro-1H-inden-1-yl]methyl]-1,3-benzodioxole-4-carboxylic acid(Non-covalent)

CWU.8: 13 residues within 4Å: Chain A: Q.139, A.140, E.141, H.142, K.144, T.145, M.149 Chain B: Q.66, Y.70, L.73, T.96, A.100, W.103 12 PLIP interactions: 6 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:T.145, B:Q.66, B:L.73, B:T.96, B:A.100, B:W.103 Hydrogen bonds: A:E.141, A:H.142, A:H.142, A:T.145, B:Q.66 Salt bridges: A:H.142 CWU.15: 14 residues within 4Å: Chain A: Q.66, Y.70, L.73, T.96, A.100, W.103 Chain B: Q.139, A.140, E.141, H.142, K.144, T.145, M.149 Ligands: EDO.6 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:Q.66, A:L.73, A:T.96, A:A.100, A:W.103, B:T.145 Hydrogen bonds: 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

2013-12-11

Peptides

INTEGRASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

INTEGRASE

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