SMTL ID : 4cgf.1

Interrogating HIV integrase for compounds that bind- a SAMPL challenge

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: T.37, H.38, K.130 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.37, A:H.38 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 SO4.8: 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 SO4.9: 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

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

ACT.3: 6 residues within 4Å: Chain A: E.56, F.71, K.74, L.75, R.78 Chain B: R.78 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.71, A:K.74 Hydrogen bonds: A:A.57 Salt bridges: A:K.74, B:R.78 ACT.4: 5 residues within 4Å: Chain A: G.65, S.94, T.95, T.96 Ligands: EDO.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.95, A:T.95, A:T.96, A:T.96 ACT.5: 6 residues within 4Å: Chain A: N.155, H.156 Chain B: G.77, R.78, W.79, P.80 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.80 Hydrogen bonds: B:R.78 Salt bridges: A:H.156 ACT.10: 6 residues within 4Å: Chain A: R.78 Chain B: E.56, A.57, F.71, K.74, L.75 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.71, B:K.74 Hydrogen bonds: B:E.56 Salt bridges: B:K.74, A:R.78 ACT.11: 4 residues within 4Å: Chain B: S.94, T.95, T.96 Ligands: EDO.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.95, B:T.96 Water bridges: B:G.65 ACT.12: 7 residues within 4Å: Chain A: G.77, R.78, W.79, P.80 Chain B: N.155, H.156 Ligands: EDO.16 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.80 Hydrogen bonds: A:R.78 Salt bridges: B:H.156 ACT.13: 3 residues within 4Å: Chain B: Y.70, K.74 Ligands: ACT.14 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Water bridges: 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.14: 3 residues within 4Å: Chain A: Y.70, K.74 Ligands: ACT.13 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.70 Hydrogen bonds: A:Y.70, A:Y.70 Salt bridges: A:K.74, B:K.74, B:K.144

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

EDO.6: 4 residues within 4Å: Chain A: T.64, G.65, Q.66 Ligands: ACT.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.65, A:Q.66 EDO.15: 4 residues within 4Å: Chain B: T.64, G.65, Q.66 Ligands: ACT.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.65, B:Q.66 EDO.16: 8 residues within 4Å: Chain A: R.78, W.79, P.80 Chain B: W.79, G.168, E.169, V.172 Ligands: ACT.12 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:N.155, B:S.166 Hydrogen bonds: A:R.78

2 x UJ6: 5-{[(3S)-2-oxo-2,3-dihydro-1H-indol-3-yl]methyl}-1,3-benzodioxole-4-carboxylic acid(Non-covalent)

UJ6.7: 14 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.99, A.100, W.103 12 PLIP interactions: 7 interactions with chain A, 5 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 Water bridges: A:K.144 Salt bridges: A:H.142 UJ6.17: 14 residues within 4Å: Chain A: Q.66, Y.70, L.73, T.96, A.99, A.100, W.103 Chain B: Q.139, A.140, E.141, H.142, K.144, T.145, M.149 13 PLIP interactions: 7 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:T.145, A:Q.66, A:L.73, A:T.96, A:A.100, A:W.103 Hydrogen bonds: B:E.141, B:H.142, B:T.145, B:T.145, A:Q.66 Water bridges: B:K.144 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

2013-12-04

Peptides

INTEGRASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

INTEGRASE

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