SMTL ID : 4chz.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

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

SO4.1: 4 residues within 4Å: Chain A: T.37, H.38, N.126, K.130 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.37, A:H.38, 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.137, A:E.141, A:L.143 Water bridges: 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.65, A:T.95, A:T.95, A:T.96, A:T.96 Water bridges: A:Q.66 SO4.13: 4 residues within 4Å: Chain B: T.37, H.38, N.126, K.130 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.38, B:N.126 Salt bridges: B:H.38, B:K.130 SO4.14: 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 SO4.15: 4 residues within 4Å: Chain B: G.65, S.94, T.95, T.96 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.65, B:T.95, B:T.95, B:T.96 Water bridges: B:Q.66, B:T.96, B:T.96

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

ACT.4: 6 residues within 4Å: Chain A: E.56, A.57, F.71, K.74, L.75 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.11: 3 residues within 4Å: Chain A: Y.70, K.74 Ligands: ACT.17 7 PLIP interactions: 4 interactions with chain A, 3 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 Water bridges: B:V.59, B:Q.148 ACT.16: 6 residues within 4Å: Chain A: R.78 Chain B: E.56, A.57, F.71, K.74, L.75 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.71, B:K.74 Hydrogen bonds: B:E.56, B:E.56, B:A.57 Salt bridges: B:K.74, A:R.78 ACT.17: 3 residues within 4Å: Chain B: Y.70, K.74 Ligands: ACT.11 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.148 Salt bridges: A:K.74, B:K.74 Water bridges: B:Y.70

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

CL.5: 3 residues within 4Å: Chain A: V.43, A.62, E.63 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: E.67, Y.70 Chain B: K.144 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain B: V.43, E.63 Ligand excluded by PLIP

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

EDO.7: 6 residues within 4Å: Chain A: N.155, H.156, R.158, S.166, E.169 Ligands: EDO.19 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.158, A:S.166 EDO.8: 9 residues within 4Å: Chain A: A.76, G.77, R.78, W.79, P.80 Chain B: Y.54, N.155, H.156, G.168 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.155, A:G.77 EDO.9: 5 residues within 4Å: Chain A: Q.139, A.140, E.141, H.142, T.145 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.139, A:E.141, A:H.142, A:H.142, A:T.145 EDO.19: 10 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 Ligands: EDO.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.77 EDO.20: 4 residues within 4Å: Chain B: Q.139, E.141, H.142, T.145 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.141, B:H.142, B:H.142

1 x H75: 2-(4-bromophenyl)-5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-3(2H)-one(Non-covalent)

H75.10: 9 residues within 4Å: Chain A: V.48, V.50, G.53, I.55, V.121, M.125, E.128, L.129, H.154 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.55, A:V.121, A:M.125 Water bridges: A:R.170 pi-Cation interactions: A:H.154

1 x LYS: LYSINE(Covalent)

LYS.12: 4 residues within 4Å: Chain B: D.178, I.179, Q.180, T.181 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.178, B:T.181

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

2013-12-18

Peptides

INTEGRASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

INTEGRASE

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