SMTL ID : 4ck1.1

Interrogating HIV integrase for compounds that bind- a SAMPL challenge

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: T.37, H.38, K.130 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: 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 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: 7 residues within 4Å: Chain A: E.56, A.57, E.58, F.71, K.74, L.75 Chain B: R.78 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Salt bridges: B:R.78, A:K.74 Hydrogen bonds: A:E.56, A:E.56, A:A.57 SO4.4: 5 residues within 4Å: Chain A: G.65, S.94, T.95, T.96 Ligands: EDO.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.95, A:T.96, A:T.96, A:T.96 SO4.8: 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 SO4.9: 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:E.40, B:K.42, B:K.144 Salt bridges: B:K.42, B:H.142 SO4.10: 6 residues within 4Å: Chain B: G.65, S.94, T.95, T.96 Ligands: EDO.13, EDO.14 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.95, B:T.96, B:T.96 Water bridges: B:T.95, B:T.95 SO4.11: 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 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.77 Water bridges: A:V.81, B:N.155, B:G.168 Salt bridges: B:H.156

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

EDO.5: 4 residues within 4Å: Chain A: T.64, G.65, Q.66 Ligands: SO4.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.65, A:Q.66 EDO.13: 5 residues within 4Å: Chain B: T.64, G.65, Q.66 Ligands: SO4.10, EDO.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.65, B:Q.66 EDO.14: 8 residues within 4Å: Chain B: E.63, T.64, G.65, S.90, N.91, S.94 Ligands: SO4.10, EDO.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.65, B:N.91

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

CL.6: 3 residues within 4Å: Chain A: V.43, A.62, E.63 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain B: V.43, A.62, E.63 Ligand excluded by PLIP

2 x OM1: (4-CARBOXY-1,3-BENZODIOXOL-5-YL)METHYL-[[2-[(4-METHOXYPHENYL)METHYLCARBAMOYL]PHENYL]METHYL]AZANIUM(Non-covalent)

OM1.7: 15 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, A.69, Y.70, L.73, T.96, A.99, A.100 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:Q.66, B:A.99 Hydrogen bonds: B:Q.66, A:Q.139, A:E.141, A:H.142, A:T.145, A:T.145 Salt bridges: A:H.142 OM1.16: 15 residues within 4Å: Chain A: Q.66, A.69, Y.70, L.73, T.96, A.99, A.100 Chain B: D.138, Q.139, A.140, E.141, H.142, K.144, T.145, M.149 10 PLIP interactions: 3 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:Q.66, A:A.99 Hydrogen bonds: A:Q.66, B:Q.139, B:E.141, B:H.142, B:H.142, B:T.145 Water bridges: B:E.141 Salt bridges: B:H.142

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

ACT.12: 6 residues within 4Å: Chain A: R.78 Chain B: E.56, A.57, F.71, K.74, L.75 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

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

2014-01-22

Peptides

INTEGRASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

INTEGRASE

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