SMTL ID : 4cjf.1

Interrogating HIV integrase for compounds that bind- a SAMPL challenge

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 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 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: 4 residues within 4Å: Chain A: K.42, R.137, 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 SO4.9: 3 residues within 4Å: Chain B: T.37, H.38, K.130 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.38 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

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

CL.3: 2 residues within 4Å: Chain A: H.156 Chain B: G.77 Ligand excluded by PLIP

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 4 residues within 4Å: Chain A: G.65, S.94, T.95, T.96 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.65 Water bridges: A:Q.66, A:T.95 DMS.11: 5 residues within 4Å: Chain B: G.65, S.94, T.95, T.96 Ligands: EDO.13 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.95

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

ACT.5: 7 residues within 4Å: Chain A: E.56, F.71, K.74, L.75, R.78 Chain B: R.78 Ligands: ACT.14 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.71, A:K.74, A:L.75 Salt bridges: A:K.74, A:R.78, B:R.78 ACT.6: 3 residues within 4Å: Chain A: Y.70, K.74 Ligands: ACT.7 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Salt bridges: B:K.74, B:K.144, A:K.74 Hydrogen bonds: A:Y.70 Water bridges: A:Y.70 ACT.7: 3 residues within 4Å: Chain B: Y.70, K.74 Ligands: ACT.6 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:K.74, A:K.74 ACT.12: 9 residues within 4Å: Chain A: G.77, R.78, W.79, P.80 Chain B: Y.54, N.155, H.156, G.168 Ligands: EDO.15 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Water bridges: B:N.155, B:S.166 Salt bridges: B:H.156 Hydrophobic interactions: A:P.80 ACT.14: 7 residues within 4Å: Chain A: R.78 Chain B: E.56, F.71, K.74, L.75, R.78 Ligands: ACT.5 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Salt bridges: A:R.78, B:K.74, B:R.78 Hydrophobic interactions: B:F.71 Hydrogen bonds: B:E.56

2 x RVN: 5-[(E)-(2-oxidanylidene-1H-indol-3-ylidene)methyl]-1,3-benzodioxole-4-carboxylic acid(Non-covalent)

RVN.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 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:L.73, B:T.96, B:A.100, B:W.103, A:T.145 Hydrogen bonds: B:Q.66, A:E.141, A:H.142, A:H.142, A:T.145 Salt bridges: A:H.142 RVN.16: 13 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 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:E.141, B:H.142, B:T.145, A:Q.66 Salt bridges: B:H.142 Hydrophobic interactions: A:Q.66, A:L.73, A:T.96, A:A.100, A:W.103

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

EDO.13: 4 residues within 4Å: Chain B: T.64, G.65, Q.66 Ligands: DMS.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.65, B:Q.66 EDO.15: 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: 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

2014-01-08

Peptides

INTEGRASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

INTEGRASE

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