SMTL ID : 4chn.1

Interrogating HIV integrase for compounds that bind- a SAMPL challenge

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

5 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, A:N.126 Salt bridges: A:H.38, A:K.130 SO4.2: 4 residues within 4Å: Chain A: A.140, E.141, H.142, T.145 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.141, A:E.141, A:H.142, A:T.145, A:T.145 Water bridges: A:H.142 Salt bridges: A:H.142 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, 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 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.137, B:L.143 Water bridges: B:K.144 Salt bridges: B:K.42 SO4.11: 4 residues within 4Å: Chain B: A.140, E.141, H.142, T.145 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.141, B:H.142, B:H.142 Salt bridges: B:H.142

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

ACT.3: 7 residues within 4Å: Chain A: E.56, A.57, E.58, F.71, K.74, L.75 Chain B: R.78 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:E.56, A:F.71, A:K.74 Hydrogen bonds: A:E.56, A:A.57, A:E.58 Salt bridges: A:K.74, B:R.78 ACT.12: 7 residues within 4Å: Chain A: R.78 Chain B: E.56, A.57, E.58, F.71, K.74, L.75 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain B Salt bridges: A:R.78, B:K.74 Hydrophobic interactions: B:F.71, B:K.74 Hydrogen bonds: B:E.56, B:E.56, B:A.57

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

EDO.4: 3 residues within 4Å: Chain A: D.178, I.179, Q.180 No protein-ligand interaction detected (PLIP) EDO.5: 4 residues within 4Å: Chain A: E.63, T.64, G.65 Ligands: GOL.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.65 Water bridges: A:E.63, A:Q.66 EDO.6: 3 residues within 4Å: Chain A: H.156, K.157, R.158 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.156, A:R.158

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: G.65, Q.66, S.94, T.95, T.96 Ligands: EDO.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.94, A:T.95, A:T.96 GOL.13: 5 residues within 4Å: Chain B: G.65, Q.66, S.94, T.95, T.96 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.65, B:Q.66, B:T.95, B:T.95 Water bridges: B:T.95

2 x ONZ: 2-(1,3-benzodioxol-4-ylcarbonylamino)ethanoic acid(Non-covalent)

ONZ.8: 13 residues within 4Å: Chain A: Y.54, N.155, H.156, R.158, S.166, G.168, E.169, V.172 Chain B: G.77, R.78, W.79, P.80, I.179 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:P.80, A:Y.54, A:V.172 Hydrogen bonds: A:S.166 Salt bridges: A:H.156, A:R.158 ONZ.14: 13 residues within 4Å: Chain A: G.77, R.78, W.79, P.80, I.179 Chain B: Y.54, N.155, H.156, R.158, S.166, G.168, E.169, V.172 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:P.80, B:Y.54, B:V.172 Hydrogen bonds: B:S.166 Salt bridges: B:H.156, B:R.158 pi-Stacking: B:H.156

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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