SMTL ID : 4cea.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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: 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 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 SO4.3: 8 residues within 4Å: Chain A: E.56, A.57, E.58, F.71, K.74, L.75 Chain B: R.78 Ligands: SO4.10 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.56, A:A.57, A:A.57, A:F.71 Salt bridges: A:K.74, B:R.78 SO4.8: 3 residues within 4Å: Chain B: T.37, H.38, K.130 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.37, B:T.37, B:H.38, 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:K.42, B:K.42, B:K.144 Salt bridges: B:K.42, B:H.142 SO4.10: 8 residues within 4Å: Chain A: R.78 Chain B: E.56, A.57, E.58, F.71, K.74, L.75 Ligands: SO4.3 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.56, B:A.57, B:E.58 Salt bridges: B:K.74, A:R.78

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

CL.4: 1 residues within 4Å: Chain A: H.156 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain B: H.156 Ligand excluded by PLIP

1 x ACY: ACETIC ACID(Non-functional Binders)

ACY.5: 2 residues within 4Å: Chain A: Y.70, K.74 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Water bridges: B:K.144, B:Q.148 Salt bridges: B:K.74, B:K.144, A:K.74

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: G.65, Q.66, S.94, T.95, T.96 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.65, A:Q.66, A:T.95, A:T.95, A:T.96 Water bridges: A:T.64, A:T.64, A:T.95 GOL.12: 6 residues within 4Å: Chain B: T.64, G.65, Q.66, S.94, T.96 Ligands: ZSW.7 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.64, B:T.64, B:G.65, B:Q.66, B:Q.66, B:T.96, B:T.96

2 x ZSW: (R)-[2-[[(2R)-butan-2-yl]carbamoyl]phenyl]methyl-[[(2S)-5-carboxy-2-(2-carboxyethyl)-2,3-dihydro-1,4-benzodioxin-6-yl]methyl]-prop-2-enyl-azanium(Non-covalent)

ZSW.7: 13 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, E.67, Y.70, T.96 Ligands: GOL.12 11 PLIP interactions: 4 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:Q.66, B:Y.70, B:Y.70, B:T.96 Hydrogen bonds: A:Q.139, A:E.141, A:H.142, A:T.145 Water bridges: A:K.144, A:K.144 Salt bridges: A:H.142 ZSW.13: 12 residues within 4Å: Chain A: Q.66, E.67, Y.70, T.96 Chain B: D.138, Q.139, A.140, E.141, H.142, K.144, T.145, M.149 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Q.139, B:E.141, B:H.142 Water bridges: B:E.141, B:K.144, A:T.64 Salt bridges: B:H.142 Hydrophobic interactions: A:Q.66, A:Y.70, A:Y.70

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

2013-11-20

Peptides

INTEGRASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

INTEGRASE

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