SMTL ID : 4ceb.1

Interrogating HIV integrase for compounds that bind- a SAMPL challenge

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 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: 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 SO4.6: 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, B:N.126 Salt bridges: B:H.38, B:K.130 SO4.7: 6 residues within 4Å: Chain B: E.40, K.42, R.137, E.141, H.142, L.143 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.137, B:E.141, B:L.143 Water bridges: B:K.42, B:K.42, B:K.144 Salt bridges: B:K.42, B:H.142

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

ACY.3: 6 residues within 4Å: Chain A: E.56, A.57, F.71, K.74, L.75 Chain B: R.78 7 PLIP interactions: 6 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 Salt bridges: A:K.74, B:R.78 ACY.8: 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:E.56, B:F.71, B:K.74 Hydrogen bonds: B:E.56, B:A.57 Salt bridges: B:K.74, A:R.78

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

EDO.4: 5 residues within 4Å: Chain A: H.156, G.168 Chain B: R.78, W.79, P.80 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.156 EDO.9: 5 residues within 4Å: Chain A: R.78, W.79, P.80 Chain B: H.156, G.168 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.156

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: G.65, Q.66, S.94, T.95, T.96 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.66, A:T.95 Water bridges: A:G.65, A:G.65 GOL.10: 5 residues within 4Å: Chain B: G.65, Q.66, S.94, T.95, T.96 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.66, B:T.95, B:T.96 Water bridges: B:G.65, B:G.65, B:G.65

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

ZSV.11: 15 residues within 4Å: Chain A: D.138, Q.139, A.140, E.141, H.142, T.145, M.149 Chain B: Q.66, E.67, A.69, Y.70, L.73, T.96, A.99, A.100 12 PLIP interactions: 6 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:Q.66, B:Y.70, B:Y.70, B:A.99 Hydrogen bonds: B:Q.66, A:Q.139, A:E.141, A:H.142, A:T.145 Water bridges: B:T.64, A:E.141 Salt bridges: A:H.142 ZSV.12: 15 residues within 4Å: Chain A: Q.66, E.67, A.69, Y.70, L.73, T.96, A.99, A.100 Chain B: D.138, Q.139, A.140, E.141, H.142, T.145, M.149 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:Q.139, B:E.141, B:H.142, B:T.145, B:T.145 Salt bridges: B:H.142 Hydrophobic interactions: A:Q.66, A:Y.70, A:Y.70, A:T.96, A:A.99

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

Related Entries With Identical Sequence