SMTL ID : 4cf8.1

Interrogating HIV integrase for compounds that bind- a SAMPL challenge

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 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 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 SO4.9: 3 residues within 4Å: Chain B: T.37, H.38, K.130 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.38 Water bridges: B:E.123, B:N.126, B:K.130 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 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

5 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 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Salt bridges: B:R.78, A:K.74 Hydrophobic interactions: A:E.56, A:F.71 Hydrogen bonds: A:A.57 ACY.4: 7 residues within 4Å: Chain A: N.155, H.156 Chain B: A.76, G.77, R.78, W.79, P.80 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.80 Hydrogen bonds: B:W.79 Salt bridges: A:H.156 ACY.11: 6 residues within 4Å: Chain A: R.78 Chain B: E.56, A.57, F.71, K.74, L.75 8 PLIP interactions: 1 interactions with chain A, 7 interactions with chain B Salt bridges: A:R.78, B:K.74 Hydrophobic interactions: B:E.56, B:F.71, B:K.74 Hydrogen bonds: B:E.56, B:E.56, B:A.57 ACY.12: 9 residues within 4Å: Chain A: A.76, G.77, R.78, W.79, P.80 Chain B: N.155, H.156, G.168 Ligands: ACY.13 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:N.155 Salt bridges: B:H.156 Hydrogen bonds: A:G.77 ACY.13: 8 residues within 4Å: Chain A: R.78, W.79, P.80 Chain B: Y.54, W.79, G.168, V.172 Ligands: ACY.12 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.78 Hydrophobic interactions: B:Y.54

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

EDO.5: 4 residues within 4Å: Chain A: T.64, G.65, Q.66 Ligands: GOL.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.65, A:Q.66 Water bridges: A:T.64

3 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.14: 3 residues within 4Å: Chain B: V.43, A.62, E.63 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain B: D.35, C.36, D.87 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: G.65, S.94, T.95, T.96 Ligands: EDO.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.65, A:T.95, A:T.95, A:T.96, A:T.96, A:T.96 GOL.16: 4 residues within 4Å: Chain B: G.65, S.94, T.95, T.96 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.65, B:T.95, B:T.96, B:T.96 Water bridges: B:Q.66

2 x V7H: (2S)-2-(3-hydroxy-3-oxopropyl)-6-[[[2-[(phenylmethyl)carbamoyl]phenyl]methylamino]methyl]-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid(Non-covalent)

V7H.8: 14 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, Y.70, T.96, A.99, A.100, W.103 16 PLIP interactions: 8 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:Q.66, B:Y.70, B:Y.70, B:A.99, B:A.100, B:W.103, A:T.145 Water bridges: B:T.64, B:Q.66, A:E.141 Hydrogen bonds: A:Q.139, A:E.141, A:H.142, A:H.142, A:T.145 Salt bridges: A:H.142 V7H.17: 15 residues within 4Å: Chain A: Q.66, E.67, Y.70, T.96, A.99, A.100, W.103 Chain B: D.138, Q.139, A.140, E.141, H.142, K.144, T.145, M.149 14 PLIP interactions: 7 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:T.145, A:Q.66, A:Y.70, A:Y.70, A:A.99, A:A.100, A:W.103 Hydrogen bonds: B:Q.139, B:E.141, B:H.142, B:T.145, B:T.145 Salt bridges: B:H.142 Water bridges: A:Q.66

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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