SMTL ID : 4cgd.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

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: T.37, H.38, K.130 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: 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 SO4.8: 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 Water bridges: 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 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

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 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.71, A:K.74 Hydrogen bonds: A:E.56, A:A.57 Salt bridges: A:K.74, B:R.78 ACY.10: 7 residues within 4Å: Chain A: R.78 Chain B: E.56, A.57, F.71, K.74, L.75, R.78 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.71, B:K.74 Hydrogen bonds: B:R.78 Salt bridges: B:K.74, A:R.78

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

EDO.4: 8 residues within 4Å: Chain A: G.77, R.78, W.79, P.80 Chain B: Y.54, N.155, H.156, G.168 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.77

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

CL.5: 3 residues within 4Å: Chain A: H.38, V.43, E.63 Ligand excluded by PLIP

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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.66, A:T.95, A:T.95, A:T.96 GOL.11: 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:Q.66, B:T.95, B:T.95 Water bridges: B:G.65, B:G.65

2 x 8P3: 2-[(2-oxo-2,3-dihydro-1H-indol-1-yl)methyl]benzoic acid(Non-covalent)

8P3.7: 9 residues within 4Å: Chain A: A.140, E.141, H.142, T.145 Chain B: Q.66, T.96, A.99, A.100, W.103 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.141, A:H.142, A:T.145, A:T.145 Salt bridges: A:H.142 Hydrophobic interactions: B:T.96, B:W.103 8P3.12: 10 residues within 4Å: Chain A: Q.66, T.96, A.99, A.100, W.103 Chain B: A.140, E.141, H.142, T.145, M.149 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.141, B:H.142, B:T.145 Salt bridges: B:H.142 Hydrophobic interactions: A:T.96, A:W.103

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

2013-12-04

Peptides

INTEGRASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

INTEGRASE

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