SMTL ID : 4cf9.1

Interrogating HIV integrase for compounds that bind- a SAMPL challenge

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

6 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: 7 residues within 4Å: Chain A: E.40, K.42, R.137, E.141, H.142, L.143 Ligands: 5EY.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.141, A:L.143 Water bridges: A:K.144 Salt bridges: A:K.42, A:R.137, A:H.142 SO4.3: 4 residues within 4Å: Chain A: G.65, S.94, T.95, T.96 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.65, A:T.95, A:T.96, A:T.96, A:T.96 Water bridges: A:Q.66 SO4.7: 4 residues within 4Å: Chain B: C.36, 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 SO4.8: 5 residues within 4Å: Chain B: K.42, R.137, E.141, H.142, L.143 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.40, B:R.137, B:L.143 Water bridges: B:K.144 Salt bridges: B:K.42, B:H.142 SO4.9: 4 residues within 4Å: Chain B: G.65, S.94, T.95, T.96 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.65, B:S.94, B:T.95, B:T.96, B:T.96 Water bridges: B:Q.66

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

EDO.4: 6 residues within 4Å: Chain A: R.78, W.79, P.80 Chain B: H.156, G.168, E.169 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.156, B:G.168

2 x 5EY: (3R)-3-(3-hydroxy-3-oxopropyl)-6-[(E)-[(2R)-2-oxidanyl-2,3-dihydroinden-1-ylidene]methyl]-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid(Non-covalent)

5EY.5: 15 residues within 4Å: Chain A: Q.139, A.140, E.141, H.142, K.144, T.145, M.149 Chain B: Q.66, Y.70, L.73, T.96, A.100, W.103 Ligands: SO4.2, EE2.6 15 PLIP interactions: 11 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:H.142, A:K.144, A:K.144, A:T.145, B:L.73, B:T.96, B:A.100, B:W.103 Hydrogen bonds: A:E.141, A:H.142, A:T.145 Water bridges: A:L.143 Salt bridges: A:H.142, A:H.142, A:K.144 5EY.11: 14 residues within 4Å: Chain A: Q.66, Y.70, L.73, T.96, A.100, W.103 Chain B: Q.139, A.140, E.141, H.142, K.144, T.145, M.149 Ligands: EE2.12 14 PLIP interactions: 10 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:H.142, B:K.144, B:T.145, A:L.73, A:T.96, A:A.100, A:W.103 Hydrogen bonds: B:E.141, B:H.142, B:T.145, B:T.145 Salt bridges: B:H.142, B:H.142, B:K.144

2 x EE2: (2R)-2-(3-hydroxy-3-oxopropyl)-6-[(E)-[(2S)-2-oxidanyl-2,3-dihydroinden-1-ylidene]methyl]-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid(Non-covalent)

EE2.6: 16 residues within 4Å: Chain A: Q.139, A.140, E.141, H.142, K.144, T.145, M.149 Chain B: Q.66, E.67, A.69, Y.70, L.73, T.96, A.100, W.103 Ligands: 5EY.5 12 PLIP interactions: 6 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:T.145, B:Q.66, B:Y.70, B:L.73, B:T.96, B:A.100, B:W.103 Hydrogen bonds: A:E.141, A:H.142, A:T.145 Salt bridges: A:H.142, A:K.144 EE2.12: 16 residues within 4Å: Chain A: Q.66, E.67, A.69, Y.70, L.73, T.96, A.100, W.103 Chain B: Q.139, A.140, E.141, H.142, K.144, T.145, M.149 Ligands: 5EY.11 13 PLIP interactions: 7 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:T.145, A:Q.66, A:L.73, A:T.96, A:A.100, A:W.103 Hydrogen bonds: B:E.141, B:H.142, B:T.145, B:T.145 Salt bridges: B:H.142, B:K.144 Water bridges: A:E.67

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

ACT.10: 7 residues within 4Å: Chain A: R.78 Chain B: E.56, A.57, E.58, F.71, K.74, L.75 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Salt bridges: A:R.78, B:K.74 Hydrophobic interactions: B:K.74 Hydrogen bonds: B:E.56, B:A.57, B:E.58

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

2013-11-27

Peptides

INTEGRASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

INTEGRASE

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