SMTL ID : 4ck3.1

Interrogating HIV integrase for compounds that bind- a SAMPL challenge

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: T.37, H.38, K.130 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.38 Water bridges: A:T.37, A:T.37, 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: 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:S.94, A:T.95, A:T.96, A:T.96 Water bridges: A:Q.66 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:T.37, B:H.38 Salt bridges: B:H.38, B:K.130 SO4.7: 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 SO4.8: 4 residues within 4Å: Chain B: G.65, S.94, T.95, T.96 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.65, B:T.95, B:T.95, B:T.95, B:T.96, B:T.96 Water bridges: B:Q.66 SO4.9: 9 residues within 4Å: Chain A: A.76, G.77, R.78, W.79, P.80 Chain B: Y.54, N.155, H.156, G.168 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.77 Water bridges: A:V.81, B:N.155, B:G.168 Salt bridges: B:H.156

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

ACT.4: 4 residues within 4Å: Chain A: H.38, V.43, A.62, E.63 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.43 Hydrogen bonds: A:E.63 Salt bridges: A:H.38 ACT.10: 3 residues within 4Å: Chain B: Y.70, K.74 Ligands: ACT.11 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.70 Hydrogen bonds: B:Y.70 Salt bridges: B:K.74, A:K.74 Water bridges: A:Q.148 ACT.11: 3 residues within 4Å: Chain A: Y.70, K.74 Ligands: ACT.10 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Water bridges: B:V.59, B:Q.148 Salt bridges: B:K.74, A:K.74 Hydrophobic interactions: A:Y.70 ACT.12: 4 residues within 4Å: Chain B: H.38, V.43, A.62, E.63 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.63 Salt bridges: B:H.38

2 x K1T: 5-[(2S)-2-{[(4-aminobutanoyl)amino]methyl}-4-methylpentyl]-1,3-benzodioxole-4-carboxylic acid(Non-covalent)

K1T.5: 13 residues within 4Å: Chain A: D.138, Q.139, A.140, E.141, H.142, T.145, M.149 Chain B: Q.66, Y.70, T.96, A.99, A.100, W.103 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:Q.66, B:Y.70, B:T.96, A:T.145 Hydrogen bonds: A:E.141, A:H.142, A:T.145, A:T.145 Salt bridges: A:H.142 K1T.13: 13 residues within 4Å: Chain A: Q.66, Y.70, T.96, A.99, A.100, W.103 Chain B: D.138, Q.139, A.140, E.141, H.142, T.145, M.149 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:T.145, A:Y.70, A:T.96 Hydrogen bonds: B:D.138, B:E.141, B:H.142, B:T.145, A:Q.66 Salt bridges: B:H.142

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

2014-01-22

Peptides

INTEGRASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

INTEGRASE

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