SMTL ID : 4ovl.1

Interrogating HIV integrase for compounds that bind- a SAMPL challenge

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 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: 5 residues within 4Å: Chain A: K.42, R.137, E.141, H.142, L.143 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.137, A:L.143 Water bridges: A:K.42, A:K.42, A:K.144 Salt bridges: A:K.42, A:H.142 SO4.10: 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 SO4.11: 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:R.137, B:L.143 Water bridges: B:K.144, B:K.144 Salt bridges: B:K.42, B:H.142 SO4.12: 8 residues within 4Å: Chain A: R.78 Chain B: E.56, A.57, E.58, F.71, K.74, L.75, R.78 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.56, B:A.57, B:E.58, B:E.58 Salt bridges: B:K.74, A:R.78 SO4.13: 5 residues within 4Å: Chain B: G.65, S.94, T.95, T.96 Ligands: EDO.14 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.65, B:T.95, B:T.95, B:T.96 Water bridges: B:Q.66

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

ACY.3: 3 residues within 4Å: Chain A: Y.70, K.74 Ligands: ACY.15 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.70 Salt bridges: A:K.74, B:K.74 Water bridges: B:V.59, B:Q.148 ACY.4: 8 residues within 4Å: Chain A: N.155, H.156 Chain B: A.76, G.77, R.78, W.79, P.80 Ligands: ACY.6 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:N.155 Salt bridges: A:H.156 Water bridges: B:V.81 ACY.5: 5 residues within 4Å: Chain A: E.56, F.71, K.74, L.75, R.78 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:K.74 Hydrogen bonds: A:E.56 Salt bridges: A:K.74, B:R.78 ACY.6: 7 residues within 4Å: Chain A: W.79, G.168, V.172 Chain B: R.78, W.79, P.80 Ligands: ACY.4 No protein-ligand interaction detected (PLIP) ACY.7: 8 residues within 4Å: Chain A: G.77, R.78, W.79, P.80 Chain B: N.155, H.156, G.168 Ligands: ACY.16 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:H.156, A:V.81 Salt bridges: B:H.156 ACY.15: 3 residues within 4Å: Chain B: Y.70, K.74 Ligands: ACY.3 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Water bridges: A:V.59, A:Q.148 Salt bridges: A:K.74, B:K.74 Hydrophobic interactions: B:Y.70 Hydrogen bonds: B:Y.70, B:Y.70 ACY.16: 8 residues within 4Å: Chain A: R.78, W.79, P.80 Chain B: Y.54, W.79, G.168, V.172 Ligands: ACY.7 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.78 Hydrophobic interactions: B:Y.54

2 x 1TD: 3-[(E)-(2-oxidanylidene-1H-indol-3-ylidene)methyl]benzoic acid(Non-covalent)

1TD.8: 10 residues within 4Å: Chain A: A.140, E.141, H.142, T.145, M.149 Chain B: Q.66, L.73, A.99, A.100, W.103 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:E.141, A:H.142, A:T.145 Salt bridges: A:H.142 Hydrophobic interactions: B:Q.66, B:L.73, B:A.100, B:W.103 Water bridges: B:A.99 1TD.17: 10 residues within 4Å: Chain A: Q.66, L.73, A.99, A.100, W.103 Chain B: A.140, E.141, H.142, T.145, M.149 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.73, A:A.100, A:W.103 Water bridges: A:A.99 Hydrogen bonds: B:E.141, B:H.142, B:T.145 Salt bridges: B:H.142

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 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:Q.66, A:S.94, A:T.95, A:T.96 Water bridges: A:G.65, A:G.65

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

EDO.14: 5 residues within 4Å: Chain B: G.65, S.90, T.93, S.94 Ligands: SO4.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.65

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

2014-03-05

Peptides

Integrase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Integrase

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