SMTL ID : 3ovn.1

Fragment-based approach to the design of ligands targeting a novel site on HIV-1 integrase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

1 x GLC- FRU: beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose(Non-covalent)

GLC-FRU.1: 13 residues within 4Å: Chain A: E.38, V.39, P.41, E.47, Y.50, K.54, K.124 Chain B: E.38, V.39, E.47, Y.50, K.54, K.124 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:V.39, B:K.124, A:E.38, A:E.47, A:E.47, A:Y.50, A:K.54, B:E.38, B:E.47, B:K.54, A:V.39, A:K.124, A:K.124 Water bridges: B:V.39, A:F.51, B:E.47, A:V.39

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

SO4.2: 6 residues within 4Å: Chain A: E.20, K.22, R.117, E.121, H.122, L.123 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.117, A:L.123 Water bridges: A:K.124 Salt bridges: A:K.22, A:H.122 SO4.6: 2 residues within 4Å: Chain B: H.122, L.123 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.123 Water bridges: B:K.22, B:K.124 Salt bridges: B:K.22, B:H.122

2 x MPV: 1-methyl-3-(thiophen-2-yl)-1H-pyrazol-5-amine(Non-covalent)

MPV.3: 7 residues within 4Å: Chain A: G.148, E.149, V.152 Chain B: R.58, P.60, I.155, I.159 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.60, B:I.155, B:I.159, A:V.152 MPV.7: 10 residues within 4Å: Chain A: R.58, W.59, P.60, I.155, T.157 Chain B: Y.34, H.136, G.148, E.149, V.152 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.60, A:I.155, B:Y.34, B:V.152 Hydrogen bonds: A:I.155 Water bridges: A:T.157

4 x CD: CADMIUM ION(Non-covalent)

CD.4: 4 residues within 4Å: Chain A: C.16, H.18, E.43 Ligands: CD.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.16, A:H.18, A:E.43, H2O.1 CD.5: 4 residues within 4Å: Chain A: C.16, E.43, D.67 Ligands: CD.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.16, A:E.43, A:D.67, H2O.1 CD.8: 4 residues within 4Å: Chain B: C.16, E.43, D.67 Ligands: CD.9 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:C.16, B:D.67, H2O.2, H2O.3, H2O.3 CD.9: 4 residues within 4Å: Chain B: C.16, H.18, E.43 Ligands: CD.8 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:C.16, B:H.18, B:E.43, H2O.2, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wielens, J. et al., Fragment-based design of ligands targeting a novel site on the integrase enzyme of human immunodeficiency virus 1. Chemmedchem (2011)

Release Date

2011-03-09

Peptides

POL polyprotein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

POL polyprotein

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