SMTL ID : 3ao1.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

4 x CD: CADMIUM ION(Non-covalent)

CD.1: 4 residues within 4Å: Chain A: C.16, H.18, E.43 Ligands: CD.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.16, A:H.18, A:E.43 CD.2: 4 residues within 4Å: Chain A: C.16, E.43, D.67 Ligands: CD.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:C.16, A:E.43, A:D.67, H2O.1, H2O.1 CD.6: 4 residues within 4Å: Chain B: C.16, E.43, D.67 Ligands: CD.7 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:C.16, B:E.43, B:D.67, H2O.2, H2O.3 CD.7: 4 residues within 4Å: Chain B: C.16, H.18, E.43 Ligands: CD.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.16, B:H.18, B:E.43, H2O.3

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

SO4.3: 6 residues within 4Å: Chain A: E.20, K.22, R.117, E.121, H.122, L.123 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.20, A:R.117, A:L.123 Water bridges: A:K.22, A:K.124 Salt bridges: A:K.22, A:H.122

3 x BZX: 1,3-benzodioxol-5-ol(Non-covalent)

BZX.4: 10 residues within 4Å: Chain A: Y.34, N.135, H.136, G.148, V.152 Chain B: G.57, R.58, W.59, P.60, I.155 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.60 BZX.5: 2 residues within 4Å: Chain A: H.136 Chain B: P.60 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.60 Water bridges: B:V.61, B:A.84 BZX.8: 10 residues within 4Å: Chain A: G.57, R.58, W.59, P.60 Chain B: Y.34, N.135, H.136, G.148, E.149, V.152 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.152, A:P.60 Water bridges: B:S.146, B:S.146, B:E.149, B:E.149

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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