SMTL ID : 3ao5.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

GLC-FRU.1: 12 residues within 4Å: Chain A: E.38, V.39, Y.50, K.54, K.124, Q.128 Chain B: E.38, V.39, I.40, Y.50, K.54, K.124 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:E.38, B:E.38, B:V.39, B:K.54, B:K.124, A:Y.50, A:Y.50, A:K.54, B:K.54, B:K.54, A:E.38, A:V.39, A:Q.128 Water bridges: B:Y.50

2 x BBY: 5-(7-bromo-1,3-benzodioxol-5-yl)-1-methyl-1H-pyrazol-3-amine(Non-covalent)

BBY.2: 13 residues within 4Å: Chain A: Y.34, N.135, H.136, R.138, S.146, G.148, E.149, V.152 Chain B: G.57, R.58, W.59, P.60, I.155 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.60, B:P.60, A:E.149 Halogen bonds: B:G.57 Hydrogen bonds: A:R.138 BBY.10: 13 residues within 4Å: Chain A: G.57, R.58, W.59, P.60 Chain B: Y.34, W.59, N.135, H.136, R.138, S.146, G.148, E.149, V.152 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.60, A:P.60, B:E.149 Halogen bonds: A:G.57 Hydrogen bonds: B:R.138

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 7 residues within 4Å: Chain A: C.16, L.25, E.43, D.67, N.71, F.72 Ligands: CD.9 Ligand excluded by PLIP CL.11: 7 residues within 4Å: Chain B: C.16, L.25, E.43, D.67, N.71, F.72 Ligands: CD.15 Ligand excluded by PLIP

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

SO4.4: 5 residues within 4Å: Chain A: K.22, R.117, E.121, H.122, L.123 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.117, A:E.121, A:L.123 Water bridges: A:K.124 Salt bridges: A:K.22, A:H.122 SO4.5: 4 residues within 4Å: Chain A: C.16, T.17, H.18, K.110 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.17, A:H.18 Salt bridges: A:H.18, A:K.110 SO4.6: 3 residues within 4Å: Chain A: G.74, A.75, T.76 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.75, A:T.76, A:T.76 SO4.7: 5 residues within 4Å: Chain A: A.120, E.121, H.122, T.125 Chain B: Q.46 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.121, A:H.122, A:T.125, B:Q.46, B:Q.46 Salt bridges: A:H.122 SO4.12: 5 residues within 4Å: Chain B: K.22, R.117, E.121, H.122, L.123 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.117, B:E.121, B:L.123 Salt bridges: B:K.22, B:H.122 SO4.13: 4 residues within 4Å: Chain B: C.16, T.17, H.18, K.110 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.18, B:H.18 Salt bridges: B:K.110

4 x CD: CADMIUM ION(Non-covalent)

CD.8: 4 residues within 4Å: Chain A: C.16, H.18, E.43 Ligands: CD.9 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.16, A:H.18, A:E.43 CD.9: 5 residues within 4Å: Chain A: C.16, E.43, D.67 Ligands: CL.3, CD.8 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.14: 4 residues within 4Å: Chain B: C.16, H.18, E.43 Ligands: CD.15 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.16, B:H.18, B:E.43, B:E.43 CD.15: 5 residues within 4Å: Chain B: C.16, E.43, D.67 Ligands: CL.11, CD.14 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.2

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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