SMTL ID : 3vqp.1

HIV-1 IN core domain in complex with 2,3-dihydro-1,4-benzodioxin-5-ylmethanol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

4 x CD: CADMIUM ION(Non-covalent)

CD.1: 4 residues within 4Å: Chain A: C.11, H.13, E.38 Ligands: CD.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.11, A:H.13, A:E.38, H2O.1 CD.2: 5 residues within 4Å: Chain A: C.11, E.38, D.62 Ligands: CD.1, CL.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.11, A:E.38, A:D.62, H2O.1 CD.7: 4 residues within 4Å: Chain B: C.11, E.38, D.62 Ligands: CD.8 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:C.11, B:E.38, B:D.62, H2O.1, H2O.2 CD.8: 4 residues within 4Å: Chain B: C.11, H.13, E.38 Ligands: CD.7 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:C.11, B:H.13, B:E.38, H2O.2, H2O.2

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

CL.3: 7 residues within 4Å: Chain A: D.10, C.11, L.20, E.38, D.62, F.67 Ligands: CD.2 Ligand excluded by PLIP

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

SO4.4: 3 residues within 4Å: Chain A: C.11, T.12, H.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.11, A:H.13 SO4.5: 5 residues within 4Å: Chain A: E.15, R.112, E.116, H.117, L.118 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.15, A:L.118 Salt bridges: A:R.112, A:H.117

1 x DBJ: 2,3-dihydro-1,4-benzodioxin-5-ylmethanol(Non-covalent)

DBJ.6: 12 residues within 4Å: Chain A: Y.29, W.54, N.130, H.131, G.143, E.144, V.147 Chain B: G.52, R.53, W.54, P.55, I.150 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.55, B:I.150, A:V.147 Water bridges: A:S.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wielens, J. et al., Parallel screening of low molecular weight fragment libraries: do differences in methodology affect hit identification?. J Biomol Screen (2013)

Release Date

2013-01-30

Peptides

POL polyprotein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

POL polyprotein

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