SMTL ID : 4e91.1 (1 other biounit)

Crystal Structure of the N-Terminal Domain of HIV-1 Capsid in Complex With Inhibitor BD3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x 0OE: 4-{2-[5-(3-chlorophenyl)-1H-pyrazol-4-yl]-1-[3-(1H-imidazol-1-yl)propyl]-1H-benzimidazol-5-yl}benzoic acid(Non-covalent)

0OE.1: 12 residues within 4Å: Chain A: W.80, M.96, R.97, E.98, W.117, H.120, P.122, P.123, I.124, P.125, I.129, R.132 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.80, A:W.80, A:E.98, A:P.122, A:I.124, A:I.124, A:P.125, A:I.129 Water bridges: A:H.120 Salt bridges: A:R.132 pi-Stacking: A:H.120 Halogen bonds: A:W.117

1 x 0OF: (3S)-1-ethyl-3-[3-hydroxy-5-(pyridin-3-yl)phenyl]-5-phenyl-7-(trifluoromethyl)-1H-1,5-benzodiazepine-2,4(3H,5H)-dione(Non-covalent)

0OF.2: 19 residues within 4Å: Chain A: W.23, V.27, E.28, A.31, F.32, S.33, V.36, F.40, M.55, L.56, V.59, G.60, G.61, H.62, A.65, M.66, L.138, I.141, V.142 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:A.31, A:F.32, A:V.36, A:V.36, A:L.56, A:V.59, A:A.65, A:L.138, A:L.138, A:I.141, A:I.141, A:V.142 Hydrogen bonds: A:F.32, A:H.62 Water bridges: A:E.28, A:V.59, A:V.59

4 x IOD: IODIDE ION(Non-functional Binders)

IOD.3: 2 residues within 4Å: Chain A: P.17, R.18 Ligand excluded by PLIP IOD.4: 2 residues within 4Å: Chain A: S.44, M.55 Ligand excluded by PLIP IOD.5: 2 residues within 4Å: Chain A: P.34, E.35 Ligand excluded by PLIP IOD.6: 2 residues within 4Å: Chain A: Q.63, A.64 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lemke, C.T. et al., Distinct Effects of Two HIV-1 Capsid Assembly Inhibitor Families That Bind the Same Site within the N-Terminal Domain of the Viral CA Protein. J.Virol. (2012)

Release Date

2012-04-25

Peptides

Gag protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Gag protein

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