SMTL ID : 4inb.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x 1F6: (3Z)-3-{[(2-methoxyethyl)amino]methylidene}-1-methyl-5-phenyl-7-(trifluoromethyl)-1H-1,5-benzodiazepine-2,4(3H,5H)-dione(Non-covalent)

1F6.1: 18 residues within 4Å: Chain A: W.23, V.27, E.28, A.31, F.32, S.33, V.36, F.40, L.56, V.59, G.60, G.61, H.62, A.65, M.66, L.138, I.141, V.142 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.27, A:F.32, A:V.36, A:V.59, A:L.138, A:I.141, A:V.142 Hydrogen bonds: A:V.27, A:F.32, A:H.62 1F6.3: 18 residues within 4Å: Chain B: W.23, V.27, E.28, A.31, F.32, S.33, V.36, F.40, L.56, V.59, G.60, G.61, H.62, A.65, M.66, L.138, I.141, V.142 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:V.27, B:F.32, B:V.36, B:V.59, B:L.138, B:I.141, B:V.142 Hydrogen bonds: B:V.27, B:F.32, B:H.62, B:H.62

2 x NA: SODIUM ION(Non-functional Binders)

NA.2: 2 residues within 4Å: Chain A: G.106, S.109 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.109 Water bridges: A:Q.50 NA.4: 2 residues within 4Å: Chain B: G.106, S.109 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.106 Water bridges: B:Q.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goudreau, N. et al., Monitoring Binding of HIV-1 Capsid Assembly Inhibitors Using (19) F Ligand-and (15) N Protein-Based NMR and X-ray Crystallography: Early Hit Validation of a Benzodiazepine Series. Chemmedchem (2013)

Release Date

2013-02-27

Peptides

Gag protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Gag protein

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