SMTL ID : 4e92.3 (2 other biounits)

Crystal Structure of the N-Terminal Domain of HIV-1 Capsid in Complex With Inhibitor BM4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 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: 17 residues within 4Å: Chain A: W.80, H.84, M.96, E.98, W.117, H.120, P.122, I.124, P.125, I.129, R.132 Chain B: P.34, E.35, I.37, P.38, I.135, N.139 15 PLIP interactions: 6 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:P.34, B:I.37, B:I.37, B:P.38, A:W.80, A:W.80, A:P.122, A:I.124, A:I.124, A:I.129 Hydrogen bonds: B:N.139, B:N.139 Salt bridges: A:R.132 pi-Stacking: A:H.120 Halogen bonds: A:W.117 0OE.3: 17 residues within 4Å: Chain A: P.34, E.35, I.37, P.38, I.135, N.139 Chain B: W.80, H.84, E.98, W.117, H.120, P.122, P.123, I.124, P.125, I.129, R.132 17 PLIP interactions: 10 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:W.80, B:W.80, B:P.122, B:I.124, B:I.124, B:P.125, B:I.129, A:P.34, A:P.34, A:I.37, A:I.37, A:P.38 Salt bridges: B:R.132 pi-Stacking: B:H.120 Halogen bonds: B:W.117 Hydrogen bonds: A:N.139, A:N.139

2 x 0OG: 3-{5-[3-ethyl-5-(5-methylfuran-2-yl)-1H-pyrazol-1-yl]-1-[(6-oxo-1,6-dihydropyridin-3-yl)methyl]-1H-benzimidazol-2-yl}-4-hydroxybenzoic acid(Non-covalent)

0OG.2: 14 residues within 4Å: Chain A: V.27, A.31, F.32, S.33, V.36, V.59, H.62, A.65, M.66, L.69, L.138, I.141, V.142, Y.145 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:A.31, A:F.32, A:V.36, A:V.36, A:H.62, A:A.65, A:L.69, A:I.141, A:V.142 Hydrogen bonds: A:F.32 Water bridges: A:A.64 pi-Stacking: A:F.32 pi-Cation interactions: A:H.62 0OG.4: 14 residues within 4Å: Chain B: V.27, A.31, F.32, S.33, V.36, V.59, H.62, A.65, M.66, L.69, L.138, I.141, V.142, Y.145 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:V.27, B:A.31, B:V.36, B:V.59, B:H.62, B:A.65, B:L.69, B:I.141, B:V.142 Hydrogen bonds: B:F.32, B:H.62, B:Y.145, B:Y.145 pi-Stacking: B:F.32, B:F.32, B:F.32 pi-Cation interactions: B:H.62

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Gag protein

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