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PDBsum entry 4dvr
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Immune system/transcription inhibitor
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PDB id
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4dvr
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Contents |
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288 a.a.
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211 a.a.
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219 a.a.
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PDB id:
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| Name: |
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Immune system/transcription inhibitor
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Title:
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Crystal structure of yu2 gp120 core in complex with fab 48d and nbd- 557
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Structure:
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Envelope glycoprotein gp120. Chain: g. Fragment: unp residues 82-122. 199-297. 319-479. Synonym: env polyprotein,env polyprotein,env polyprotein. Engineered: yes. Fab 48d light chain. Chain: l. Engineered: yes. Fab 48d heavy chain.
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Source:
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Human immunodeficiency virus type 1 group m subtype b (isolate yu-2). HIV-1. Organism_taxid: 362651. Strain: isolate yu-2. Gene: env. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell_line: hek293f.
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Resolution:
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2.50Å
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R-factor:
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0.233
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R-free:
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0.289
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Authors:
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Y.D.Kwon,P.D.Kwong
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Key ref:
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Y.D.Kwon
et al.
(2014).
Crystal structures of HIV-1 gp120 envelope glycoprotein in complex with NBD analogues that target the CD4-binding site.
Plos One,
9,
e85940.
PubMed id:
DOI:
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Date:
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23-Feb-12
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Release date:
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27-Feb-13
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PROCHECK
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Headers
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References
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P35961
(ENV_HV1Y2) -
Envelope glycoprotein gp160 from Human immunodeficiency virus type 1 group M subtype B (isolate YU-2)
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Seq:
Struc:
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843 a.a.
288 a.a.*
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DOI no:
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Plos One
9:e85940
(2014)
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PubMed id:
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Crystal structures of HIV-1 gp120 envelope glycoprotein in complex with NBD analogues that target the CD4-binding site.
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Y.D.Kwon,
J.M.LaLonde,
Y.Yang,
M.A.Elban,
A.Sugawara,
J.R.Courter,
D.M.Jones,
A.B.Smith,
A.K.Debnath,
P.D.Kwong.
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ABSTRACT
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Efforts to develop therapeutic agents that inhibit HIV-1 entry have led to the
identification of several small molecule leads. One of the most promising is the
NBD series, which binds within a conserved gp120 cavity and possesses
para-halogen substituted aromatic rings, a central oxalamide linker, and a
tetramethylpiperidine moiety. In this study, we characterized structurally the
interactions of four NBD analogues containing meta-fluoro substitution on the
aromatic ring and various heterocyclic ring replacements of the
tetramethylpiperidine group. The addition of a meta-fluorine to the aromatic
ring improved surface complementarity and did not alter the position of the
analogue relative to gp120. By contrast, heterocyclic ring replacements of the
tetramethylpiperidine moiety exhibited diverse positioning and interactions with
the vestibule of the gp120 cavity. Overall, the biological profile of
NBD-congeners was modulated by ligand interactions with the gp120-cavity
vestibule. Herein, six co-crystal structures of NBD-analogues with gp120 provide
a structural framework for continued small molecule-entry inhibitor optimization.
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