2KP8

Ligand bound to a model peptide that mimics the open fusogenic form


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Non-peptide entry inhibitors of HIV-1 that target the gp41 coiled coil pocket.

Stewart, K.D.Huth, J.R.Ng, T.I.McDaniel, K.Hutchinson, R.N.Stoll, V.S.Mendoza, R.R.Matayoshi, E.D.Carrick, R.Mo, H.Severin, J.Walter, K.Richardson, P.L.Barrett, L.W.Meadows, R.Anderson, S.Kohlbrenner, W.Maring, C.Kempf, D.J.Molla, A.Olejniczak, E.T.

(2010) Bioorg Med Chem Lett 20: 612-617

  • DOI: https://doi.org/10.1016/j.bmcl.2009.11.076
  • Primary Citation of Related Structures:  
    2KP8

  • PubMed Abstract: 

    The ectodomain of HIV-1 gp41 mediates the fusion of viral and host cellular membranes. The peptide-based drug Enfuvirtide(1) is precedent that antagonists of this fusion activity may act as anti HIV-agents. Here, NMR screening was used to discover non-peptide leads against this target and resulted in the discovery of a new benzamide 1 series. This series is non-peptide, low molecular weight, and analogs have activity in a cell fusion assay with EC50 values ranging 3-41microM. Structural work on the gp41/benzamide 1 complex was determined by NMR spectroscopy using a designed model peptide system that mimics an open pocket of the fusogenic form of the protein.


  • Organizational Affiliation

    Pharmaceutical Discovery Division, Abbott Laboratories, 100 Abbott Park Rd., R46Y, AP10, Abbott Park, IL 60064-6098, United States. kent.d.stewart@abbott.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Model peptide
A, B, C
72Escherichia coliMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XIG
Query on XIG

Download Ideal Coordinates CCD File 
D [auth B]5-{[(4'-methoxybiphenyl-4-yl)methyl][(1S)-1,2,3,4-tetrahydronaphthalen-1-yl]carbamoyl}benzene-1,2,4-tricarboxylic acid
C34 H29 N O8
RDVWBTCVLAKXDT-PMERELPUSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
XIG PDBBind:  2KP8 Kd: 1.00e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2022-03-16
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-07-26
    Changes: Database references