2JPR

Joint refinement of the HIV-1 CA-NTD in complex with the assembly inhibitor CAP-1


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 20 
  • Selection Criteria: all calculated structures submitted 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the Antiviral Assembly Inhibitor CAP-1 Complex with the HIV-1 CA Protein

Kelly, B.N.Kyere, S.Kinde, I.Tang, C.Howard, B.R.Robinson, H.Sundquist, W.I.Summers, M.F.Hill, C.P.

(2007) J Mol Biol 373: 355-366

  • DOI: https://doi.org/10.1016/j.jmb.2007.07.070
  • Primary Citation of Related Structures:  
    2JPR, 2PWM, 2PWO, 2PXR

  • PubMed Abstract: 

    The CA domain of the human immunodeficiency virus type 1 (HIV-1) Gag polyprotein plays critical roles in both the early and late phases of viral replication and is therefore an attractive antiviral target. Compounds with antiviral activity were recently identified that bind to the N-terminal domain of CA (CA N) and inhibit capsid assembly during viral maturation. We have determined the structure of the complex between CA N and the antiviral assembly inhibitor N-(3-chloro-4-methylphenyl)-N'-{2-[({5-[(dimethylamino)-methyl]-2-furyl}-methyl)-sulfanyl]ethyl}-urea) (CAP-1) using a combination of NMR spectroscopy and X-ray crystallography. The protein undergoes a remarkable conformational change upon CAP-1 binding, in which Phe32 is displaced from its buried position in the protein core to open a deep hydrophobic cavity that serves as the ligand binding site. The aromatic ring of CAP-1 inserts into the cavity, with the urea NH groups forming hydrogen bonds with the backbone oxygen of Val59 and the dimethylamonium group interacting with the side-chains of Glu28 and Glu29. Elements that could be exploited to improve binding affinity are apparent in the structure. The displacement of Phe32 by CAP-1 appears to be facilitated by a strained main-chain conformation, which suggests a potential role for a Phe32 conformational switch during normal capsid assembly.


  • Organizational Affiliation

    Department of Biochemistry, University of Utah, Salt Lake City, UT 84112-5650, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gag-Pol polyprotein145Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)Mutation(s): 0 
Gene Names: gag-pol
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12497 
Go to UniProtKB:  P12497
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12497
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JPR
Query on JPR

Download Ideal Coordinates CCD File 
B [auth A]1-(3-chloro-4-methylphenyl)-3-{2-[({5-[(dimethylamino)methyl]-2-furyl}methyl)thio]ethyl}urea
C18 H24 Cl N3 O2 S
WEYNBWVKOYCCQT-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
JPR BindingDB:  2JPR Kd: 8.00e+5 (nM) from 1 assay(s)
IC50: 6.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 20 
  • Selection Criteria: all calculated structures submitted 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2022-03-09
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2024-05-29
    Changes: Data collection