1HTG

X-RAY CRYSTALLOGRAPHIC STUDIES OF A SERIES OF PENICILLIN-DERIVED ASYMMETRIC INHIBITORS OF HIV-1 PROTEASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

X-ray crystallographic studies of a series of penicillin-derived asymmetric inhibitors of HIV-1 protease.

Jhoti, H.Singh, O.M.Weir, M.P.Cooke, R.Murray-Rust, P.Wonacott, A.

(1994) Biochemistry 33: 8417-8427

  • DOI: https://doi.org/10.1021/bi00194a005
  • Primary Citation of Related Structures:  
    1HTE, 1HTF, 1HTG

  • PubMed Abstract: 

    In the development of a treatment for AIDS, the HIV-1 protease has been identified as a good target enzyme for inhibitor design. We previously reported a series of dimeric penicillin-derived C2-symmetric HIV-1 protease inhibitors [Humber, D., et al. (1993) J. Med. Chem. 36, 3120-3128]. In an attempt to reduce the size and optimize the binding of these C2-symmetric inhibitors, molecular modeling studies led to a novel series of monomeric penicillin-derived inhibitors of HIV-1 protease. The binding modes of these monomeric inhibitors have been characterized by X-ray crystallographic and NMR studies. Crystal structures of HIV-1 protease complexed to three inhibitors (GR123976, GR126045, and GR137615) from this series identify the molecular details of the interactions. The binding of GR123976 (IC50 = 2.3 microM) exhibits good hydrophobic contacts but few electrostatic interactions. A strategy of structure-based design and chemical synthesis led to the elaboration of GR123976 to optimize interactions with the protein. Crystallographic analysis of HIV-1 protease complexed to GR126045 and GR137615 identified these interactions with the catalytic aspartates and the protein binding pockets. The crystal structures of the three complexes confirm the presence of the major interactions modeled in order to optimize potency and reveal details of the molecular recognition by HIV-1 protease of this novel series of nonpeptidic inhibitors.


  • Organizational Affiliation

    Department of Biomolecular Structure, Glaxo Research & Development Limited, Greenford, Middlesex, England.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HIV-1 PROTEASE
A, B
99Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Explore P03366 
Go to UniProtKB:  P03366
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03366
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
G37
Query on G37

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
2-(BENZYLCARBAMOYL-PHENYLACETYLAMINO-METHYL)-5,5-DIMETHYL-THIAZOLIDINE-4-CARBOXYLIC ACID 3-[(1H-BENZIMIDAZOL-2-YLMETHYLCARBAMOYL)-1-BENZYL-2-HYDROXYPROPYL]-AMIDE
C42 H47 N7 O5 S
ZABIWLDXHYJWLT-QGNCIQMXSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
G37 BindingDB:  1HTG Ki: 3.2 (nM) from 1 assay(s)
Binding MOAD:  1HTG IC50: 3.8 (nM) from 1 assay(s)
PDBBind:  1HTG IC50: 3.8 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.3α = 90
b = 87.4β = 90
c = 46.6γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-07-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Advisory, Derived calculations, Other
  • Version 1.4: 2024-02-07
    Changes: Advisory, Data collection, Database references, Derived calculations