2PSV

Crystal Structure of wild type HIV-1 protease in complex with CARB-KB45


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Design of Mutation-resistant HIV Protease Inhibitors with the Substrate Envelope Hypothesis.

Chellappan, S.Kiran Kumar Reddy, G.S.Ali, A.Nalam, M.N.Anjum, S.G.Cao, H.Kairys, V.Fernandes, M.X.Altman, M.D.Tidor, B.Rana, T.M.Schiffer, C.A.Gilson, M.K.

(2007) Chem.Biol.Drug Des. 69: 298-313

  • DOI: 10.1111/j.1747-0285.2007.00514.x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • There is a clinical need for HIV protease inhibitors that can evade resistance mutations. One possible approach to designing such inhibitors relies upon the crystallographic observation that the substrates of HIV protease occupy a rather constant reg ...

    There is a clinical need for HIV protease inhibitors that can evade resistance mutations. One possible approach to designing such inhibitors relies upon the crystallographic observation that the substrates of HIV protease occupy a rather constant region within the binding site. In particular, it has been hypothesized that inhibitors which lie within this region will tend to resist clinically relevant mutations. The present study offers the first prospective evaluation of this hypothesis, via computational design of inhibitors predicted to conform to the substrate envelope, followed by synthesis and evaluation against wild-type and mutant proteases, as well as structural studies of complexes of the designed inhibitors with HIV protease. The results support the utility of the substrate envelope hypothesis as a guide to the design of robust protease inhibitors.


    Organizational Affiliation

    Center for Advanced Research in Biotechnology, University of Maryland, Biotechnology Institute, Rockville, MD 20850, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protease
A, B
99Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: pol
Find proteins for O38707 (Human immunodeficiency virus 1)
Go to UniProtKB:  O38707
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
MUV
Query on MUV

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Download CCD File 
A
N-{(1S,2R)-1-BENZYL-3-[(CYCLOPROPYLMETHYL)(2-FURYLSULFONYL)AMINO]-2-HYDROXYPROPYL}-N'-METHYLSUCCINAMIDE
C23 H31 N3 O6 S
IKOPFHKAECNGQI-VQTJNVASSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MUVKi: 58 nM (91) BINDINGDB
MUVKi: 58 nM BINDINGMOAD
MUVKi: 58 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.165 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.692α = 90.00
b = 57.593β = 90.00
c = 61.836γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
AMoREphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-05
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Advisory, Refinement description