2BPY

HIV-1 protease-inhibitor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Rapid X-ray diffraction analysis of HIV-1 protease-inhibitor complexes: inhibitor exchange in single crystals of the bound enzyme.

Munshi, S.Chen, Z.Li, Y.Olsen, D.B.Fraley, M.E.Hungate, R.W.Kuo, L.C.

(1998) Acta Crystallogr D Biol Crystallogr 54: 1053-1060

  • DOI: 10.1107/s0907444998003588
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The ability to replace an inhibitor bound to the HIV-1 protease in single crystals with other potent inhibitors offers the possibility of investigating a series of protease inhibitors rapidly and conveniently with the use of X-ray crystallography. Th ...

    The ability to replace an inhibitor bound to the HIV-1 protease in single crystals with other potent inhibitors offers the possibility of investigating a series of protease inhibitors rapidly and conveniently with the use of X-ray crystallography. This approach affords a fast turnaround of structural information for iterative rational drug designs and obviates the need for studying the complex structures by co-crystallization. The replacement approach has been successfully used with single crystals of the HIV-1 protease complexed with a weak inhibitor. The structures of the complexes obtained by the replacement method are similar to those determined by co-crystallization.


    Related Citations: 
    • Crystal Structure at 1.9-A Resolution of Human Immunodeficiency Virus (HIV) II Protease Complexed with L-735,524, an Orally Bioavailable Inhibitor of the HIV Proteases
      Chen, Z., Li, Y., Chen, E., Hall, D.L., Darke, P.L., Culberson, C., Shafer, J.A., Kuo, L.C.
      (1994) J Biol Chem 269: 26344

    Organizational Affiliation

    Department of Antiviral Research, Merck Research Laboratories, West Point, PA 19486, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 PROTEASE
A, B
99Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: HIV-1 PROTEASE FROM THE NY5 ISOLATE
EC: 3.4.23.16 (PDB Primary Data), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P04587 (Human immunodeficiency virus type 1 group M subtype B (isolate BH5))
Go to UniProtKB:  P04587
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3IN
Query on 3IN

Download CCD File 
B
N-[2(S)-CYCLOPENTYL-1(R)-HYDROXY-3(R)METHYL]-5-[(2(S)-TERTIARY-BUTYLAMINO-CARBONYL)-4-(N1-(2)-(N-METHYLPIPERAZINYL)-3-CHLORO-PYRAZINYL-5-CARBONYL)-PIPERAZINO]-4(S)-HYDROXY-2(R)-PHENYLMETHYL-PENTANAMIDE
C37 H55 Cl N8 O5
SQZXWXXIPWXBCL-CYTJBAGBSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3INKi:  39.79999923706055   nM  PDBBind
3INKi:  39.79999923706055   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.64α = 90
b = 87.28β = 90
c = 46.83γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 1998-01-22 
  • Released Date: 1999-02-23 
  • Deposition Author(s): Munshi, S., Chen, Z.

Revision History 

  • Version 1.0: 1999-02-23
    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: 2012-05-09
    Changes: Structure summary