2BPY

HIV-1 protease-inhibitor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Work: 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.,Sect.D 54: 1053-1060

  • Primary Citation of Related Structures:  2BPV, 2BPW, 2BPX, 2BPZ

  • 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 type 1 group M subtype BGene Names: gag-pol
EC: 3.4.23.16, 3.1.-.-, 2.7.7.49, 2.7.7.7, 3.1.26.13, 2.7.7.-, 3.1.13.2
Find proteins for P04587 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P04587
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3IN
Query on 3IN

Download SDF File 
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: 39.8 nM BINDINGMOAD
3INKi: 39.8 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Work: 0.197 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 58.640α = 90.00
b = 87.280β = 90.00
c = 46.830γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2012-05-09
    Type: Structure summary