4E43

HIV protease (PR) dimer with acetate in exo site and peptide in active site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Fragment-based screen against HIV protease.

Perryman, A.L.Zhang, Q.Soutter, H.H.Rosenfeld, R.McRee, D.E.Olson, A.J.Elder, J.E.Stout, C.D.

(2010) Chem.Biol.Drug Des. 75: 257-268

  • DOI: 10.1111/j.1747-0285.2009.00943.x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We have employed a fragment-based screen against wild-type (NL4-3) HIV protease (PR) using the Active Sight fragment library and X-ray crystallography. The experiments reveal two new binding sites for small molecules. PR was co-crystallized with frag ...

    We have employed a fragment-based screen against wild-type (NL4-3) HIV protease (PR) using the Active Sight fragment library and X-ray crystallography. The experiments reveal two new binding sites for small molecules. PR was co-crystallized with fragments, or crystals were soaked in fragment solutions, using five crystal forms, and 378 data sets were collected to 2.3-1.3 A resolution. Fragment binding induces a distinct conformation and specific crystal form of TL-3 inhibited PR during co-crystallization. One fragment, 2-methylcyclohexanol, binds in the 'exo site' adjacent to the Gly(16)Gly(17)Gln(18)loop where the amide of Gly(17)is a specific hydrogen bond donor, and hydrophobic contacts occur with the side chains of Lys(14)and Leu(63). Another fragment, indole-6-carboxylic acid, binds on the 'outside/top of the flap' via hydrophobic contacts with Trp(42), Pro(44), Met(46), and Lys(55), a hydrogen bond with Val(56), and a salt-bridge with Arg(57). 2-acetyl-benzothiophene also binds at this site. This study is the first fragment-based crystallographic screen against HIV PR, and the first time that fragments were screened against an inhibitor-bound drug target to search for compounds that both bind to novel sites and stabilize the inhibited conformation of the target.


    Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protease
A, B
99Human immunodeficiency virus type 1 group M subtype DMutation(s): 1 
Gene Names: gag-pol
Find proteins for P12499 (Human immunodeficiency virus type 1 group M subtype D)
Go to UniProtKB:  P12499
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Random peptide
C
6N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

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

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BME
Query on BME

Download SDF File 
Download CCD File 
B
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A, B
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.193 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 58.290α = 90.00
b = 86.259β = 90.00
c = 46.299γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
PDB_EXTRACTdata extraction
SCALAdata scaling
MOSFLMdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-03-11 
  • Released Date: 2012-05-30 
  • Deposition Author(s): Stout, C.D.
  • This entry supersedes: 3KF1

Revision History 

  • Version 1.0: 2012-05-30
    Type: Initial release
  • Version 1.1: 2012-06-06
    Type: Other