3KFS

HIV Protease (PR) dimer with inhibitor TL-3 bound and fragment 2F4 in the outside/top of flap


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 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.David Stout, C.

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

  • DOI: 10.1111/j.1747-0285.2009.00943.x
  • Primary Citation of Related Structures:  3KF0, 3KF1, 3KFN, 3KFP, 3KFR, 4E43

  • 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 DGene 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 P12499 (Human immunodeficiency virus type 1 group M subtype D)
Go to UniProtKB:  P12499
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BME
Query on BME

Download SDF File 
Download CCD File 
A, B
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
2FX
Query on 2FX

Download SDF File 
Download CCD File 
B
1-benzothiophen-2-ylacetic acid
C10 H8 O2 S
SAAWNQLNUJBOLW-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
3TL
Query on 3TL

Download SDF File 
Download CCD File 
A
benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate
TL-3, C2 symmetric inhibitor
C50 H64 N6 O10
BJJPNOGMLLUCER-KUTQPOQPSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000434 (3TL)
Query on PRD_000434
AN-[(benzyloxy)carbonyl]-L-alanyl-N-[(1R)-1-benzyl-2-oxoethyl]-L-valinamidePeptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 28.950α = 90.00
b = 66.350β = 90.00
c = 92.970γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALAdata scaling
REFMACrefinement
Blu-Icedata collection
MOSFLMdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-10-28 
  • Released Date: 2010-02-23 
  • Deposition Author(s): Stout, C.D.

Revision History 

  • Version 1.0: 2010-02-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2013-02-27
    Type: Other