RCSB PDB - 5VEA: HIV Protease (PR) with TL-3 in active site and 4-methylbenzene-1,2-diamine in exosite

 5VEA

HIV Protease (PR) with TL-3 in active site and 4-methylbenzene-1,2-diamine in exosite


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 3TLClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Fragment-based campaign for the identification of potential exosite binders of HIV-1 Protease

Forli, S.Tiefenbrunn, T.Baksh, M.M.Chang, M.W.Perryman, A.Garg, D.Happer, M.Lin, Y.-C.Goodsell, D.Angelina, E.L.De Vera, I.Kojetin, D.Torbett, B.E.Finn, M.G.Elder, J.Stout, C.D.Olson, A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HIV-1 protease99Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: pol
EC: 3.4.23.16
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12497 
Go to UniProtKB:  P12497
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12497
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3TL
Query on 3TL

Download Ideal Coordinates CCD File 
B [auth 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
C50 H64 N6 O10
BJJPNOGMLLUCER-KUTQPOQPSA-N
9AY
Query on 9AY

Download Ideal Coordinates CCD File 
C [auth A]4-methylbenzene-1,2-diamine
C7 H10 N2
DGRGLKZMKWPMOH-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
3TL BindingDB:  5VEA Ki: 1.5 (nM) from 1 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.763α = 90
b = 62.763β = 90
c = 82.238γ = 120
Software Package:
Software NamePurpose
MOSFLMdata collection
SCALAdata scaling
MOLREPdata processing
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 3TLClick on this verticalbar to view details

Entry History 

Deposition Data

  • Released Date: 2018-04-25 
  • Deposition Author(s): Stout, C.D.

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-25
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Refinement description