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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Ligand Structure Quality Assessment 


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
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(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

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Ligand Structure Quality Assessment 


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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