3SRK

A new class of suicide inhibitor blocks nucleotide binding to pyruvate kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 
    0.266 (Depositor), 0.264 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

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 PTKClick on this verticalbar to view detailsBest fitted LSAClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

A new class of suicide inhibitor blocks nucleotide binding to pyruvate kinase

Morgan, H.P.Walsh, M.Blackburn, E.A.Wear, M.A.Boxer, M.Shen, M.McNae, I.W.Michels, P.A.M.Auld, D.S.Fothergill-Gilmore, L.A.Walkinshaw, M.D.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyruvate kinase
A, B
499Leishmania mexicanaMutation(s): 0 
Gene Names: PYK
EC: 2.7.1.40
UniProt
Find proteins for Q27686 (Leishmania mexicana)
Explore Q27686 
Go to UniProtKB:  Q27686
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ27686
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PTK
Query on PTK

Download Ideal Coordinates CCD File 
F [auth A]pyrene-1,3,6,8-tetrasulfonic acid
C16 H10 O12 S4
CZLSHVQVNDDHDQ-UHFFFAOYSA-N
LSA
Query on LSA

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
1,2-BENZISOTHIAZOL-3(2H)-ONE 1,1-DIOXIDE
C7 H5 N O3 S
CVHZOJJKTDOEJC-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
H [auth B],
I [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free:  0.266 (Depositor), 0.264 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.42α = 90
b = 130.16β = 90
c = 166.49γ = 90
Software Package:
Software NamePurpose
DNAdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

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 PTKClick on this verticalbar to view detailsBest fitted LSAClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-18
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Structure summary