5JCT | pdb_00005jct

Crystal Structure of Human Pirin in complex with a Chemical Probe pyrrolidine 24


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 
    0.204 (Depositor), 0.211 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5JCT

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery of a Chemical Probe Bisamide (CCT251236): An Orally Bioavailable Efficacious Pirin Ligand from a Heat Shock Transcription Factor 1 (HSF1) Phenotypic Screen.

Cheeseman, M.D.Chessum, N.E.Rye, C.S.Pasqua, A.E.Tucker, M.J.Wilding, B.Evans, L.E.Lepri, S.Richards, M.Sharp, S.Y.Ali, S.Rowlands, M.O'Fee, L.Miah, A.Hayes, A.Henley, A.T.Powers, M.Te Poele, R.De Billy, E.Pellegrino, L.Raynaud, F.Burke, R.van Montfort, R.L.Eccles, S.A.Workman, P.Jones, K.

(2017) J Med Chem 60: 180-201

  • DOI: https://doi.org/10.1021/acs.jmedchem.6b01055
  • Primary Citation Related Structures: 
    5JCT

  • PubMed Abstract: 

    Phenotypic screens, which focus on measuring and quantifying discrete cellular changes rather than affinity for individual recombinant proteins, have recently attracted renewed interest as an efficient strategy for drug discovery. In this article, we describe the discovery of a new chemical probe, bisamide (CCT251236), identified using an unbiased phenotypic screen to detect inhibitors of the HSF1 stress pathway. The chemical probe is orally bioavailable and displays efficacy in a human ovarian carcinoma xenograft model. By developing cell-based SAR and using chemical proteomics, we identified pirin as a high affinity molecular target, which was confirmed by SPR and crystallography.


  • Organizational Affiliation
    • Cancer Research UK Cancer Therapeutics Unit at The Institute of Cancer Research , London SW7 3RP, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 35.19 kDa 
  • Atom Count: 2,666 
  • Modeled Residue Count: 287 
  • Deposited Residue Count: 310 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Pirin310Homo sapiensMutation(s): 0 
Gene Names: PIR
EC: 1.13.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for O00625 (Homo sapiens)
Explore O00625 
Go to UniProtKB:  O00625
PHAROS:  O00625
GTEx:  ENSG00000087842 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00625
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6JQ

Query on 6JQ



Download:Ideal Coordinates CCD File
F [auth A]N-{5-[(2,3-dihydro-1,4-benzodioxine-6-carbonyl)amino]-2-methylphenyl}-2-[3-(pyrrolidin-1-yl)propyl]quinoline-6-carboxamide
C33 H34 N4 O4
VJPIHBNUZAVUAJ-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS

Query on DMS



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
FE

Query on FE



Download:Ideal Coordinates CCD File
B [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free:  0.204 (Depositor), 0.211 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.148α = 90
b = 67.415β = 90
c = 107.062γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomC309/A8274
Cancer Research UKUnited KingdomC309/A11566

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-01-25
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description