6I83

Crystal structure of phosphorylated RET V804M tyrosine kinase domain complexed with PDD00018366

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

Discovery and Optimization of wt-RET/KDR-Selective Inhibitors of RETV804MKinase.

Newton, R., Waszkowycz, B., Seewooruthun, C., Burschowsky, D., Richards, M., Hitchin, S., Begum, H., Watson, A., French, E., Hamilton, N., Jones, S., Lin, L.Y., Waddell, I., Echalier, A., Bayliss, R., Jordan, A.M., Ogilvie, D.

(2020) ACS Med Chem Lett 11: 497-505

  • DOI: https://doi.org/10.1021/acsmedchemlett.9b00615
  • Primary Citation of Related Structures:  
    6I82, 6I83

  • PubMed Abstract: 

    A combination of focused library and virtual screening, hit expansion, and rational design has resulted in the development of a series of inhibitors of RET V804M kinase, the anticipated drug-resistant mutant of RET kinase. These agents do not inhibit the wild type (wt) isoforms of RET or KDR and therefore offer a potential adjunct to RET inhibitors currently undergoing clinical evaluation.

    • Organizational Affiliation: 

    Drug Discovery Unit, Cancer Research UK, Manchester Institute, University of Manchester, Alderley Park, Macclesfield SK10 4TG, U.K.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proto-oncogene tyrosine-protein kinase receptor Ret314Homo sapiensMutation(s): 1 
Gene Names: RET, CDHF12, CDHR16, PTC, RET51
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P07949 (Homo sapiens)
Explore P07949 
Go to UniProtKB:  P07949
PHAROS:  P07949
GTEx:  ENSG00000165731 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07949
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
H72
Query on H72
Download Ideal Coordinates CCD File 
B [auth A]4-[5-(pyridin-3-ylmethylamino)pyrazolo[1,5-a]pyrimidin-3-yl]benzamide
C19 H16 N6 O
LMGXQBQAUALFTB-UHFFFAOYSA-N
FMT
Query on FMT
Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
A
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Binding Affinity Annotations 
IDSourceBinding Affinity
H72 Binding MOAD:  6I83 IC50: 25 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.38α = 90
b = 70.04β = 102.22
c = 78.73γ = 90
Software Package:
Software NamePurpose
GDAdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomGrant C480/A11411
Cancer Research UKUnited KingdomC5759/A17098
Cancer Research UKUnited KingdomC1362/A20263

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-11
    Type: Initial release
  • Version 1.1: 2020-04-22
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description