Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 34.32 kDa 
• Atom Count: 2,536 
• Modelled Residue Count: 274 
• Deposited Residue Count: 288 
• Unique protein chains: 1

 6PDJ

Tyrosine-protein kinase LCK bound to Compound 11

• PDB DOI:  https://doi.org/10.2210/pdb6PDJ/pdb

• Classification: SIGNALING PROTEIN/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2019-06-19 Released: 2019-10-09 
• Deposition Author(s): Critton, D.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.217 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 

Literature

Discovery of Pyridazinone and Pyrazolo[1,5-a]pyridine Inhibitors of C-Terminal Src Kinase.

O'Malley, D.P., Ahuja, V., Fink, B., Cao, C., Wang, C., Swanson, J., Wee, S., Gavai, A.V., Tokarski, J., Critton, D., Paiva, A.A., Johnson, B.M., Szapiel, N., Xie, D.

(2019) ACS Med Chem Lett 10: 1486-1491

• PubMed: 31620238 
• DOI: https://doi.org/10.1021/acsmedchemlett.9b00354
• Primary Citation of Related Structures:  
  6PDJ


• PubMed Abstract: 
  

C-terminal Src kinase (CSK) functions as a negative regulator of T cell activation through inhibitory phosphorylation of LCK, so inhibitors of CSK are of interest as potential immuno-oncology agents. Screening of an internal kinase inhibitor collection identified pyridazinone lead 1 , and a series of modifications led to optimized compound 13 . Compound 13 showed potent activity in biochemical and cellular assays in vitro and demonstrated the ability to increase T cell proliferation induced by T cell receptor signaling. Compound 13 gave extended exposure in mice upon oral dosing and produced a functional response (decrease in LCK phosphorylation) in mouse spleens at 6 h post dose.

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Organizational Affiliation: 

Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase Lck	A	288	Homo sapiens	Mutation(s): 0  Gene Names: LCK EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P06239 (Homo sapiens) Explore P06239  Go to UniProtKB:  P06239
PHAROS:  P06239

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ODJ (Subject of Investigation/LOI)	B [auth A]	N-{4-[(6-methoxypyrazolo[1,5-a]pyridine-3-carbonyl)amino]-3-methylphenyl}-1-methyl-1H-indazole-3-carboxamide C25 H22 N6 O3 LXWXQRLCBZDGSZ-UHFFFAOYSA-N
CXS	C [auth A]	3-CYCLOHEXYL-1-PROPYLSULFONIC ACID C9 H19 N O3 S PJWWRFATQTVXHA-UHFFFAOYSA-N
SO4	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NI	F [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Binding Affinity Annotations
ID	Source	Binding Affinity
PTR	BindingDB:  6PDJ	Kd: 4.00e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.217 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.016	α = 90
b = 74.163	β = 90
c = 104.527	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
AutoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-10-09 
Deposition Author(s): Critton, D.A.

Revision History  

• Version 1.0: 2019-10-09
  Type: Initial release
  
• Version 1.1: 2019-10-30
  Changes: Data collection, Database references