Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 38.55 kDa 
• Atom Count: 2,303 
• Modelled Residue Count: 281 
• Deposited Residue Count: 335 
• Unique protein chains: 1

 3KRL

cFMS Tyrosine kinase in complex with 5-Cyano-furan-2-carboxylic acid [4-(4-methyl-piperazin-1-yl)-2-piperidin-1-yl-phenyl]-amide

• PDB DOI:  https://doi.org/10.2210/pdb3KRL/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2009-11-18 Released: 2010-12-01 
• Deposition Author(s): Schubert, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.264 
• R-Value Work: 0.209 
• R-Value Observed: 0.212 

Literature

Optimization of a Potent Class of Arylamide Colony-Stimulating Factor-1 Receptor Inhibitors Leading to Anti-inflammatory Clinical Candidate 4-Cyano-N-[2-(1-cyclohexen-1-yl)-4-[1-[(dimethylamino)acetyl]-4-piperidinyl]phenyl]-1H-imidazole-2-carboxamide (JNJ-28312141).

Illig, C.R., Manthey, C.L., Wall, M.J., Meegalla, S.K., Chen, J., Wilson, K.J., Ballentine, S.K., Desjarlais, R.L., Schubert, C., Crysler, C.S., Chen, Y., Molloy, C.J., Chaikin, M.A., Donatelli, R.R., Yurkow, E., Zhou, Z., Player, M.R., Tomczuk, B.E.

(2011) J Med Chem 54: 7860-7883

• PubMed: 22039836 
• DOI: https://doi.org/10.1021/jm200900q
• Primary Citation of Related Structures:  
  3KRJ, 3KRL


• PubMed Abstract: 
  

A class of potent inhibitors of colony-stimulating factor-1 receptor (CSF-1R or FMS), as exemplified by 8 and 21, was optimized to improve pharmacokinetic and pharmacodynamic properties and potential toxicological liabilities. Early stage absorption, distribution, metabolism, and excretion assays were employed to ensure the incorporation of druglike properties resulting in the selection of several compounds with good activity in a pharmacodynamic screening assay in mice. Further investigation, utilizing the type II collagen-induced arthritis model in mice, culminated in the selection of anti-inflammatory development candidate JNJ-28312141 (23, FMS IC(50) = 0.69 nM, cell assay IC(50) = 2.6 nM). Compound 23 also demonstrated efficacy in rat adjuvant and streptococcal cell wall-induced models of arthritis and has entered phase I clinical trials.

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Organizational Affiliation: 

Johnson & Johnson Pharmaceutical Research & Development, Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrophage colony-stimulating factor 1 receptor, Basic fibroblast growth factor receptor 1	A	335	Homo sapiens	Mutation(s): 1  Gene Names: CSF1R, FGFR1 EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P11362 (Homo sapiens) Explore P11362  Go to UniProtKB:  P11362
PHAROS:  P11362
Find proteins for P07333 (Homo sapiens) Explore P07333  Go to UniProtKB:  P07333
PHAROS:  P07333
UniProt Groups	P11362P07333

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KRL	B [auth A]	5-cyano-N-[4-(4-methylpiperazin-1-yl)-2-piperidin-1-ylphenyl]furan-2-carboxamide C22 H27 N5 O2 UUPPIQKPNBIUKY-UHFFFAOYSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
KRL	Binding MOAD:  3KRL	IC50: 0.8 (nM) from 1 assay(s)
	PDBBind:  3KRL	IC50: 0.8 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.264 
• R-Value Work: 0.209 
• R-Value Observed: 0.212 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.111	α = 90
b = 81.111	β = 90
c = 142.57	γ = 120

Software Package:

Software Name	Purpose
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-01 
Deposition Author(s): Schubert, C.

Revision History  

• Version 1.0: 2010-12-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-12-14
  Changes: Database references
• Version 1.3: 2017-08-23
  Changes: Source and taxonomy
• Version 1.4: 2021-10-13
  Changes: Database references, Derived calculations