3LCD

Inhibitor Bound to A DFG-In structure of the Kinase Domain of CSF-1R

• PDB DOI: https://doi.org/10.2210/pdb3LCD/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2010-01-10 Released: 2010-03-02 
• Deposition Author(s): Kamtekar, S., Day, J.E., Reitz, B.A., Mathis, K.J., Meyers, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.265 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 

Literature

Structure-based drug design enables conversion of a DFG-in binding CSF-1R kinase inhibitor to a DFG-out binding mode

Meyers, M.J., Pelc, M., Kamtekar, S., Day, J., Poda, G.I., Hall, M.K., Michener, M.L., Reitz, B.A., Mathis, K.J., Pierce, B.S., Parikh, M.D., Mischke, D.A., Long, S.A., Parlow, J.J., Anderson, D.R., Thorarensen, A.

(2010) Bioorg Med Chem Lett 20: 1543-1547

• PubMed: 20137931 
• DOI: https://doi.org/10.1016/j.bmcl.2010.01.078
• Primary Citation of Related Structures:  
  3LCD, 3LCO


• PubMed Abstract: 
  

  The work described herein demonstrates the utility of structure-based drug design (SBDD) in shifting the binding mode of an HTS hit from a DFG-in to a DFG-out binding mode resulting in a class of novel potent CSF-1R kinase inhibitors suitable for lead development.

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Organizational Affiliation: 

Pfizer Global Research & Development, St. Louis Laboratories, 700 Chesterfield Parkway West, Chesterfield, MO 63017, United States. [e-mail]

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: 38.05 kDa 
• Atom Count: 2,345 
• Modelled Residue Count: 290 
• Deposited Residue Count: 329 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrophage colony-stimulating factor 1 receptor	A	329	Homo sapiens	Mutation(s): 0  Gene Names: CSF-1R, CSF1R, FMS EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P07333 (Homo sapiens) Explore P07333  Go to UniProtKB:  P07333
PHAROS:  P07333 GTEx:  ENSG00000182578

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BDY	D [auth A]	N~3~-(2,6-dichlorobenzyl)-5-(4-{[(2R)-2-(pyrrolidin-1-ylmethyl)pyrrolidin-1-yl]carbonyl}phenyl)pyrazine-2,3-diamine C27 H30 Cl2 N6 O PVBCEWZVPUKFNT-HXUWFJFHSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
BDY	PDBBind:  3LCD	IC50: 40 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.265 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.649	α = 90
b = 74.125	β = 90
c = 91.024	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-02 
Deposition Author(s): Kamtekar, S., Day, J.E., Reitz, B.A., Mathis, K.J., Meyers, M.J.

Revision History  

• Version 1.0: 2010-03-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-07-26
  Changes: Data collection, Refinement description, Source and taxonomy
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary