8CGC

Structure of CSF1R in complex with a pyrollopyrimidine (compound 23)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.152 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Synthesis and Development of Highly Selective Pyrrolo[2,3- d ]pyrimidine CSF1R Inhibitors Targeting the Autoinhibited Form.

Aarhus, T.I.Bjornstad, F.Wolowczyk, C.Larsen, K.U.Rognstad, L.Leithaug, T.Unger, A.Habenberger, P.Wolf, A.Bjorkoy, G.Pridans, C.Eickhoff, J.Klebl, B.Hoff, B.H.Sundby, E.

(2023) J Med Chem 66: 6959-6980

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c00428
  • Primary Citation of Related Structures:  
    8CGC

  • PubMed Abstract: 

    Colony-stimulating factor-1 receptor (CSF1R) is a receptor tyrosine kinase that controls the differentiation and maintenance of most tissue-resident macrophages, and the inhibition of CSF1R has been suggested as a possible therapy for a range of human disorders. Herein, we present the synthesis, development, and structure-activity relationship of a series of highly selective pyrrolo[2,3- d ]pyrimidines, showing subnanomolar enzymatic inhibition of this receptor and with excellent selectivity toward other kinases in the platelet-derived growth factor receptor (PDGFR) family. The crystal structure of the protein and 23 revealed that the binding conformation of the protein is DFG-out-like. The most promising compounds in this series were profiled for cellular potency and subjected to pharmacokinetic profiling and in vivo stability, indicating that this compound class could be relevant in a potential disease setting. Additionally, these compounds inhibited primarily the autoinhibited form of the receptor, contrasting the behavior of pexidartinib, which could explain the exquisite selectivity of these structures.


  • Organizational Affiliation

    Department of Materials Science & Engineering, Norwegian University of Science and Technology (NTNU), NO-7491 Trondheim, Norway.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Macrophage colony-stimulating factor 1 receptor343Homo sapiensMutation(s): 0 
Gene Names: CSF1RFMS
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07333
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UIK (Subject of Investigation/LOI)
Query on UIK

Download Ideal Coordinates CCD File 
D [auth A][4-[4-[methyl-[(3-methylphenyl)methyl]amino]-7~{H}-pyrrolo[2,3-d]pyrimidin-6-yl]phenyl]methanol
C22 H22 N4 O
KXUSCHVJJBSONI-UHFFFAOYSA-N
LMR
Query on LMR

Download Ideal Coordinates CCD File 
B [auth A](2S)-2-hydroxybutanedioic acid
C4 H6 O5
BJEPYKJPYRNKOW-REOHCLBHSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.152 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.013α = 90
b = 81.013β = 90
c = 143.237γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-24
    Type: Initial release
  • Version 1.1: 2023-06-07
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection