3LCD: Inhibitor

Inhibitor Bound to A DFG-In structure of the Kinase Domain of CSF-1R. Determined by X-ray diffraction at 2.5 Å resolution. Released 2 Mar 2010.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,345
Mol. weight: 38.05 kDa
Ligands: BDY
Released: 2 Mar 2010

Explore 3LCD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3LCD contains 19 α-helices and 14 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 19 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	566-568	3
α-helix	570-572	3
α-helix	573-575	3
β-strand	576	1	1
α-helix	579-581	3
β-strand	582-590	9	1
β-strand	594-602	9	1
β-strand	610-618	9	1
α-helix	624-640	17
β-strand	646	1	2
β-strand	649-653	5	1
β-strand	660-664	5	1
β-strand	670	1	2
α-helix	671-742	13
α-helix	752-770	19
β-strand	774-775	2	3
α-helix	781-783	3
β-strand	784-786	3	2
α-helix	788-790	3
β-strand	792-794	3	2
β-strand	801-802	2	3
β-strand	809-810	2	4
α-helix	819-821	3
α-helix	824-828	5
β-strand	831-832	2	4
α-helix	834-849	16
α-helix	853-854	2
α-helix	863-870	8
α-helix	875-878	4
α-helix	883-892	10
α-helix	897-899	3
α-helix	901-902	2
α-helix	903-912	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Macrophage colony-stimulating factor 1 receptor	A	protein	329	Homo sapiens	P07333 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3LCD_1 Macrophage colony-stimulating factor 1 receptor (chains A)
GVDYKYKQKPKYQVRWKIIESYEGNSYTFIDPTQLPYNEKWEFPRNNLQFGKTLGAGAFG
KVVEATAFGLGKEDAVLKVAVKMLKSTAHADEKEALMSELKIMSHLGQHENIVNLLGACT
HGGPVLVITEYCCYGDLLNFLRRKAEADLDKEDGRPLELRDLLHFSSQVAQGMAFLASKN
CIHRDVAARNVLLTNGHVAKIGDFGLARDIMNDSNYIVKGNARLPVKWMAPESIFDCVYT
VQSDVWSYGILLWEIFSLGLNPYPGILVNSKFYKLVKDGYQMAQPAFAPKNIYSIMQACW
ALEPTHRPTFQQICSFLQEQAQEDRRERD

Ligands and cofactors

ID	Name	Formula	Copies
BDY	N~3~-(2,6-dichlorobenzyl)-5-(4-{[(2R)-2-(pyrrolidin-1-ylmethyl)pyrrolidin-1-yl]…	C27 H30 Cl2 N6 O	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

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. et al. Bioorg Med Chem Lett (2010) 20:1543-1547. DOI 10.1016/j.bmcl.2010.01.078 · PubMed

Other PDB entries of the same protein (UniProt P07333 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8JOT 1.69 Å, Crystal structure of CSF-1R kinase domain with sulfatinib
6T2W 1.7 Å, Crystal structure of the CSF1R kinase domain with a dihydropurinone inhibitor (compound 4)
2I1M 1.8 Å, cFMS tyrosine kinase (tie2 KID) in complex with an arylamide inhibitor
6IG8 1.8 Å, Crystal structure of CSF-1R kinase domain with a small molecular inhibitor, JTE-952
2I0Y 1.9 Å, cFMS tyrosine kinase (FGF KID) in complex with an arylamide inhibitor
8CGC 1.93 Å, Structure of CSF1R in complex with a pyrollopyrimidine (compound 23)
3DPK 1.95 Å, cFMS tyrosine kinase in complex with a pyridopyrimidinone inhibitor
3BEA 2.02 Å, cFMS tyrosine kinase (tie2 KID) in complex with a pyrimidinopyridone inhibitor
3KRJ 2.1 Å, cFMS tyrosine kinase in complex with 4-Cyano-1H-imidazole-2-carboxylic acid…
6N33 2.25 Å, Crystal structure of fms kinase domain with a small molecular inhibitor, PLX5622
8W1L 2.26 Å, Structure of CSF1R kinase domain in complex with Cpd 32
3KRL 2.4 Å, cFMS Tyrosine kinase in complex with 5-Cyano-furan-2-carboxylic acid…

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