8w1l

Structure of CSF1R kinase domain in complex with Cpd 32

Method: X-RAY DIFFRACTION D_max: 64.3 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Macrophage colony-stimulating factor 1 receptor,CSF1R

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 538–678 Chain A； UniProt 774–922	Mutation：residues 679-752 replaced by residues 577-597 of FGFR1	A1AE3 [3-({3-methoxy-4-[(6-methoxypyridin-3-yl)methoxy]phenyl}methyl)-3H-imidazo[4,5-b]pyridin-6-yl](2-oxa-6-azaspiro[3.3]heptan-6-yl)methanone × 1 GOL GLYCEROL × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6.5；293 K；0.1 M MES, pH 6.5, 21.3% polyethylene glycol 3350 and 0.25 M ammonium sulfate	Resolution 2.26 Å R-free 0.226

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 8W1L	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2I0V c-FMS tyrosine kinase in complex with a quinolone inhibitor Deposited 2006-08-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 538–678（141 aa） Fragment：Kinase Domain Chain A 753–922（170 aa） Fragment：Kinase Domain	Not recorded	SO4 SULFATE ION × 1 6C3 6-CHLORO-3-(3-METHYLISOXAZOL-5-YL)-4-PHENYLQUINOLIN-2(1H)-ONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；298 K；PEG 3350, sodium acetate, Li2SO4, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.296
2I0Y cFMS tyrosine kinase (FGF KID) in complex with an arylamide inhibitor Deposited 2006-08-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 538–678（141 aa） Fragment：Kinase Domain Chain A 753–922（170 aa） Fragment：Kinase Domain	Not recorded	5CN 5-CYANO-FURAN-2-CARBOXYLIC ACID [5-HYDROXYMETHYL-2-(4-METHYL-PIPERIDIN-1-YL)-PHENYL]-AMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；298 K；PEG 3350, sodium acetate, Li2SO4, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.263
2I1M cFMS tyrosine kinase (tie2 KID) in complex with an arylamide inhibitor Deposited 2006-08-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 538–678（141 aa） Fragment：Kinase Domain Chain A 753–922（170 aa） Fragment：Kinase Domain	Not recorded	5CN 5-CYANO-FURAN-2-CARBOXYLIC ACID [5-HYDROXYMETHYL-2-(4-METHYL-PIPERIDIN-1-YL)-PHENYL]-AMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；298 K；PEG 3350, sodium acetate, Li2SO4, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.282
2OGV Crystal Structure of the Autoinhibited Human c-Fms Kinase Domain Deposited 2007-01-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 543–681（139 aa） Fragment：Kinase domain: Residues 543-918 Chain A 741–918（178 aa） Fragment：Kinase domain: Residues 543-918	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；30% PEG 8000, 0.2M Ammonium sulfate, 0.1M MES pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.279
3BEA cFMS tyrosine kinase (tie2 KID) in complex with a pyrimidinopyridone inhibitor Deposited 2007-11-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 538–678（141 aa） Chain A 753–922（170 aa）	Mutation：A695L Mutation：A695L	SO4 SULFATE ION × 3 IXH 8-(2,3-dihydro-1H-inden-5-yl)-2-({4-[(3R,5S)-3,5-dimethylpiperazin-1-yl]phenyl}amino)-5-oxo-5,8-dihydropyrido[2,3-d]pyrimidine-6-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；298 K；PEG 3350, sodium acetate, Li2SO4, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.02 Å R-free 0.230
3DPK cFMS tyrosine kinase in complex with a pyridopyrimidinone inhibitor Deposited 2008-07-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 538–678（141 aa） Fragment：KINASE DOMAIN Chain A 753–922（170 aa） Fragment：KINASE DOMAIN	Mutation：Native kinase insert domain replaced by FGF receptor kinase insert domain Mutation：Native kinase insert domain replaced by FGF receptor kinase insert domain	SO4 SULFATE ION × 3 8C5 8-cyclohexyl-N-methoxy-5-oxo-2-{[4-(2-pyrrolidin-1-ylethyl)phenyl]amino}-5,8-dihydropyrido[2,3-d]pyrimidine-6-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；298 K；PEG 3350, SODIUM ACETATE, LI2SO4, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.95 Å R-free 0.244
3KRJ cFMS tyrosine kinase in complex with 4-Cyano-1H-imidazole-2-carboxylic acid (2-cyclohex-1-enyl-4-piperidin-4-yl-phenyl)-amide Deposited 2009-11-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 538–678（141 aa） Fragment：UNP residues 538-678, 753-922 Chain A 753–922（170 aa） Fragment：UNP residues 538-678, 753-922	Mutation：C584S Mutation：C584S	ACT ACETATE ION × 1 KRJ 4-cyano-N-(2-cyclohex-1-en-1-yl-4-piperidin-4-ylphenyl)-1H-imidazole-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；13-19%PRG3350 100mM NaAcetate, pH 5.6 200mM (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.260
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 Deposited 2009-11-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 538–678（141 aa） Fragment：UNP residues 538-678, 753-922 Chain A 753–922（170 aa） Fragment：UNP residues 538-678, 753-922	Mutation：C584S Mutation：C584S	KRL 5-cyano-N-[4-(4-methylpiperazin-1-yl)-2-piperidin-1-ylphenyl]furan-2-carboxamide × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；13-19% PEG3350 100mM NaAc pH 5.6 200mM (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.40 Å R-free 0.264
3LCD Inhibitor Bound to A DFG-In structure of the Kinase Domain of CSF-1R Deposited 2010-01-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 538–681（144 aa） Fragment：Kinase Domain Chain A 741–919（179 aa） Fragment：Kinase Domain	Mutation：KID domain replaced by linker Mutation：KID domain replaced by linker	SO4 SULFATE ION × 2 BDY N~3~-(2,6-dichlorobenzyl)-5-(4-{[(2R)-2-(pyrrolidin-1-ylmethyl)pyrrolidin-1-yl]carbonyl}phenyl)pyrazine-2,3-diamine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；Equal volumes of protein:ligand (10 mg/ml protein, 1 mM ligand, 200 mM NaCl, 50 mM Potassium dihydrogen phosphate pH 7.5, 5% glycerol, 0.25 mM TCEP) and well solution (0.1 M sodium acetate pH 5.5, 0.2 M Lithium sulfate, 5 mM DTT, 1.5% glycerol, 10-25% PEG 3350) were mixed and set up., VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.265
3LCO Inhibitor Bound to A DFG-Out structure of the Kinase Domain of CSF-1R Deposited 2010-01-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 550–695（146 aa） Fragment：Kinase Domain Chain A 742–919（178 aa） Fragment：Kinase Domain	Not recorded	LC0 3-({4-methoxy-5-[(4-methoxybenzyl)oxy]pyridin-2-yl}methoxy)-5-(1-methyl-1H-pyrazol-4-yl)pyrazin-2-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；11 mg/mL protein incubated with 4 mM inhibitor at 4C overnight followed by addition of 1 ug Arg-C (per 50 ul sample) at 22C for 24 hours, followed by addition of 0.5 uL of 5 mg/mL leupeptin, followed by mixing with equal volumes of well solution:22.5-35% PEG 4000, 0.1M Tris-HCL pH 8.5, 0.2M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.40 Å R-free 0.289
4DKD Crystal Structure of Human Interleukin-34 Bound to Human CSF-1R Deposited 2012-02-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 20–299（280 aa） Fragment：D1-D3, UNP residues 20-299	Not recorded	BMA beta-D-mannopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1M Calcium acetate, 0.1M Mes pH 6.0, 15% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.00 Å R-free 0.287
4HW7 Crystal structure of FMS kinase domain with a small molecular inhibitor, PLX647-OME Deposited 2012-11-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 542–919（378 aa） Fragment：FMS kinase domain with KID	Mutation：C667T, C830S, C907T	64M 5-[(5-methoxy-1H-pyrrolo[2,3-b]pyridin-3-yl)methyl]-N-[4-(trifluoromethyl)benzyl]pyridin-2-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；20% PEG8K, 0.2M MgCl and 0.1M Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.90 Å R-free 0.267
4HW7 Crystal structure of FMS kinase domain with a small molecular inhibitor, PLX647-OME Deposited 2012-11-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 542–919（378 aa） Fragment：FMS kinase domain with KID	Mutation：C667T, C830S, C907T	64M 5-[(5-methoxy-1H-pyrrolo[2,3-b]pyridin-3-yl)methyl]-N-[4-(trifluoromethyl)benzyl]pyridin-2-amine × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；20% PEG8K, 0.2M MgCl and 0.1M Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.90 Å R-free 0.267
4LIQ Structure of the extracellular domain of human CSF-1 receptor in complex with the Fab fragment of RG7155 Deposited 2013-07-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 2–512（511 aa） Fragment：ectodomain, UNP residues 2-512	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；25% PEG 3350, 0.2M lithium sulfate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.60 Å R-free 0.237
4R7H Crystal structure of FMS KINASE domain with a small molecular inhibitor, PLX3397 Deposited 2014-08-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 541–919（379 aa） Fragment：FMS kinase domain with KID (UNP residues 538-919)	Mutation：C667T, C830S, C907T	P31 5-[(5-chloro-1H-pyrrolo[2,3-b]pyridin-3-yl)methyl]-N-{[6-(trifluoromethyl)pyridin-3-yl]methyl}pyridin-2-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；20% PEG8K, 0.2M MGCL AND 0.1M TRIS, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.80 Å R-free 0.248
4R7H Crystal structure of FMS KINASE domain with a small molecular inhibitor, PLX3397 Deposited 2014-08-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 541–919（379 aa） Fragment：FMS kinase domain with KID (UNP residues 538-919)	Mutation：C667T, C830S, C907T	P31 5-[(5-chloro-1H-pyrrolo[2,3-b]pyridin-3-yl)methyl]-N-{[6-(trifluoromethyl)pyridin-3-yl]methyl}pyridin-2-amine × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；20% PEG8K, 0.2M MGCL AND 0.1M TRIS, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.80 Å R-free 0.248
4R7I Crystal structure of FMS kinase domain with a small molecular inhibitor, GLEEVEC Deposited 2014-08-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 541–919（379 aa） Fragment：FMS kinase domain with KID (UNP residues 538-919)	Mutation：C667T, C830S, C907T	STI 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；20% PEG8K, 0.2M MGCL AND 0.1M TRIS, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.75 Å R-free 0.236
4R7I Crystal structure of FMS kinase domain with a small molecular inhibitor, GLEEVEC Deposited 2014-08-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 541–919（379 aa） Fragment：FMS kinase domain with KID (UNP residues 538-919)	Mutation：C667T, C830S, C907T	STI 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；20% PEG8K, 0.2M MGCL AND 0.1M TRIS, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.75 Å R-free 0.236
4WRL Structure of the human CSF-1:CSF-1R complex Deposited 2014-10-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 20–296（277 aa） Fragment：UNP residues 20-296 Chain C 20–296（277 aa） Fragment：UNP residues 20-296	Mutation：N240Q Mutation：N240Q	SIA N-acetyl-alpha-neuraminic acid × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.2 M Lithium sulfate monohydrate, 0.1 M Tris pH 8.5 and 28% w/v PEG 3350	Resolution 2.80 Å R-free 0.261
4WRM Structure of the human CSF-1:CSF-1R complex Deposited 2014-10-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 20–504（485 aa） Fragment：UNP RESIDUES 20-504	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1 M NaCl, 0.1 M Tris pH 8.0 and 8% w/v PEG 20000	Resolution 6.85 Å R-free 0.359
6IG8 Crystal structure of CSF-1R kinase domain with a small molecular inhibitor, JTE-952 Deposited 2018-09-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 550–695（146 aa） Chain A 742–919（178 aa）	Mutation：S688A Mutation：S688A	MG MAGNESIUM ION × 2 GOL GLYCEROL × 1 A7O (3-{4-[(4-cyclopropylphenyl)methoxy]-3-methoxyphenyl}azetidin-1-yl)(4-{[(2S)-2,3-dihydroxypropoxy]methyl}pyridin-2-yl)methanone × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；11 mg/mL protein, 22.5-35% PEG 4000, 0.1M Tris-HCL pH 8.5, 0.2M MgCl2	Resolution 1.80 Å R-free 0.192
6N33 Crystal structure of fms kinase domain with a small molecular inhibitor, PLX5622 Deposited 2018-11-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 542–919（378 aa）	Mutation：C667T, C830S, C907T	622 6-fluoro-N-[(5-fluoro-2-methoxypyridin-3-yl)methyl]-5-[(5-methyl-1H-pyrrolo[2,3-b]pyridin-3-yl)methyl]pyridin-2-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；20% PEG8K, 0.2M MGCL2 AND 0.1M TRIS, PH 7.5	Resolution 2.25 Å R-free 0.220
6T2W Crystal structure of the CSF1R kinase domain with a dihydropurinone inhibitor (compound 4) Deposited 2019-10-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 542–919（378 aa） Fragment：kinase domain (amino acids Q542-R919) with internal deletion of amino acids 697-740	Not recorded	M9T 2-[(4-methoxy-2-methyl-phenyl)amino]-7-methyl-9-(4-oxidanylcyclohexyl)purin-8-one × 1 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；277 K；16% PEG3350, 0.15 M Ammonium Sulfate, 0.1 M PCTP pH 5.5	Resolution 1.70 Å R-free 0.187
6WXJ CSF1R signaling is a regulator of pathogenesis in progressive MS Deposited 2020-05-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 538–678（141 aa） Chain A 753–922（170 aa）	Not recorded	UF4 4-(3-{[(2S)-2-(6-methoxypyridin-3-yl)-2,3-dihydro-1,4-benzodioxin-6-yl]methyl}-3H-imidazo[4,5-b]pyridin-6-yl)-2-methylbut-3-yn-2-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；294 K；0.1 M MES, pH 6.5, 21.3% polyethylene glycol 3350 and 0.25 M ammonium sulfate	Resolution 2.62 Å R-free 0.272
7MFC Crystal structure of CSF1R in complex with vimseltinib Deposited 2021-04-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 542–919（378 aa） Fragment：Kinase domain, UNP residues 542-919 with deletion of 696-741	Mutation：C677T, C830S, C907T	Z6V Vimseltinib × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；CSF1R at 4mg/ml with 0.5mM vimseltinib: Crystallization: 100mM Tris base / HCl pH 7.71, 18% PEG 8000, 100mM MgCl2: Cryo: 20% glycerol	Resolution 2.80 Å R-free 0.256
7TNH Crystal structure of CSF1R kinase domain in complex with DP-6233 Deposited 2022-01-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 549–678（130 aa） Chain A 753–922（170 aa）	Not recorded	NA SODIUM ION × 1 CL CHLORIDE ION × 4 I9W 2,2-dimethyl-N-[(6-methyl-5-{[2-(1-methyl-1H-pyrazol-4-yl)pyridin-4-yl]oxy}pyridin-2-yl)carbamoyl]propanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；CSF1R at 10.7 mg/mL in 50 mM Tris pH 7.5, 200 mM NaCl, 5% glycerol with 5-fold excess of arylamide compound against 10% PEG 10,000, 0.1 M MES pH 6.5 and 0.1 M magnesium acetate soaked over two nights with 1 mM DP-6233 and 20% ethylene glycol as cryo	Resolution 2.70 Å R-free 0.269
8CGC Structure of CSF1R in complex with a pyrollopyrimidine (compound 23) Deposited 2023-02-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 542–919（378 aa）	Mutation：S688A	LMR (2S)-2-hydroxybutanedioic acid × 1 GOL GLYCEROL × 1 UIK [4-[4-[methyl-[(3-methylphenyl)methyl]amino]-7~{H}-pyrrolo[2,3-d]pyrimidin-6-yl]phenyl]methanol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.3 M DL-Malic acid pH 7.0, 23.0% w/v PEG 3350	Resolution 1.93 Å R-free 0.206
8JOT Crystal structure of CSF-1R kinase domain with sulfatinib Deposited 2023-06-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 542–919（378 aa）	Mutation：C137T,C300S,C377T	UKI Sulfatinib × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；19% PEG8K, 0.2 M MgCl and 0.1 M Tris, pH 7.5	Resolution 1.69 Å R-free 0.207

25 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CSF1R_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–142； UniProt 538–678 Author chain A； PDBConstruct 185–333； UniProt 774–922

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8w1l
Deposition date deposition_date	2024-02-16
最后修订 last_revision	2024-05-29
Structure title title	Structure of CSF1R kinase domain in complex with Cpd 32
Keywords keywords	Inhibitor complex, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	19.83 Å
Radius of gyration Rg (electron density) rg_electron	18.83 Å
Forward intensity I(0) i0	16314100.00
Molecular weight molecular_weight	31045.0 kDa
Excluded volume excluded_volume	39010 Å³
Envelope volume envelope_volume	45048 Å³
Hydration-shell volume shell_volume	19918 Å³
Envelope diameter envelope_diameter	65.8 Å
Shell Rg shell_rg	25.22 Å
Envelope Rg envelope_rg	18.98 Å
Shape Rg shape_rg	18.84 Å
Total Rg total_rg	19.70 Å
Total atoms total_atoms	2193
Residues n_residues	282
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	64.3 Å
Rg (real space) rg_real	19.73 Å
Rg uncertainty (real space) rg_real_error	0.41 Å
I(0) (real space) i0_real	1.6310e+07
I(0) uncertainty (real space) i0_real_error	1.8270e+05
Rg (reciprocal space) rg_reciprocal	19.75 Å
I(0) (reciprocal space) i0_reciprocal	16310000.0000
Solution quality estimate total_estimate	0.8080
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	57.9 Å
Skewness Skewness skewness	0.238
Kurtosis Kurtosis kurtosis	-0.364
Angular range angular_range	— – 0.4000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4861000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.833; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Macrophage colony-stimulating factor 1 receptor,CSF1R
Molecular weight formula_weight	37850.3 kDa
EC 编号 ec_number	2.7.10.1
Mutation mutation	residues 679-752 replaced by residues 577-597 of FGFR1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2270

GYKYKQKPKYQVRWKIIESYEGNSYTFIDPTQLPYNEKWEFPRNNLQFGKTLGAGAFGKVVEATAFGLGKEDAVLKVAVKMLKSTAHADEKEALMSELKIMSHLGQHENIVNLLGACTHGGPVLVITEYCCYGDLLNFLRRKRPPGLEYSYNPSHNPEEQLSSRDLLHFSSQVAQGMAFLASKNCIHRDVAARNVLLTNGHVAKIGDFGLARDIMNDSNYIVKGNARLPVKWMAPESIFDCVYTVQSDVWSYGILLWEIFSLGLNPYPGILVNSKFYKLVKDGYQMAQPAFAPKNIYSIMQACWALEPTHRPTFQQICSFLQEQAQEDRRERD

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	;[3-({3-methoxy-4-[(6-methoxypyridin-3-yl)methoxy]phenyl}methyl)-3H-imidazo[4,5-b]pyridin-6-yl](2-oxa-6-azaspiro[3.3]heptan-6-yl)methanone ;
Molecular weight formula_weight	501.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	77

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8. Citations (1)

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Unit-cell length a length_a	81.020 Å
Unit-cell length b length_b	81.020 Å
Unit-cell length c length_c	146.060 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	9

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	trigonal

Resolution resolution	2.260 Å
Low-resolution limit resolution_low	32.390 Å
R factor r_factor	0.1776
R_work r_work	0.1723
R_free r_free	0.2255

fit	/app/data/saxs_computation/w1/8w1l/8w1l.fit
pddf	/app/data/pr_computation/w1/8w1l/8w1l.pr.out
profile	/app/data/saxs_computation/w1/8w1l/8w1l.dat