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. 蛋白身份与相关结构 Protein Identity & Related Structures

Macrophage colony-stimulating factor 1 receptor,CSF1R

Homo sapiens

当前结构中的状态

Assembly	聚集状态	构建体	突变与修饰	配体、离子与共同组分	实验方法与环境	结构质量
1	蛋白单体单体蛋白 × 1 PDB 声明：monomeric（1）与蛋白拷贝数一致	链 A； UniProt 538–678 链 A； UniProt 774–922	突变：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结晶条件：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	分辨率 2.26 Å R-free 0.226

数据库中的同蛋白其他状态

以下每一行都是同一 UniProt 蛋白在另一个 PDB 条目中的 biological assembly， “相对当前条目”直接指出证据层面的不同；没有差异标签表示当前已读取字段一致。

其他 PDB	相对当前条目 8W1L	Assembly / 聚集状态	构建体	突变与修饰	配体、离子与非聚合物	实验方法与环境	结构质量
2I0V c-FMS tyrosine kinase in complex with a quinolone inhibitor 提交 2006-08-11	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 538–678（141 aa）片段：Kinase Domain 链 A 753–922（170 aa）片段：Kinase Domain	未记录	SO4 SULFATE ION × 1 6C3 6-CHLORO-3-(3-METHYLISOXAZOL-5-YL)-4-PHENYLQUINOLIN-2(1H)-ONE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 5.2；298 K；PEG 3350, sodium acetate, Li2SO4, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	分辨率 2.80 Å R-free 0.296
2I0Y cFMS tyrosine kinase (FGF KID) in complex with an arylamide inhibitor 提交 2006-08-11	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 538–678（141 aa）片段：Kinase Domain 链 A 753–922（170 aa）片段：Kinase Domain	未记录	5CN 5-CYANO-FURAN-2-CARBOXYLIC ACID [5-HYDROXYMETHYL-2-(4-METHYL-PIPERIDIN-1-YL)-PHENYL]-AMIDE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 5.2；298 K；PEG 3350, sodium acetate, Li2SO4, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	分辨率 1.90 Å R-free 0.263
2I1M cFMS tyrosine kinase (tie2 KID) in complex with an arylamide inhibitor 提交 2006-08-14	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 538–678（141 aa）片段：Kinase Domain 链 A 753–922（170 aa）片段：Kinase Domain	未记录	5CN 5-CYANO-FURAN-2-CARBOXYLIC ACID [5-HYDROXYMETHYL-2-(4-METHYL-PIPERIDIN-1-YL)-PHENYL]-AMIDE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 5.2；298 K；PEG 3350, sodium acetate, Li2SO4, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	分辨率 1.80 Å R-free 0.282
2OGV Crystal Structure of the Autoinhibited Human c-Fms Kinase Domain 提交 2007-01-09	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 543–681（139 aa）片段：Kinase domain: Residues 543-918 链 A 741–918（178 aa）片段：Kinase domain: Residues 543-918	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 2.70 Å R-free 0.279
3BEA cFMS tyrosine kinase (tie2 KID) in complex with a pyrimidinopyridone inhibitor 提交 2007-11-16	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 信息不足单体；蛋白 × 1 PDB 声明：monomeric	链 A 538–678（141 aa）链 A 753–922（170 aa）	突变：A695L 突变：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结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 5.2；298 K；PEG 3350, sodium acetate, Li2SO4, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	分辨率 2.02 Å R-free 0.230
3DPK cFMS tyrosine kinase in complex with a pyridopyrimidinone inhibitor 提交 2008-07-08	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 信息不足单体；蛋白 × 1 PDB 声明：monomeric	链 A 538–678（141 aa）片段：KINASE DOMAIN 链 A 753–922（170 aa）片段：KINASE DOMAIN	突变：Native kinase insert domain replaced by FGF receptor kinase insert domain 突变：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结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 5.2；298 K；PEG 3350, SODIUM ACETATE, LI2SO4, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	分辨率 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 提交 2009-11-18	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 信息不足单体；蛋白 × 1 PDB 声明：monomeric	链 A 538–678（141 aa）片段：UNP residues 538-678, 753-922 链 A 753–922（170 aa）片段：UNP residues 538-678, 753-922	突变：C584S 突变：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结晶条件 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	分辨率 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 提交 2009-11-18	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 信息不足单体；蛋白 × 1 PDB 声明：monomeric	链 A 538–678（141 aa）片段：UNP residues 538-678, 753-922 链 A 753–922（170 aa）片段：UNP residues 538-678, 753-922	突变：C584S 突变：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结晶条件 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	分辨率 2.40 Å R-free 0.264
3LCD Inhibitor Bound to A DFG-In structure of the Kinase Domain of CSF-1R 提交 2010-01-10	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 538–681（144 aa）片段：Kinase Domain 链 A 741–919（179 aa）片段：Kinase Domain	突变：KID domain replaced by linker 突变：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结晶条件 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	分辨率 2.50 Å R-free 0.265
3LCO Inhibitor Bound to A DFG-Out structure of the Kinase Domain of CSF-1R 提交 2010-01-11	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 550–695（146 aa）片段：Kinase Domain 链 A 742–919（178 aa）片段：Kinase Domain	未记录	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结晶条件 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	分辨率 3.40 Å R-free 0.289
4DKD Crystal Structure of Human Interleukin-34 Bound to Human CSF-1R 提交 2012-02-03	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合异源复合物；蛋白 × 3 PDB 声明：trimeric	链 C 20–299（280 aa）片段：D1-D3, UNP residues 20-299	未记录	BMA beta-D-mannopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 3.00 Å R-free 0.287
4HW7 Crystal structure of FMS kinase domain with a small molecular inhibitor, PLX647-OME 提交 2012-11-07	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 542–919（378 aa）片段：FMS kinase domain with KID	突变：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结晶条件 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	分辨率 2.90 Å R-free 0.267
4HW7 Crystal structure of FMS kinase domain with a small molecular inhibitor, PLX647-OME 提交 2012-11-07	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白同源多聚体同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 542–919（378 aa）片段：FMS kinase domain with KID	突变：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结晶条件 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	分辨率 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 提交 2013-07-03	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合异源复合物；蛋白 × 3 PDB 声明：trimeric	链 E 2–512（511 aa）片段：ectodomain, UNP residues 2-512	未记录	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 2.60 Å R-free 0.237
4R7H Crystal structure of FMS KINASE domain with a small molecular inhibitor, PLX3397 提交 2014-08-27	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 541–919（379 aa）片段：FMS kinase domain with KID (UNP residues 538-919)	突变：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结晶条件 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	分辨率 2.80 Å R-free 0.248
4R7H Crystal structure of FMS KINASE domain with a small molecular inhibitor, PLX3397 提交 2014-08-27	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白同源多聚体同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 541–919（379 aa）片段：FMS kinase domain with KID (UNP residues 538-919)	突变：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结晶条件 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	分辨率 2.80 Å R-free 0.248
4R7I Crystal structure of FMS kinase domain with a small molecular inhibitor, GLEEVEC 提交 2014-08-27	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 541–919（379 aa）片段：FMS kinase domain with KID (UNP residues 538-919)	突变：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结晶条件 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	分辨率 2.75 Å R-free 0.236
4R7I Crystal structure of FMS kinase domain with a small molecular inhibitor, GLEEVEC 提交 2014-08-27	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白同源多聚体同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 541–919（379 aa）片段：FMS kinase domain with KID (UNP residues 538-919)	突变：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结晶条件 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	分辨率 2.75 Å R-free 0.236
4WRL Structure of the human CSF-1:CSF-1R complex 提交 2014-10-24	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合异源复合物；蛋白 × 4 PDB 声明：tetrameric	链 A 20–296（277 aa）片段：UNP residues 20-296 链 C 20–296（277 aa）片段：UNP residues 20-296	突变：N240Q 突变：N240Q	SIA N-acetyl-alpha-neuraminic acid × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 2.80 Å R-free 0.261
4WRM Structure of the human CSF-1:CSF-1R complex 提交 2014-10-24	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 20–504（485 aa）片段：UNP RESIDUES 20-504	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 6.85 Å R-free 0.359
6IG8 Crystal structure of CSF-1R kinase domain with a small molecular inhibitor, JTE-952 提交 2018-09-25	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 550–695（146 aa）链 A 742–919（178 aa）	突变：S688A 突变：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结晶条件 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	分辨率 1.80 Å R-free 0.192
6N33 Crystal structure of fms kinase domain with a small molecular inhibitor, PLX5622 提交 2018-11-14	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 542–919（378 aa）	突变：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结晶条件 VAPOR DIFFUSION, SITTING DROP；277 K；20% PEG8K, 0.2M MGCL2 AND 0.1M TRIS, PH 7.5	分辨率 2.25 Å R-free 0.220
6T2W Crystal structure of the CSF1R kinase domain with a dihydropurinone inhibitor (compound 4) 提交 2019-10-09	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 542–919（378 aa）片段：kinase domain (amino acids Q542-R919) with internal deletion of amino acids 697-740	未记录	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结晶条件 VAPOR DIFFUSION；pH 5.5；277 K；16% PEG3350, 0.15 M Ammonium Sulfate, 0.1 M PCTP pH 5.5	分辨率 1.70 Å R-free 0.187
6WXJ CSF1R signaling is a regulator of pathogenesis in progressive MS 提交 2020-05-10	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 538–678（141 aa）链 A 753–922（170 aa）	未记录	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结晶条件 VAPOR DIFFUSION；294 K；0.1 M MES, pH 6.5, 21.3% polyethylene glycol 3350 and 0.25 M ammonium sulfate	分辨率 2.62 Å R-free 0.272
7MFC Crystal structure of CSF1R in complex with vimseltinib 提交 2021-04-08	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 542–919（378 aa）片段：Kinase domain, UNP residues 542-919 with deletion of 696-741	突变：C677T, C830S, C907T	Z6V Vimseltinib × 1	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 2.80 Å R-free 0.256
7TNH Crystal structure of CSF1R kinase domain in complex with DP-6233 提交 2022-01-21	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 信息不足单体；蛋白 × 1 PDB 声明：monomeric	链 A 549–678（130 aa）链 A 753–922（170 aa）	未记录	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结晶条件 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	分辨率 2.70 Å R-free 0.269
8CGC Structure of CSF1R in complex with a pyrollopyrimidine (compound 23) 提交 2023-02-03	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 542–919（378 aa）	突变：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结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.3 M DL-Malic acid pH 7.0, 23.0% w/v PEG 3350	分辨率 1.93 Å R-free 0.206
8JOT Crystal structure of CSF-1R kinase domain with sulfatinib 提交 2023-06-08	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 542–919（378 aa）	突变：C137T,C300S,C377T	UKI Sulfatinib × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；277.15 K；19% PEG8K, 0.2 M MgCl and 0.1 M Tris, pH 7.5	分辨率 1.69 Å R-free 0.207

共 25 个其他 PDB 条目、28 个 assembly。打开独立比较页并筛选聚集状态

查看构建体与数据证据

UniProt名称	CSF1R_HUMAN
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 2–142； UniProt 538–678 作者链 A； PDB构建体 185–333； UniProt 774–922

页面优先展示蛋白身份、当前 assembly、共同组分、聚集状态和跨 PDB 结构链接。链映射与序列区间收在“数据证据”中；数据库内部编号、导入时间和 assembly 操作表达式仅用于维护，因此不在读者页面展示。

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

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

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2. 结构基本信息 2. Structure Basics

条目编号 entry_id	8w1l
沉积日期 deposition_date	2024-02-16
最后修订 last_revision	2024-05-29
结构标题 title	Structure of CSF1R kinase domain in complex with Cpd 32
关键词 keywords	Inhibitor complex, TRANSFERASE; TRANSFERASE
实验方法 method	X-RAY DIFFRACTION

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3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	19.83 Å
回转半径 Rg (电子) rg_electron	18.83 Å
零角强度 I(0) i0	16314100.00
分子量 molecular_weight	31045.0 kDa
排除体积 excluded_volume	39010 Å³
包络体积 envelope_volume	45048 Å³
水化壳体积 shell_volume	19918 Å³
包络直径 envelope_diameter	65.8 Å
壳层 Rg shell_rg	25.22 Å
包络 Rg envelope_rg	18.98 Å
形状 Rg shape_rg	18.84 Å
总 Rg total_rg	19.70 Å
总原子数 total_atoms	2193
残基数 n_residues	282
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	64.3 Å
Rg (实空间) rg_real	19.73 Å
Rg 误差 (实空间) rg_real_error	0.41 Å
I(0) (实空间) i0_real	1.6310e+07
I(0) 误差 (实空间) i0_real_error	1.8270e+05
Rg (倒空间) rg_reciprocal	19.75 Å
I(0) (倒空间) i0_reciprocal	16310000.0000
解质量估计 total_estimate	0.8080
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	57.9 Å
偏度 Skewness skewness	0.238
峰度 Kurtosis kurtosis	-0.364
角度范围 angular_range	— – 0.4000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	4861000.0000
实空间数据点数 n_real_points	72
GNOM 版本 gnom_version	4.1.3
质量判据 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. 晶体学与实验 5. Crystallography & Experiment

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6. 实体与聚合物信息 Entities & Polymers (5)

实体 1 Entity 1 polymer

描述 description	Macrophage colony-stimulating factor 1 receptor,CSF1R
分子量 formula_weight	37850.3 kDa
EC 编号 ec_number	2.7.10.1
突变 mutation	residues 679-752 replaced by residues 577-597 of FGFR1
来源方法 src_method	man
拷贝数 entity_count	1

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	2270

GYKYKQKPKYQVRWKIIESYEGNSYTFIDPTQLPYNEKWEFPRNNLQFGKTLGAGAFGKVVEATAFGLGKEDAVLKVAVKMLKSTAHADEKEALMSELKIMSHLGQHENIVNLLGACTHGGPVLVITEYCCYGDLLNFLRRKRPPGLEYSYNPSHNPEEQLSSRDLLHFSSQVAQGMAFLASKNCIHRDVAARNVLLTNGHVAKIGDFGLARDIMNDSNYIVKGNARLPVKWMAPESIFDCVYTVQSDVWSYGILLWEIFSLGLNPYPGILVNSKFYKLVKDGYQMAQPAFAPKNIYSIMQACWALEPTHRPTFQQICSFLQEQAQEDRRERD

来源 Source

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

实体 2 Entity 2 non-polymer

描述 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 ;
分子量 formula_weight	501.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

实体 3 Entity 3 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

实体 4 Entity 4 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

实体 5 Entity 5 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	77

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8. 引用文献 (1)

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晶胞边长 a length_a	81.020 Å
晶胞边长 b length_b	81.020 Å
晶胞边长 c length_c	146.060 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	120.00 °
晶胞分子数 Z z_pdb	9

空间群 space_group	H 3
空间群编号 int_tables_number	146
晶系 crystal_system	trigonal

分辨率 resolution	2.260 Å
最低分辨率 resolution_low	32.390 Å
R 因子 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