6d20

Crystal structure of Tyrosine-protein kinase receptor in complex with 5-(4-fluorophenyl)thieno[2,3-d]pyrimidin-4(3H)-one and 5-{[2,4-dichloro-5-(pyridin-2-yl)benzene-1-carbonyl]amino}-N-(2-hydroxy-2-methylpropyl)-1-phenyl-1H-pyrazole-3-carboxamide Inhibitors

Method: X-RAY DIFFRACTION D_max: 72.4 Å Quality: REASONABLE

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

High affinity nerve growth factor receptor

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 381–698	未记录	FQD 5-(4-fluorophenyl)thieno[2,3-d]pyrimidin-4(3H)-one × 1 FQG 5-{[2,4-dichloro-5-(pyridin-2-yl)benzene-1-carbonyl]amino}-N-(2-hydroxy-2-methylpropyl)-1-phenyl-1H-pyrazole-3-carboxamide × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 8；294 K；Well volume: 30.0 uL Well Ingredients: Polymer: 10.0 %w/v (6.0 uL of stock 50.0 %w/v) PEG 3350 Buffer: 16.0 %v/v (4.8 uL of stock 100.0 %v/v) tacsimate (pH 8.00) Organic (non-volatile): 10.0 %v/v (3.0 uL of stock 100.0 %v/v) Ethylene glycol Additive: 0.025 M (1.5 uL of stock 0.5 M) TCEP hydrochloride Plate setup temperature: 13 C Plate incubation temperature: 21 C Drop volume from well: 0.2 uL Drop protein volume: 0.4 uL Protein: 6.30 mg/mL (0.17 mM) Compound1: 1.00 mM (to aid crystallization). Compound23 (allostric inhibitor): 1.3ul 50mM compound23 DMSO stock in 133ul protein (0.50 mM)	分辨率 1.94 Å R-free 0.207

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 6D20	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
1HE7 Human Nerve growth factor receptor TrkA 提交 2000-11-20	构建体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 蛋白同源多聚体同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 282–413（132 aa）片段：LIGAND BINDING DOMAIN, SPANS RESIDUES 285-380	未记录	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray结晶条件 pH 4.7；10 MG/ML PROTEIN + 0.1-0.3M NACL, 0.1M NA-CITRATE, PH 4.6 - 4.8	分辨率 2.00 Å R-free 0.276
1SHC SHC PTB DOMAIN COMPLEXED WITH A TRKA RECEPTOR PHOSPHOPEPTIDE, NMR, MINIMIZED AVERAGE STRUCTURE 提交 1996-03-27	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验方法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 B 489–500（12 aa）	非标准单体：是（mmCIF未提供具体位点）	未记录非水小分子	SOLUTION NMR mmCIF 未提供已读取条件	分辨率未提供
1WWA NGF BINDING DOMAIN OF HUMAN TRKA RECEPTOR 提交 1999-04-29	构建体不同配体/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 X 278–408（131 aa）片段：LIGAND BINDING DOMAIN	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 pH 6.5；pH 6.5	分辨率 2.50 Å R-free 0.258
1WWA NGF BINDING DOMAIN OF HUMAN TRKA RECEPTOR 提交 1999-04-29	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 Y 278–408（131 aa）片段：LIGAND BINDING DOMAIN	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 pH 6.5；pH 6.5	分辨率 2.50 Å R-free 0.258
1WWA NGF BINDING DOMAIN OF HUMAN TRKA RECEPTOR 提交 1999-04-29	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 3 蛋白同源多聚体同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 X 278–408（131 aa）片段：LIGAND BINDING DOMAIN 链 Y 278–408（131 aa）片段：LIGAND BINDING DOMAIN	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 pH 6.5；pH 6.5	分辨率 2.50 Å R-free 0.258
1WWW NGF IN COMPLEX WITH DOMAIN 5 OF THE TRKA RECEPTOR 提交 1999-03-12	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 × 4 PDB 声明：tetrameric	链 X 282–382（101 aa）片段：DOMAIN 5 链 Y 282–382（101 aa）片段：DOMAIN 5	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 pH 5；pH 5.0	分辨率 2.20 Å R-free 0.266
2IFG Structure of the extracellular segment of human TRKA in complex with nerve growth factor 提交 2006-09-20	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 36–382（347 aa）链 B 36–382（347 aa）	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 pH 7.5；PEG, GLYCINE, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, pH 7.50	分辨率 3.40 Å R-free 0.331
2N90 TrkA transmembrane domain NMR structure in DPC micelles 提交 2015-10-29	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 410–447（38 aa）链 B 410–447（38 aa）	未记录	未记录非水小分子	SOLUTION NMR NMR测量条件 pH 5.9；318 K；压力 ambient NMR样品组成 1 mM [U-100% 13C; U-100% 15N] protein, 1 mM protein, 40 mM [U-100% 2H] DPC, 20 mM potassium phosphate, 95% H2O/5% D2O \| 95% H2O/5% D2O	分辨率未提供
4AOJ Human TrkA in complex with the inhibitor AZ-23 提交 2012-03-28	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 蛋白同源多聚体同源多聚体；蛋白 × 12 PDB 声明：dodecameric	链 A 473–796（324 aa）片段：KINASE DOMAIN, RESIDUES 473-796 链 B 473–796（324 aa）片段：KINASE DOMAIN, RESIDUES 473-796 链 C 473–796（324 aa）片段：KINASE DOMAIN, RESIDUES 473-796	未记录	V4Z 5-chloranyl-N2-[(1S)-1-(5-fluoranylpyridin-2-yl)ethyl]-N4-(3-propan-2-yloxy-1H-pyrazol-5-yl)pyrimidine-2,4-diamine × 12 ZN ZINC ION × 24	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 8；HANGING DROP METHOD. 1 UL TRKA AT 10 MG/ML IN 10 MG/ML IN 20 MM TRIS PH 8.5, 0.1% CHAPS, 1MM TCEP, 8.7% GLYCEROL MIXED WITH 1 UL MOTHER LIQUOR CONTAINING 35% W/V GLYCEROL, 140 MM NA/K TARTRATE, 100 MM HEPES PH 8.0 SUPPLEMENTED WITH 40 MM ZINC CHLORIDE.	分辨率 2.75 Å R-free 0.242
4CRP Solution structure of a TrkAIg2 domain construct for use in drug discovery 提交 2014-02-28	构建体不同突变/修饰不同配体/离子不同实验方法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 282–383（102 aa）片段：EXTRACELLULAR NGF BINDING DOMAIN, RESIDUES 270-383	突变：YES	未记录非水小分子	SOLUTION NMR NMR测量条件 pH 6.9；293 K；离子强度（mmCIF原始值）10；压力 1.0 NMR样品组成 90% H2O, 10% D2O	分辨率未提供
4F0I Crystal structure of apo TrkA 提交 2012-05-04	构建体不同配体/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 498–796（299 aa）片段：UNP residues 498-796	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 5.6；277 K；0.1 M Na citrate, pH 5.6, 14% PEG 3350, 5% 2-Propanol , VAPOR DIFFUSION, SITTING DROP, temperature 277K	分辨率 2.30 Å R-free 0.241
4F0I Crystal structure of apo TrkA 提交 2012-05-04	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 498–796（299 aa）片段：UNP residues 498-796	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 5.6；277 K；0.1 M Na citrate, pH 5.6, 14% PEG 3350, 5% 2-Propanol , VAPOR DIFFUSION, SITTING DROP, temperature 277K	分辨率 2.30 Å R-free 0.241
4GT5 Crystal structure of the inactive TrkA kinase domain 提交 2012-08-28	构建体不同配体/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 498–796（299 aa）片段：receptor tyrosine kinase (UNP residues 498-796)	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；294.15 K；1.5 M sodium chloride, 0.1 M MES, pH 6.5, 0.2 M sodium/potassium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 294.15K	分辨率 2.40 Å R-free 0.248
4PMM The structure of TrkA kinase bound to the inhibitor N-(3-cyclopropyl-1-phenyl-1H-pyrazol-5-yl)-2-{4-[3-methoxy-4-(4-methyl-1H-imidazol-1-yl)phenyl]-1H-1,2,3-triazol-1-yl}acetamide 提交 2014-05-22	构建体不同配体/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 501–787（287 aa）片段：kinase domain (UNP residues 501-787)	未记录	31V N-(3-cyclopropyl-1-phenyl-1H-pyrazol-5-yl)-2-{4-[3-methoxy-4-(4-methyl-1H-imidazol-1-yl)phenyl]-1H-1,2,3-triazol-1-yl}acetamide × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 1 ACT ACETATE ION × 3	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M Bis-Tris, 2.3M AmmoniumAcetate	分辨率 2.00 Å R-free 0.199
4PMP The structure of TrkA kinase bound to the inhibitor 1-cyclopropyl-1-[3-(1,3-thiazol-2-yl)benzyl]-3-[4-(trifluoromethoxy)phenyl]urea 提交 2014-05-22	构建体不同配体/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 501–787（287 aa）片段：kinase domain (UNP residues 501-787)	未记录	31W 1-cyclopropyl-1-[3-(1,3-thiazol-2-yl)benzyl]-3-[4-(trifluoromethoxy)phenyl]urea × 1 CL CHLORIDE ION × 1 ACT ACETATE ION × 3	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M Bis-Tris, 2.3M AmmoniumAcetate	分辨率 1.80 Å R-free 0.185
4PMS The structure of TrkA kinase bound to the inhibitor 4-naphthalen-1-yl-1-[(5-phenyl-1,2,4-oxadiazol-3-yl)methyl]-1H-pyrrolo[3,2-c]pyridine-2-carboxylic acid 提交 2014-05-22	构建体不同配体/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 501–787（287 aa）片段：kinase domain (UNP residues 501-787)	未记录	31X 4-(naphthalen-1-yl)-1-[(5-phenyl-1,2,4-oxadiazol-3-yl)methyl]-1H-pyrrolo[3,2-c]pyridine-2-carboxylic acid × 1 CL CHLORIDE ION × 1 ACT ACETATE ION × 3	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M Bis-Tris, 2.3M AmmoniumAcetate	分辨率 2.80 Å R-free 0.240
4PMT The structure of TrkA kinase bound to the inhibitor N~4~-(4-morpholin-4-ylphenyl)-N~6~-(pyridin-3-ylmethyl)pyrido[3,2-d]pyrimidine-4,6-diamine 提交 2014-05-22	构建体不同配体/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 501–787（287 aa）片段：kinase domain (UNP residues 501-787)	未记录	31Y N~4~-[4-(morpholin-4-yl)phenyl]-N~6~-(pyridin-3-ylmethyl)pyrido[3,2-d]pyrimidine-4,6-diamine × 1 CL CHLORIDE ION × 1 ACT ACETATE ION × 3	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M Bis-Tris, 2.3M AmmoniumAcetate	分辨率 2.10 Å R-free 0.209
4YNE (R)-2-Phenylpyrrolidine Substitute Imidazopyridazines: a New Class of Potent and Selective Pan-TRK Inhibitors 提交 2015-03-09	构建体不同配体/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 502–796（295 aa）	未记录	4EK 6-[(2R)-2-(3-fluorophenyl)pyrrolidin-1-yl]-3-(pyridin-2-yl)imidazo[1,2-b]pyridazine × 1 SO4 SULFATE ION × 5 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；0.8M (NH4)2SO4, 0.1M Citrate pH 5.0	分辨率 2.02 Å R-free 0.216
4YPS (R)-2-Phenylpyrrolidine Substitute Imidazopyridazines: a New Class of Potent and Selective Pan-TRK Inhibitors 提交 2015-03-13	构建体不同配体/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 502–796（295 aa）	未记录	4F6 4-{6-[(3R)-3-(3-fluorophenyl)morpholin-4-yl]imidazo[1,2-b]pyridazin-3-yl}benzonitrile × 1 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；0.8M (NH4)2SO4, 0.1M Citrate pH 5.0	分辨率 2.10 Å R-free 0.257
5H3Q Crystal Structure of TrkA kinase with ligand 提交 2016-10-26	构建体不同配体/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 473–796（324 aa）	未记录	7HF 1-[(3S,4R)-4-[3,4-bis(fluoranyl)phenyl]-1-(2-methoxyethyl)pyrrolidin-3-yl]-3-(5-ethoxy-4-methyl-2-phenyl-pyrazol-3-yl)urea × 1 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；1.2M Sodium Tartrate, 100mM Tris-HCl pH 8.5, 5 mM DTT	分辨率 2.10 Å R-free 0.215
5I8A TrkA with (6~{R})-3-methylsulfanyl-6-phenyl-1-(1~{H}-pyrazol-3-yl)-6,7-dihydro-5~{H}-thieno[3,4-c]pyridin-4-one 提交 2016-02-18	构建体不同配体/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 400–689（290 aa）片段：catalytic domain, UNP residues 400-689	未记录	69C (6R)-3-(methylsulfanyl)-6-phenyl-1-(1H-pyrazol-3-yl)-6,7-dihydrothieno[3,4-c]pyridin-4(5H)-one × 1 CL CHLORIDE ION × 1 ACT ACETATE ION × 3	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1M Bis-Tris pH 6.5, 2.3M Ammonium Acetate	分辨率 2.33 Å R-free 0.209
5JFS Crystal structure of TrkA in complex with PF-00593174 提交 2016-04-19	构建体不同配体/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 404–698（295 aa）	未记录	6K0 N-{4-[4-amino-7-(propan-2-yl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonyl]pyridin-2-yl}-N'-(2,4-difluorophenyl)urea × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；277 K；protein was concentrated to 10mg/ml. Crystals of complexes were grown using the hanging drop vapour diffusion method from 0.1M HEPES pH7.5, 0.1M MgCl2 and 10% EtOH at 4C	分辨率 2.07 Å R-free 0.191
5JFV Crystal structure of TrkA in complex with PF-05206283 提交 2016-04-19	构建体不同配体/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 404–698（295 aa）	未记录	6K1 N-{5-[4-amino-7-(propan-2-yl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonyl]pyridin-3-yl}-2-(4-chlorophenyl)acetamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；277 K；protein was concentrated to 10mg/ml. Crystals of complexes were grown using the hanging drop vapour diffusion method from 0.1M HEPES pH7.5, 0.1M MgCl2 and 10% EtOH at 4C	分辨率 1.59 Å R-free 0.192
5JFW Crystal structure of TrkA in complex with PF-05247452 提交 2016-04-19	构建体不同配体/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 404–698（295 aa）	未记录	6K2 2-(4-cyanophenyl)-N-{5-[7-(propan-2-yl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonyl]pyridin-3-yl}acetamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；277 K；protein was concentrated to 10mg/ml. Crystals of complexes were grown using the hanging drop vapour diffusion method from 0.1M HEPES pH7.5, 0.1M MgCl2 and 10% EtOH at 4C	分辨率 1.52 Å R-free 0.209
5JFX Crystal structure of TrkA in complex with PF-06273340 提交 2016-04-19	构建体不同配体/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 404–698（295 aa）	未记录	6K4 N-{5-[2-amino-7-(1-hydroxy-2-methylpropan-2-yl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonyl]pyridin-3-yl}-2-(5-chloropyridin-2-yl)acetamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；277 K；protein was concentrated to 10mg/ml. Crystals of complexes were grown using the hanging drop vapour diffusion method from 0.1M HEPES pH7.5, 0.1M MgCl2 and 10% EtOH at 4C	分辨率 1.63 Å R-free 0.232
5KMI TrkA JM-kinase with 1-(9{H}-fluoren-9-yl)-3-(2-methyl-4-phenyl-pyrimidin-5-yl)urea 提交 2016-06-27	构建体不同配体/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 376–698（323 aa）片段：catalytic domain with juxtamembrane region, UNP residues 376-698	未记录	6UE 1-(9~{H}-fluoren-9-yl)-3-(2-methyl-4-phenyl-pyrimidin-5-yl)urea × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；50mM MES pH 6.5, 150 mM NaCl, 5mM TCEP, 0.1% beta-OctylGlucoside	分辨率 1.87 Å R-free 0.247
5KMJ TrkA JM-kinase with {N}-(2-pyridylmethyl)-2-[2-(2-thienyl)indol-1-yl]acetamide 提交 2016-06-27	构建体不同配体/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 376–698（323 aa）片段：catalytic domain with juxtamembrane region, UNP residues 376-698	未记录	6UF ~{N}-(pyridin-2-ylmethyl)-2-(2-thiophen-2-ylindol-1-yl)ethanamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；50mM MES pH 6.5, 150 mM NaCl, 5mM TCEP, 0.1% beta-OctylGlucoside	分辨率 2.04 Å R-free 0.226
5KMK TrkA JM-kinase with 2-fluoro-{N}-[2-(4-fluorophenyl)-6-methyl-3-pyridyl]-4-(trifluoromethyl)benzamide 提交 2016-06-27	构建体不同配体/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 376–698（323 aa）片段：catalytic domain with juxtamembrane region, UNP residues 376-698	未记录	6UG 2-fluoranyl-~{N}-[2-(4-fluorophenyl)-6-methyl-pyridin-3-yl]-4-(trifluoromethyl)benzamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；50mM MES pH 6.5, 150 mM NaCl, 5mM TCEP, 0.1% beta-OctylGlucoside	分辨率 2.24 Å R-free 0.281
5KML TrkA JM-kinase with 1-(5-methyl-3-phenyl-1,2-oxazol-4-yl)-3-[[2-(trifluoromethyl)phenyl]methyl]urea 提交 2016-06-27	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 376–698（323 aa）片段：catalytic domain with juxtamembrane region, UNP residues 376-698	非标准单体：是（mmCIF未提供具体位点）	6UH 1-(5-methyl-3-phenyl-1,2-oxazol-4-yl)-3-[[2-(trifluoromethyl)phenyl]methyl]urea × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；50mM MES pH 6.5, 150 mM NaCl, 5mM TCEP, 0.1% beta-OctylGlucoside	分辨率 2.01 Å R-free 0.232
5KMM TrkA JM-kinase with 1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-(1-naphthyl)urea 提交 2016-06-27	构建体不同配体/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 376–698（323 aa）片段：catalytic domain with juxtamembrane region, UNP residues 376-698	未记录	6UJ 1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-naphthalen-1-yl-urea × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；50mM MES pH 6.5, 150 mM NaCl, 5mM TCEP, 0.1% beta-OctylGlucoside	分辨率 2.12 Å R-free 0.264
5KMN TrkA JM-kinase with 1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-[[2-(trifluoromethyl)phenyl]methyl]urea 提交 2016-06-27	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 376–698（323 aa）片段：catalytic domain with juxtamembrane region, UNP residues 376-698	非标准单体：是（mmCIF未提供具体位点）	6UK 1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-[[2-(trifluoromethyl)phenyl]methyl]urea × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；50mM MES pH 6.5, 150 mM NaCl, 5mM TCEP, 0.1% beta-OctylGlucoside	分辨率 2.14 Å R-free 0.222
5KMO TrkA JM-kinase with 1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-(2-pyridyl)urea 提交 2016-06-27	构建体不同配体/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 376–698（323 aa）片段：catalytic domain with juxtamembrane region, UNP resdiues 376-698	未记录	6UM 1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-pyridin-2-yl-urea × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；50mM MES pH 6.5, 150 mM NaCl, 5mM TCEP, 0.1% beta-OctylGlucoside	分辨率 2.67 Å R-free 0.243
5KVT THE STRUCTURE OF TRKA KINASE DOMAIN BOUND TO THE INHIBITOR ENTRECTINIB 提交 2016-07-15	构建体不同配体/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 501–787（287 aa）片段：kinase domain (UNP residues 501-787)	未记录	YMX Entrectinib × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；pH 6.5；277 K；VAPOR DIFFUSION, HANGING DROP, WELL SOLUTION: 0.1M BIS-TRIS, PH6.5, 2.6-3.0M AMMONIUMACETATE TEMPERATURE 277K	分辨率 2.45 Å R-free 0.239
5WR7 Crystal structure of Trk-A complexed with a selective inhibitor CH7057288 提交 2016-11-30	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 489–792（304 aa）片段：KINASE DOMAIN, UNP residues 489-792	非标准单体：是（mmCIF未提供具体位点）	RCH N-tert-butyl-2-[2-[6,6-dimethyl-8-(methylsulfonylamino)-11-oxidanylidene-naphtho[2,3-b][1]benzofuran-3-yl]ethynyl]-6-methyl-pyridine-4-carboxamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；277 K；0.05-0.15M KH2PO4, 0.1M MES pH 6.25, 1.5-2.5M NaCl, 0.05-0.15M NaH2PO4, 0.01M TCEP HCl	分辨率 2.76 Å R-free 0.234
6D1Y Crystal structure of Tyrosine-protein kinase receptor in complex with 2,4-dichloro-N-(3-methyl-1-phenyl-1H-pyrazol-5-yl)benzamide Inhibitor 提交 2018-04-12	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 381–698（318 aa）	未记录	FQJ 2,4-dichloro-N-(3-methyl-1-phenyl-1H-pyrazol-5-yl)benzamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；Well volume: 25.0 uL Well Ingredients: Buffer: 0.1 M (5.0 uL of stock 0.5 M) ADA (pH 6.50) Salt: 3.0 M (9.375 uL of stock 8.0 M) lithium nitrate Plate setup temperature: 13 C Plate incubation temperature: 4 C Drop volume from well: 0.1 uL Drop protein volume: 0.1 uL Protein Formulation Composition: Protein: (5.0 mg/mL) (0.14 mM) Compound: (3.00 mM)	分辨率 1.93 Å R-free 0.224
6D1Z Crystal structure of Tyrosine-protein kinase receptor in complex with 5-(4-fluorophenyl)thieno[2,3-d]pyrimidin-4(3H)-one Inhibitor 提交 2018-04-12	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 381–698（318 aa）	未记录	FQD 5-(4-fluorophenyl)thieno[2,3-d]pyrimidin-4(3H)-one × 1 GOL GLYCEROL × 1 FQM 5-{[5-(6-aminopyridin-2-yl)-2-chlorobenzene-1-carbonyl]amino}-1-phenyl-1H-pyrazole-3-carboxamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.63；294 K；Well volume: 30.0 uL Well Ingredients: Salt: 0.2571428571 M (1.9285714282 uL of stock 4.0 M) potassium formate Precipitant: 20.0 %w/v (12.0 uL of stock 50.0 %w/v) PEG 3350 Buffer: 0.1 M (3.0 uL of stock 1.0 M) Tris (pH 7.63) Plate setup temperature: 13 C Plate incubation temperature: 21 C Drop volume from well: 0.1 uL Drop protein volume: 0.3 uL Protein: 6.00 mg/mL (0.17 mM) Compound1: small molecule to aid crystallization (1.20 mM) Soak of 10mM compound 3 for > 1h into co-crystals of TrkA + compound1	分辨率 1.87 Å R-free 0.210
6DKB Crystal structure of Trk-A in complex with the Pan-Trk Kinase Inhibitor, compound 10b. 提交 2018-05-29	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 381–698（318 aa）	未记录	FKY 2-{[(3R,4S)-3-fluoro-1-{[4-(trifluoromethoxy)phenyl]acetyl}piperidin-4-yl]oxy}-5-(1-methyl-1H-imidazol-4-yl)pyridine-3-carboxamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；294 K；Well volume: 30.0 uL Drop volume from well: 0.2 uL Drop protein volume: 0.4 uL Well Ingredients: Polymer: 10.0 %w/v (6.0 uL of stock 50.0 %w/v) PEG 3350 Buffer: 16.0 %v/v (4.8 uL of stock 100.0 %v/v) tacsimate (pH 8.00) Organic (non-volatile): 10.0 %v/v (3.0 uL of stock 100.0 %v/v) Ethylene glycol Additive: 0.025 M (1.5 uL of stock 0.5 M) TCEP hydrochloride Plate setup temperature: 13 C Plate incubation temperature: 21 C	分辨率 2.68 Å R-free 0.245
6DKG Crystal structure of Trk-A in complex with the Pan-Trk Kinase Inhibitor, compound 13b. 提交 2018-05-29	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 381–698（318 aa）	未记录	22L 5-phenylthieno[2,3-d]pyrimidin-4(3H)-one × 1 GO7 2-{[(3R,4S)-3-fluoro-1-{[4-(trifluoromethoxy)phenyl]acetyl}piperidin-4-yl]oxy}-4-(2-hydroxy-2-methylpropoxy)benzamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；294 K；Compound 13b soaked for 30 min into preformed crystals of TrkA. Well volume: 50.0 uL Well Ingredients: Polymer: 9.0 %w/v (9.0 uL of stock 50.0 %w/v) PEG 3350 Buffer: 15.8 %v/v (7.9 uL of stock 100.0 %v/v) tacsimate (pH 8.00) Additive: 0.025 M (12.5 uL of stock 0.1 M) TCEP hydrochloride Plate setup temperature: 13 C Plate incubation temperature: 21 C Drop volume from well: 0.0050 uL Drop protein volume: 0.34 uL	分辨率 2.53 Å R-free 0.225
6DKI Crystal structure of Trk-A in complex with the Pan-Trk Kinase Inhibitor, compound 19. 提交 2018-05-29	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 381–698（318 aa）	未记录	22L 5-phenylthieno[2,3-d]pyrimidin-4(3H)-one × 1 GOD 6-amino-5-{[(3S)-4,4-difluoro-1-{[4-(trifluoromethoxy)phenyl]acetyl}pyrrolidin-3-yl]oxy}-N-methylpyridine-3-carboxamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；294 K；Well volume: 20.0 uL Well Ingredients: Polymer: 9.0 %w/v (3.6 uL of stock 50.0 %w/v) PEG 3350 Buffer: 15.8 %v/v (3.16 uL of stock 100.0 %v/v) tacsimate (pH 8.00) Additive: 0.025 M (5.0 uL of stock 0.1 M) TCEP hydrochloride Plate setup temperature: 13 C Plate incubation temperature: 21 C Drop volume from well: 0.01 uL Drop protein volume: 0.2 uL Protein: 6.30 mg/mL	分辨率 2.11 Å R-free 0.227
6IQN Crystal structure of TrkA kinase with ligand 提交 2018-11-08	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 蛋白同源多聚体同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 502–796（295 aa）链 B 502–796（295 aa）	未记录	AQ6 4-[[4-azanyl-3-(4-cyclohexylpiperazin-1-yl)-9,10-bis(oxidanylidene)anthracen-1-yl]amino]benzoic acid × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M MES pH6.5, 18% PEG 8000	分辨率 2.54 Å R-free 0.287
6J5L Crystal structure of Trk-A in complex with the Pan-Trk Kinase Inhibitor, compound 10e 提交 2019-01-11	构建体不同配体/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 502–796（295 aa）	未记录	B9C N-{2-[({3-[6-(piperazin-1-yl)pyridin-3-yl]-1H-indazol-5-yl}amino)methyl]phenyl}methanesulfonamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5.3；293 K；0.65 M Ammonium sulfate, 0.1 M Sodium Citrate pH 5.3	分辨率 2.30 Å R-free 0.251
6NPT TRK-A IN COMPLEX WITH LIGAND 1 提交 2019-01-18	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 393–697（305 aa）片段：KINASE DOMAIN	非标准单体：是（mmCIF未提供具体位点）	KWY 4-tert-butyl-N-(1,3-diphenyl-1H-pyrazol-5-yl)benzamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；277.15 K；The protein at a concentration of 10 mg/ml was mixed with 2mM of the ligand (diluted from 100 mM DMSO stock solution) for 1 hour on ice and crystallized at 4 deg C (hanging drop) from: 0.10 M KH2PO4/ 0.10 M NaH2PO4/ 0.10 M MES/NaOH pH 6.00 and 1.90 M NaCl (cryo: 25% glycerol in reservoir), or 18.00 % (w/v) PEG 3350, 0.20 M CaCl2, 0.10 M, MES pH=6.50 (cryo: direct).	分辨率 2.19 Å R-free 0.276
6NSP TRK-A IN COMPLEX WITH LIGAND 9 提交 2019-01-25	构建体不同配体/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 402–698（297 aa）片段：KINASE DOMAIN	未记录	L0P N-(8-methyl-2-phenylimidazo[1,2-a]pyridin-3-yl)-2-(3-oxo-2,3-dihydro-4H-1,4-benzothiazin-4-yl)acetamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；277 K；0.1M KH2PO4/ 0.1M NaH2PO4/ 0.1M MES/NaOH pH 6.0 and 1.9M NaCl (cryo: 25% glycerol in reservoir), or 18% (w/v) PEG 3350, 0.2M CaCl2, 0.1M, MES pH = 6.50 (cryo: direct).	分辨率 2.31 Å R-free 0.255
6NSS TRK-A IN COMPLEX WITH LIGAND 6 提交 2019-01-25	构建体不同配体/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 387–697（311 aa）片段：KINASE DOMAIN	未记录	L0M N-(8-methyl-2-phenylimidazo[1,2-a]pyrazin-3-yl)-2-(10H-phenoxazin-10-yl)acetamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；277 K；0.10M KH2PO4/ 0.10M NaH2PO4/ 0.1M MES/NaOH pH = 6.00 and 1.9M NaCl (cryo: 25% glycerol in reservoir), or 18% (w/v) PEG 3350, 0.2M CaCl2, 0.10M, MES pH = 6.50 (cryo: direct).	分辨率 1.97 Å R-free 0.218
6PL1 TRK-A IN COMPLEX WITH LIGAND 1B 提交 2019-06-30	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 387–697（311 aa）片段：KINASE DOMAIN	非标准单体：是（mmCIF未提供具体位点）	OOJ N-(5-{[(7-methyl-4-oxo-4H-pyrido[1,2-a]pyrimidin-2-yl)methyl]sulfanyl}-1,3,4-thiadiazol-2-yl)-N'-[3-(trifluoromethyl)phenyl]urea × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；277.15 K；20mM Tris/HCl, pH=8.5, 50mM NaCl, 2mM DTT, 0.5mM PMSF	分辨率 2.03 Å R-free 0.260
6PL2 TRK-A IN COMPLEX WITH LIGAND 1a 提交 2019-06-30	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 387–697（311 aa）片段：KINASE DOMAIN	非标准单体：是（mmCIF未提供具体位点）	OOM N-(3-tert-butyl-1-phenyl-1H-pyrazol-5-yl)-2-{[1-(4-hydroxyphenyl)-1H-tetrazol-5-yl]sulfanyl}acetamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；277.15 K；20mM Tris/HCl	分辨率 2.59 Å R-free 0.274
6PL3 TRK-A IN COMPLEX WITH LIGAND 2a 提交 2019-06-30	构建体不同配体/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 387–697（311 aa）片段：KINASE DOMAIN	未记录	OOD 2-[(3-tert-butyl-1-phenyl-1H-pyrazol-5-yl)amino]-2-oxoethyl 4-(1H-tetrazol-1-yl)benzoate × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；277.15 K；pH 8.5	分辨率 3.00 Å R-free 0.272
6PL4 TRK-A IN COMPLEX WITH LIGAND 1 提交 2019-06-30	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 387–697（311 aa）片段：KINASE DOMAIN	非标准单体：是（mmCIF未提供具体位点）	OO7 N-{[5-(methoxymethyl)-2-(trifluoromethoxy)phenyl]methyl}-N'-(8-methyl-2-phenylimidazo[1,2-a]pyrazin-3-yl)urea × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；277.15 K；pH 8.5	分辨率 2.06 Å R-free 0.239
6PMA TRK-A IN COMPLEX WITH LIGAND 提交 2019-07-01	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 387–697（311 aa）	非标准单体：是（mmCIF未提供具体位点）	OQS N-[2-chloro-5-(trifluoromethyl)phenyl]-2-[1-(4-methoxyphenyl)-4-oxo-1,4-dihydro-5H-pyrazolo[3,4-d]pyrimidin-5-yl]acetamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；277 K；0.10M KH2PO4/ 0.10M NaH2PO4/ 0.1M MES/NaOH pH = 6.00 and 1.9M NaCl (cryo: 25% glycerol in reservoir), or 18% (w/v) PEG 3350, 0.2M CaCl2, 0.10M, MES pH = 6.50 (cryo: direct).	分辨率 2.53 Å R-free 0.266
6PMB TRK-A IN COMPLEX WITH LIGAND 1a 提交 2019-07-01	构建体不同配体/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 387–697（311 aa）	未记录	OQM 2-[5,7-dimethyl-2-(pyridin-3-yl)[1,2,4]triazolo[1,5-a]pyrimidin-6-yl]-N-[3-(trifluoromethyl)phenyl]acetamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；277 K；0.10M KH2PO4/ 0.10M NaH2PO4/ 0.1M MES/NaOH pH = 6.00 and 1.9M NaCl (cryo: 25% glycerol in reservoir), or 18% (w/v) PEG 3350, 0.2M CaCl2, 0.10M, MES pH = 6.50 (cryo: direct)	分辨率 2.81 Å R-free 0.282
6PMC TRK-A IN COMPLEX WITH LIGAND 1a 提交 2019-07-01	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 387–697（311 aa）	非标准单体：是（mmCIF未提供具体位点）	OQJ N-(6-{[(5-chloro-2-methoxyphenyl)carbamoyl]amino}-1,3-benzothiazol-2-yl)benzamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；277 K；0.10M KH2PO4/ 0.10M NaH2PO4/ 0.1M MES/NaOH pH = 6.00 and 1.9M NaCl (cryo: 25% glycerol in reservoir), or 18% (w/v) PEG 3350, 0.2M CaCl2, 0.10M, MES pH = 6.50 (cryo: direct)	分辨率 2.19 Å R-free 0.298
6PME TRK-A IN COMPLEX WITH LIGAND 提交 2019-07-01	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 蛋白同源多聚体同源多聚体；蛋白 × 12 PDB 声明：dodecameric	链 A 387–697（311 aa）链 B 387–697（311 aa）链 C 387–697（311 aa）	非标准单体：是（mmCIF未提供具体位点）非标准单体：是（mmCIF未提供具体位点）非标准单体：是（mmCIF未提供具体位点）	ZN ZINC ION × 12 OOY N-[2,4-bis(morpholin-4-yl)phenyl]-3-phenoxybenzamide × 12 SRT S,R MESO-TARTARIC ACID × 8	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；277 K；0.10M KH2PO4/ 0.10M NaH2PO4/ 0.1M MES/NaOH pH = 6.00 and 1.9M NaCl (cryo: 25% glycerol in reservoir), or 18% (w/v) PEG 3350, 0.2M CaCl2, 0.10M, MES pH = 6.50 (cryo: direct).	分辨率 3.00 Å R-free 0.315
7N3T TrkA ECD complex with designed miniprotein ligand 提交 2021-06-01	构建体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 × 2 PDB 声明：dimeric	链 A 36–382（347 aa）片段：Extracellular domain, UNP residues 36-382	未记录	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 EDO 1,2-ETHANEDIOL × 5 SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.2；295 K；0.4 M ammonium sulfate, 0.1 M bis-tris pH 6.2, 16% PEG 3350.	分辨率 1.84 Å R-free 0.242
7N3T TrkA ECD complex with designed miniprotein ligand 提交 2021-06-01	构建体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 其他组合异源复合物；蛋白 × 2 PDB 声明：dimeric	链 B 36–382（347 aa）片段：Extracellular domain, UNP residues 36-382	未记录	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 EDO 1,2-ETHANEDIOL × 4 SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.2；295 K；0.4 M ammonium sulfate, 0.1 M bis-tris pH 6.2, 16% PEG 3350.	分辨率 1.84 Å R-free 0.242
7XAF The crystal structure of TrkA kinase in complex with 4^6,14-dimethyl-N-(3-(4-methyl-1H-imidazol-1-yl)-5-(trifluoromethyl)phenyl)-10-oxo-5-oxa-11,14-diaza-1(3,6)-imidazo[1,2-b]pyridazina-4(1,3)-benzenacyclo- tetradecaphan-2-yne-45-carboxamide 提交 2022-03-17	构建体不同配体/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 498–796（299 aa）	未记录	FKT 4^6,14-dimethyl-N-(3-(4-methyl-1H-imidazol-1-yl)-5-(trifluoromethyl)phenyl)-10-oxo-5-oxa-11,14-diaza-1(3,6)-imidazo[1,2-b]pyridazina-4(1,3)-benzenacyclo-tetradecaphan-2-yne-45-carboxamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.2；289 K；0.1M Na2HPO4/KH2PO4 (pH 6.2), 2M NaCl	分辨率 3.00 Å R-free 0.299
7XBI The crystal structure of human TrkA kinase bound to the inhibitor 提交 2022-03-21	构建体不同配体/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 485–795（311 aa）	未记录	CVY 4-[[2-fluoranyl-5-(trifluoromethyl)phenyl]carbamoylamino]-~{N}-[3-(1-methylpyrazol-4-yl)-1~{H}-indazol-5-yl]-2-(trifluoromethyl)benzamide × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；277 K；0.1M Na2HPO4/KH2PO4 pH=6.2, 2M NaCl	分辨率 2.16 Å R-free 0.246
8J5W The crystal structure of TrkA(F589L) kinase in complex with N-(3-cyclopropyl-5-((4-methylpiperazin-1-yl)methyl)phenyl)-4^6-methyl-14-oxo-5-oxa-13-aza-1(3,6)-imidazo[1,2-b]pyridazina-4(1,3)-benzenacyclotetradecaphan-2-yne-4^5-carboxamide 提交 2023-04-24	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 484–796（313 aa）	突变：F589L	A4U N-(3-cyclopropyl-5-((4-methylpiperazin-1-yl)methyl)phenyl)-4^6-methyl-14-oxo-5-oxa-13-aza-1(3,6)-imidazo[1,2-b]pyridazina-4(1,3)-benzenacyclotetradecaphan-2-yne-4^5-carboxamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；289 K；0.1M Na2HPO4/KH2PO4 (pH 6.2), 2M NaCl	分辨率 2.28 Å R-free 0.266
8J5X The crystal structure of TrkA(G595R) kinase in complex with N-(3-cyclopropyl-5-((4-methylpiperazin-1-yl)methyl)phenyl)-4^6-methyl-14-oxo-5-oxa-13-aza-1(3,6)-imidazo[1,2-b]pyridazina-4(1,3)-benzenacyclotetradecaphan-2-yne-4^5-carboxamide 提交 2023-04-24	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 498–796（299 aa）	突变：G595R	A4U N-(3-cyclopropyl-5-((4-methylpiperazin-1-yl)methyl)phenyl)-4^6-methyl-14-oxo-5-oxa-13-aza-1(3,6)-imidazo[1,2-b]pyridazina-4(1,3)-benzenacyclotetradecaphan-2-yne-4^5-carboxamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；289 K；0.1M Na2HPO4/KH2PO4 (pH 6.2), 2M NaCl	分辨率 2.09 Å R-free 0.220
8J61 The crystal structure of TrkA kinase in complex with 4^6-methyl-N-(3-(4-methyl-1H-imidazol-1-yl)-5-(trifluoromethyl)phenyl)-14-oxo-5-oxa-13-aza-1(3,6)-imidazo[1,2-b]pyridazina-4(1,3)-benzenacyclotetradecaphan-2-yne-4^5-carboxamide 提交 2023-04-24	构建体不同配体/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 498–796（299 aa）	未记录	A0X 4^6-methyl-N-(3-(4-methyl-1H-imidazol-1-yl)-5-(trifluoromethyl)phenyl)-14-oxo-5-oxa-13-aza-1(3,6)-imidazo[1,2-b]pyridazina-4(1,3)-benzenacyclotetradecaphan-2-yne-4^5-carboxamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；289 K；0.1M Na2HPO4/KH2PO4 (pH 6.2), 2M NaCl	分辨率 3.05 Å R-free 0.255
8J63 The crystal structure of TrkA kinase in complex with 4^6-methyl-N-(3-(4-methyl-1H-imidazol-1-yl)-5-(trifluoromethyl)phenyl)-11-oxo-5-oxa-10,14-diaza-1(3,6)-imidazo[1,2-b]pyridazina-4(1,3)-benzenacyclotetradecaphan-2-yne-4^5-carboxamide 提交 2023-04-24	构建体不同配体/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 498–796（299 aa）	未记录	A6X 4^6-methyl-N-(3-(4-methyl-1H-imidazol-1-yl)-5-(trifluoromethyl)phenyl)-11-oxo-5-oxa-10,14-diaza-1(3,6)-imidazo[1,2-b]pyridazina-4(1,3)-benzenacyclotetradecaphan-2-yne-4^5-carboxamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；289 K；0.1M Na2HPO4/KH2PO4 (pH 6.2), 2M NaCl	分辨率 3.00 Å R-free 0.289
8YTD Crystal Structure of TrkA D5 domain in complex with two different macrocyclic peptides 提交 2024-03-25	构建体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 × 3 PDB 声明：trimeric	链 A 281–382（102 aa）	未记录	EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；277 K；25% v/v ethylene glycol	分辨率 2.34 Å R-free 0.276
8YTE Crystal Structure of TrkA D5 domain in complex with macrocyclic peptide 提交 2024-03-25	构建体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 281–382（102 aa）	未记录	EDO 1,2-ETHANEDIOL × 4 GM1 AMINOMETHYLAMIDE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；293 K；0.1 M Tris pH 8.5, , 25% w/v Polyethylene glycol 3,350, 0.2 M ammonium acetate	分辨率 2.26 Å R-free 0.249
8YTE Crystal Structure of TrkA D5 domain in complex with macrocyclic peptide 提交 2024-03-25	构建体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 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 C 281–382（102 aa）	未记录	EDO 1,2-ETHANEDIOL × 5 GM1 AMINOMETHYLAMIDE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；293 K；0.1 M Tris pH 8.5, , 25% w/v Polyethylene glycol 3,350, 0.2 M ammonium acetate	分辨率 2.26 Å R-free 0.249
9DAI Crystal structure of Trk-A in complex with Staurosporin 提交 2024-08-22	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 381–698（318 aa）	突变：T165E, S171E	STU STAUROSPORINE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；286.15 K；Well volume: 30.0 uL Well Ingredients: Polymer: 10.0 %w/v PEG 3350 Buffer: 16.0 %v/v tacsimate (pH 8.00) Organic (non-volatile): 10.0 %v/v Ethylene glycol Additive: 0.025 M TCEP hydrochloride Plate setup temperature: 13 C Plate incubation temperature: 21 C Drop volume from well: 0.2 uL Drop protein volume: 0.4 uL (6.3mg/ml)	分辨率 2.86 Å R-free 0.277

共 59 个其他 PDB 条目、64 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	NTRK1_HUMAN
Isoform	P04629-4
PDB实体	1
链与序列区间	作者链 A； PDB构建体 3–320； UniProt 381–698

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	6d20
沉积日期 deposition_date	2018-04-12
结构标题 title	Crystal structure of Tyrosine-protein kinase receptor in complex with 5-(4-fluorophenyl)thieno[2,3-d]pyrimidin-4(3H)-one and 5-{[2,4-dichloro-5-(pyridin-2-yl)benzene-1-carbonyl]amino}-N-(2-hydroxy-2-methylpropyl)-1-phenyl-1H-pyrazole-3-carboxamide Inhibitors
关键词 keywords	Allosteric Inhibitor Complex Tyrosine kinase, TRANSFERASE, TRANSFERASE-Inhibitor complex; TRANSFERASE/Inhibitor
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	20.59 Å
回转半径 Rg (电子) rg_electron	19.51 Å
零角强度 I(0) i0	20238200.00
分子量 molecular_weight	34180.0 kDa
排除体积 excluded_volume	42817 Å³
包络体积 envelope_volume	50571 Å³
水化壳体积 shell_volume	21405 Å³
包络直径 envelope_diameter	68.7 Å
壳层 Rg shell_rg	26.20 Å
包络 Rg envelope_rg	19.93 Å
形状 Rg shape_rg	19.49 Å
总 Rg total_rg	20.52 Å
总原子数 total_atoms	2428
残基数 n_residues	296
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	72.4 Å
Rg (实空间) rg_real	20.52 Å
Rg 误差 (实空间) rg_real_error	0.57 Å
I(0) (实空间) i0_real	2.0240e+07
I(0) 误差 (实空间) i0_real_error	2.8240e+05
Rg (倒空间) rg_reciprocal	20.54 Å
I(0) (倒空间) i0_reciprocal	20240000.0000
解质量估计 total_estimate	0.6871
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	5
主峰位置 r_peak_primary	28.3 Å
偏度 Skewness skewness	0.298
峰度 Kurtosis kurtosis	-0.344
角度范围 angular_range	— – 0.3850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	8327000.0000
实空间数据点数 n_real_points	70
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.438; Stabil: 0.873; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; 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 (4)

实体 1 Entity 1 polymer

描述 description	High affinity nerve growth factor receptor
分子量 formula_weight	36110.5 kDa
EC 编号 ec_number	2.7.10.1
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	2652

GSTEGKGSGLQGHIIENPQYFSDACVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLPEQDKMLVAVKALKEASESARQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHGDLNRFLRSHGPDAKLLAGGEDVAPGPLGLGQLLAVASQVAAGMVYLAGLHFVHRDLATRNCLVGQGLVVKIGDFGMSRDIYSTDYYRVGGRTMLPIRWMPPESILYRKFTTESDVWSFGVVLWEIFTYGKQPWYQLSNTEAIDCITQGRELERPRACPPEVYAIMRGCWQREPQQRHSIKDVHARLQALAQAPPVYLDVLG

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	Insect cell expression vector pTIE1

实体 2 Entity 2 non-polymer

描述 description	5-(4-fluorophenyl)thieno[2,3-d]pyrimidin-4(3H)-one
分子量 formula_weight	246.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

实体 3 Entity 3 non-polymer

描述 description	5-{[2,4-dichloro-5-(pyridin-2-yl)benzene-1-carbonyl]amino}-N-(2-hydroxy-2-methylpropyl)-1-phenyl-1H-pyrazole-3-carboxamide
分子量 formula_weight	524.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

实体 4 Entity 4 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	224

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7. 折叠分类 (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d6d20a_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.144 — Protein kinase-like (PK-like)
超家族 Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
家族 Family family	d.144.1.0 — automated matches

CATH v4.4 (2 domains)

结构域编号 domain_id	6d20A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

结构域编号 domain_id	6d20A02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	510 — Transferase(Phosphotransferase); domain 1
同源超家族 H-superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

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8. 引用文献 (1)

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晶胞边长 a length_a	113.940 Å
晶胞边长 b length_b	45.810 Å
晶胞边长 c length_c	79.490 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	127.04 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	1.940 Å
最低分辨率 resolution_low	45.470 Å
R 因子 r_factor	0.1722
R_work r_work	0.1703
R_free r_free	0.2072

fit	/app/data/saxs_computation/d2/6d20/6d20.fit
pddf	/app/data/pr_computation/d2/6d20/6d20.pr.out
profile	/app/data/saxs_computation/d2/6d20/6d20.dat