8yte

Crystal Structure of TrkA D5 domain in complex with macrocyclic peptide

Method: X-RAY DIFFRACTION D_max: 70.5 Å Quality: GOOD

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

High affinity nerve growth factor receptor

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 281–382	Not recorded	Macrocyclic Peptide × 1 EDO 1,2-ETHANEDIOL × 4 GM1 AMINOMETHYLAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；293 K；0.1 M Tris pH 8.5, , 25% w/v Polyethylene glycol 3,350, 0.2 M ammonium acetate	Resolution 2.26 Å R-free 0.249
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 281–382	Not recorded	Macrocyclic Peptide × 1 EDO 1,2-ETHANEDIOL × 5 GM1 AMINOMETHYLAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；293 K；0.1 M Tris pH 8.5, , 25% w/v Polyethylene glycol 3,350, 0.2 M ammonium acetate	Resolution 2.26 Å R-free 0.249

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 8YTE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1HE7 Human Nerve growth factor receptor TrkA Deposited 2000-11-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 282–413（132 aa） Fragment：LIGAND BINDING DOMAIN, SPANS RESIDUES 285-380	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.7；10 MG/ML PROTEIN + 0.1-0.3M NACL, 0.1M NA-CITRATE, PH 4.6 - 4.8	Resolution 2.00 Å R-free 0.276
1SHC SHC PTB DOMAIN COMPLEXED WITH A TRKA RECEPTOR PHOSPHOPEPTIDE, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1996-03-27	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 489–500（12 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1WWA NGF BINDING DOMAIN OF HUMAN TRKA RECEPTOR Deposited 1999-04-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 278–408（131 aa） Fragment：LIGAND BINDING DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.50 Å R-free 0.258
1WWA NGF BINDING DOMAIN OF HUMAN TRKA RECEPTOR Deposited 1999-04-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain Y 278–408（131 aa） Fragment：LIGAND BINDING DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.50 Å R-free 0.258
1WWA NGF BINDING DOMAIN OF HUMAN TRKA RECEPTOR Deposited 1999-04-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain X 278–408（131 aa） Fragment：LIGAND BINDING DOMAIN Chain Y 278–408（131 aa） Fragment：LIGAND BINDING DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.50 Å R-free 0.258
1WWW NGF IN COMPLEX WITH DOMAIN 5 OF THE TRKA RECEPTOR Deposited 1999-03-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain X 282–382（101 aa） Fragment：DOMAIN 5 Chain Y 282–382（101 aa） Fragment：DOMAIN 5	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；pH 5.0	Resolution 2.20 Å R-free 0.266
2IFG Structure of the extracellular segment of human TRKA in complex with nerve growth factor Deposited 2006-09-20	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 36–382（347 aa） Chain B 36–382（347 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；PEG, GLYCINE, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, pH 7.50	Resolution 3.40 Å R-free 0.331
2N90 TrkA transmembrane domain NMR structure in DPC micelles Deposited 2015-10-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 410–447（38 aa） Chain B 410–447（38 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.9；318 K；Pressure ambient NMR sample composition 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	Resolution not provided
4AOJ Human TrkA in complex with the inhibitor AZ-23 Deposited 2012-03-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 473–796（324 aa） Fragment：KINASE DOMAIN, RESIDUES 473-796 Chain B 473–796（324 aa） Fragment：KINASE DOMAIN, RESIDUES 473-796 Chain C 473–796（324 aa） Fragment：KINASE DOMAIN, RESIDUES 473-796	Not recorded	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 crystallization conditions 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.	Resolution 2.75 Å R-free 0.242
4CRP Solution structure of a TrkAIg2 domain construct for use in drug discovery Deposited 2014-02-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 282–383（102 aa） Fragment：EXTRACELLULAR NGF BINDING DOMAIN, RESIDUES 270-383	Mutation：YES	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.9；293 K；Ionic strength (raw mmCIF value) 10；Pressure 1.0 NMR sample composition 90% H2O, 10% D2O	Resolution not provided
4F0I Crystal structure of apo TrkA Deposited 2012-05-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 498–796（299 aa） Fragment：UNP residues 498-796	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 2.30 Å R-free 0.241
4F0I Crystal structure of apo TrkA Deposited 2012-05-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 498–796（299 aa） Fragment：UNP residues 498-796	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 2.30 Å R-free 0.241
4GT5 Crystal structure of the inactive TrkA kinase domain Deposited 2012-08-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 498–796（299 aa） Fragment：receptor tyrosine kinase (UNP residues 498-796)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 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 Deposited 2014-05-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 501–787（287 aa） Fragment：kinase domain (UNP residues 501-787)	Not recorded	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 crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M Bis-Tris, 2.3M AmmoniumAcetate	Resolution 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 Deposited 2014-05-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 501–787（287 aa） Fragment：kinase domain (UNP residues 501-787)	Not recorded	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 crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M Bis-Tris, 2.3M AmmoniumAcetate	Resolution 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 Deposited 2014-05-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 501–787（287 aa） Fragment：kinase domain (UNP residues 501-787)	Not recorded	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 crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M Bis-Tris, 2.3M AmmoniumAcetate	Resolution 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 Deposited 2014-05-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 501–787（287 aa） Fragment：kinase domain (UNP residues 501-787)	Not recorded	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 crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M Bis-Tris, 2.3M AmmoniumAcetate	Resolution 2.10 Å R-free 0.209
4YNE (R)-2-Phenylpyrrolidine Substitute Imidazopyridazines: a New Class of Potent and Selective Pan-TRK Inhibitors Deposited 2015-03-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 502–796（295 aa）	Not recorded	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 crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；0.8M (NH4)2SO4, 0.1M Citrate pH 5.0	Resolution 2.02 Å R-free 0.216
4YPS (R)-2-Phenylpyrrolidine Substitute Imidazopyridazines: a New Class of Potent and Selective Pan-TRK Inhibitors Deposited 2015-03-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 502–796（295 aa）	Not recorded	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 crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；0.8M (NH4)2SO4, 0.1M Citrate pH 5.0	Resolution 2.10 Å R-free 0.257
5H3Q Crystal Structure of TrkA kinase with ligand Deposited 2016-10-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 473–796（324 aa）	Not recorded	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 crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；1.2M Sodium Tartrate, 100mM Tris-HCl pH 8.5, 5 mM DTT	Resolution 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 Deposited 2016-02-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 400–689（290 aa） Fragment：catalytic domain, UNP residues 400-689	Not recorded	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 crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1M Bis-Tris pH 6.5, 2.3M Ammonium Acetate	Resolution 2.33 Å R-free 0.209
5JFS Crystal structure of TrkA in complex with PF-00593174 Deposited 2016-04-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 404–698（295 aa）	Not recorded	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 crystallization conditions 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	Resolution 2.07 Å R-free 0.191
5JFV Crystal structure of TrkA in complex with PF-05206283 Deposited 2016-04-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 404–698（295 aa）	Not recorded	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 crystallization conditions 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	Resolution 1.59 Å R-free 0.192
5JFW Crystal structure of TrkA in complex with PF-05247452 Deposited 2016-04-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 404–698（295 aa）	Not recorded	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 crystallization conditions 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	Resolution 1.52 Å R-free 0.209
5JFX Crystal structure of TrkA in complex with PF-06273340 Deposited 2016-04-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 404–698（295 aa）	Not recorded	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 crystallization conditions 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	Resolution 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 Deposited 2016-06-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 376–698（323 aa） Fragment：catalytic domain with juxtamembrane region, UNP residues 376-698	Not recorded	6UE 1-(9~{H}-fluoren-9-yl)-3-(2-methyl-4-phenyl-pyrimidin-5-yl)urea × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；50mM MES pH 6.5, 150 mM NaCl, 5mM TCEP, 0.1% beta-OctylGlucoside	Resolution 1.87 Å R-free 0.247
5KMJ TrkA JM-kinase with {N}-(2-pyridylmethyl)-2-[2-(2-thienyl)indol-1-yl]acetamide Deposited 2016-06-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 376–698（323 aa） Fragment：catalytic domain with juxtamembrane region, UNP residues 376-698	Not recorded	6UF ~{N}-(pyridin-2-ylmethyl)-2-(2-thiophen-2-ylindol-1-yl)ethanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；50mM MES pH 6.5, 150 mM NaCl, 5mM TCEP, 0.1% beta-OctylGlucoside	Resolution 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 Deposited 2016-06-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 376–698（323 aa） Fragment：catalytic domain with juxtamembrane region, UNP residues 376-698	Not recorded	6UG 2-fluoranyl-~{N}-[2-(4-fluorophenyl)-6-methyl-pyridin-3-yl]-4-(trifluoromethyl)benzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；50mM MES pH 6.5, 150 mM NaCl, 5mM TCEP, 0.1% beta-OctylGlucoside	Resolution 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 Deposited 2016-06-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 376–698（323 aa） Fragment：catalytic domain with juxtamembrane region, UNP residues 376-698	Non-standard monomer：Yes (specific site not provided by mmCIF)	6UH 1-(5-methyl-3-phenyl-1,2-oxazol-4-yl)-3-[[2-(trifluoromethyl)phenyl]methyl]urea × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；50mM MES pH 6.5, 150 mM NaCl, 5mM TCEP, 0.1% beta-OctylGlucoside	Resolution 2.01 Å R-free 0.232
5KMM TrkA JM-kinase with 1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-(1-naphthyl)urea Deposited 2016-06-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 376–698（323 aa） Fragment：catalytic domain with juxtamembrane region, UNP residues 376-698	Not recorded	6UJ 1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-naphthalen-1-yl-urea × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；50mM MES pH 6.5, 150 mM NaCl, 5mM TCEP, 0.1% beta-OctylGlucoside	Resolution 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 Deposited 2016-06-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 376–698（323 aa） Fragment：catalytic domain with juxtamembrane region, UNP residues 376-698	Non-standard monomer：Yes (specific site not provided by mmCIF)	6UK 1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-[[2-(trifluoromethyl)phenyl]methyl]urea × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；50mM MES pH 6.5, 150 mM NaCl, 5mM TCEP, 0.1% beta-OctylGlucoside	Resolution 2.14 Å R-free 0.222
5KMO TrkA JM-kinase with 1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-(2-pyridyl)urea Deposited 2016-06-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 376–698（323 aa） Fragment：catalytic domain with juxtamembrane region, UNP resdiues 376-698	Not recorded	6UM 1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-pyridin-2-yl-urea × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；50mM MES pH 6.5, 150 mM NaCl, 5mM TCEP, 0.1% beta-OctylGlucoside	Resolution 2.67 Å R-free 0.243
5KVT THE STRUCTURE OF TRKA KINASE DOMAIN BOUND TO THE INHIBITOR ENTRECTINIB Deposited 2016-07-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 501–787（287 aa） Fragment：kinase domain (UNP residues 501-787)	Not recorded	YMX Entrectinib × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 2.45 Å R-free 0.239
5WR7 Crystal structure of Trk-A complexed with a selective inhibitor CH7057288 Deposited 2016-11-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 489–792（304 aa） Fragment：KINASE DOMAIN, UNP residues 489-792	Non-standard monomer：Yes (specific site not provided by mmCIF)	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 crystallization conditions 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	Resolution 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 Deposited 2018-04-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 381–698（318 aa）	Not recorded	FQJ 2,4-dichloro-N-(3-methyl-1-phenyl-1H-pyrazol-5-yl)benzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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)	Resolution 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 Deposited 2018-04-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 381–698（318 aa）	Not recorded	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 crystallization conditions 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	Resolution 1.87 Å R-free 0.210
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 Deposited 2018-04-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 381–698（318 aa）	Not recorded	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 crystallization conditions 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)	Resolution 1.94 Å R-free 0.207
6DKB Crystal structure of Trk-A in complex with the Pan-Trk Kinase Inhibitor, compound 10b. Deposited 2018-05-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 381–698（318 aa）	Not recorded	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 crystallization conditions 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	Resolution 2.68 Å R-free 0.245
6DKG Crystal structure of Trk-A in complex with the Pan-Trk Kinase Inhibitor, compound 13b. Deposited 2018-05-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 381–698（318 aa）	Not recorded	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 crystallization conditions 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	Resolution 2.53 Å R-free 0.225
6DKI Crystal structure of Trk-A in complex with the Pan-Trk Kinase Inhibitor, compound 19. Deposited 2018-05-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 381–698（318 aa）	Not recorded	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 crystallization conditions 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	Resolution 2.11 Å R-free 0.227
6IQN Crystal structure of TrkA kinase with ligand Deposited 2018-11-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 502–796（295 aa） Chain B 502–796（295 aa）	Not recorded	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 crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M MES pH6.5, 18% PEG 8000	Resolution 2.54 Å R-free 0.287
6J5L Crystal structure of Trk-A in complex with the Pan-Trk Kinase Inhibitor, compound 10e Deposited 2019-01-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 502–796（295 aa）	Not recorded	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 crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.3；293 K；0.65 M Ammonium sulfate, 0.1 M Sodium Citrate pH 5.3	Resolution 2.30 Å R-free 0.251
6NPT TRK-A IN COMPLEX WITH LIGAND 1 Deposited 2019-01-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 393–697（305 aa） Fragment：KINASE DOMAIN	Non-standard monomer：Yes (specific site not provided by mmCIF)	KWY 4-tert-butyl-N-(1,3-diphenyl-1H-pyrazol-5-yl)benzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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).	Resolution 2.19 Å R-free 0.276
6NSP TRK-A IN COMPLEX WITH LIGAND 9 Deposited 2019-01-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 402–698（297 aa） Fragment：KINASE DOMAIN	Not recorded	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 crystallization conditions 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).	Resolution 2.31 Å R-free 0.255
6NSS TRK-A IN COMPLEX WITH LIGAND 6 Deposited 2019-01-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 387–697（311 aa） Fragment：KINASE DOMAIN	Not recorded	L0M N-(8-methyl-2-phenylimidazo[1,2-a]pyrazin-3-yl)-2-(10H-phenoxazin-10-yl)acetamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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).	Resolution 1.97 Å R-free 0.218
6PL1 TRK-A IN COMPLEX WITH LIGAND 1B Deposited 2019-06-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 387–697（311 aa） Fragment：KINASE DOMAIN	Non-standard monomer：Yes (specific site not provided by mmCIF)	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 crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；20mM Tris/HCl, pH=8.5, 50mM NaCl, 2mM DTT, 0.5mM PMSF	Resolution 2.03 Å R-free 0.260
6PL2 TRK-A IN COMPLEX WITH LIGAND 1a Deposited 2019-06-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 387–697（311 aa） Fragment：KINASE DOMAIN	Non-standard monomer：Yes (specific site not provided by mmCIF)	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 crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；20mM Tris/HCl	Resolution 2.59 Å R-free 0.274
6PL3 TRK-A IN COMPLEX WITH LIGAND 2a Deposited 2019-06-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 387–697（311 aa） Fragment：KINASE DOMAIN	Not recorded	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 crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；pH 8.5	Resolution 3.00 Å R-free 0.272
6PL4 TRK-A IN COMPLEX WITH LIGAND 1 Deposited 2019-06-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 387–697（311 aa） Fragment：KINASE DOMAIN	Non-standard monomer：Yes (specific site not provided by mmCIF)	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 crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；pH 8.5	Resolution 2.06 Å R-free 0.239
6PMA TRK-A IN COMPLEX WITH LIGAND Deposited 2019-07-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 387–697（311 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	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 crystallization conditions 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).	Resolution 2.53 Å R-free 0.266
6PMB TRK-A IN COMPLEX WITH LIGAND 1a Deposited 2019-07-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 387–697（311 aa）	Not recorded	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 crystallization conditions 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)	Resolution 2.81 Å R-free 0.282
6PMC TRK-A IN COMPLEX WITH LIGAND 1a Deposited 2019-07-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 387–697（311 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	OQJ N-(6-{[(5-chloro-2-methoxyphenyl)carbamoyl]amino}-1,3-benzothiazol-2-yl)benzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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)	Resolution 2.19 Å R-free 0.298
6PME TRK-A IN COMPLEX WITH LIGAND Deposited 2019-07-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 387–697（311 aa） Chain B 387–697（311 aa） Chain C 387–697（311 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	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 crystallization conditions 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).	Resolution 3.00 Å R-free 0.315
7N3T TrkA ECD complex with designed miniprotein ligand Deposited 2021-06-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 36–382（347 aa） Fragment：Extracellular domain, UNP residues 36-382	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 EDO 1,2-ETHANEDIOL × 5 SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions 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.	Resolution 1.84 Å R-free 0.242
7N3T TrkA ECD complex with designed miniprotein ligand Deposited 2021-06-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 36–382（347 aa） Fragment：Extracellular domain, UNP residues 36-382	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 EDO 1,2-ETHANEDIOL × 4 SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions 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.	Resolution 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 Deposited 2022-03-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 498–796（299 aa）	Not recorded	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 crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；289 K；0.1M Na2HPO4/KH2PO4 (pH 6.2), 2M NaCl	Resolution 3.00 Å R-free 0.299
7XBI The crystal structure of human TrkA kinase bound to the inhibitor Deposited 2022-03-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 485–795（311 aa）	Not recorded	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 crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1M Na2HPO4/KH2PO4 pH=6.2, 2M NaCl	Resolution 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 Deposited 2023-04-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 484–796（313 aa）	Mutation：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 crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.1M Na2HPO4/KH2PO4 (pH 6.2), 2M NaCl	Resolution 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 Deposited 2023-04-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 498–796（299 aa）	Mutation：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 crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.1M Na2HPO4/KH2PO4 (pH 6.2), 2M NaCl	Resolution 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 Deposited 2023-04-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 498–796（299 aa）	Not recorded	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 crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.1M Na2HPO4/KH2PO4 (pH 6.2), 2M NaCl	Resolution 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 Deposited 2023-04-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 498–796（299 aa）	Not recorded	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 crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.1M Na2HPO4/KH2PO4 (pH 6.2), 2M NaCl	Resolution 3.00 Å R-free 0.289
8YTD Crystal Structure of TrkA D5 domain in complex with two different macrocyclic peptides Deposited 2024-03-25	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 281–382（102 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；277 K；25% v/v ethylene glycol	Resolution 2.34 Å R-free 0.276
9DAI Crystal structure of Trk-A in complex with Staurosporin Deposited 2024-08-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 381–698（318 aa）	Mutation：T165E, S171E	STU STAUROSPORINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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)	Resolution 2.86 Å R-free 0.277

59 other PDB entries and 63 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NTRK1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–102； UniProt 281–382 Author chain C； PDBConstruct 1–102； UniProt 281–382

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	8yte
Deposition date deposition_date	2024-03-25
Structure title title	Crystal Structure of TrkA D5 domain in complex with macrocyclic peptide
Keywords keywords	TRANSFERASE, cyclic peptide; 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	21.24 Å
Radius of gyration Rg (electron density) rg_electron	20.49 Å
Forward intensity I(0) i0	11018200.00
Molecular weight molecular_weight	25186.0 kDa
Excluded volume excluded_volume	31566 Å³
Envelope volume envelope_volume	37683 Å³
Hydration-shell volume shell_volume	16369 Å³
Envelope diameter envelope_diameter	72.4 Å
Shell Rg shell_rg	25.62 Å
Envelope Rg envelope_rg	20.55 Å
Shape Rg shape_rg	20.48 Å
Total Rg total_rg	21.28 Å
Total atoms total_atoms	1771
Residues n_residues	222
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	70.5 Å
Rg (real space) rg_real	21.35 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	1.1020e+07
I(0) uncertainty (real space) i0_real_error	1.5110e+05
Rg (reciprocal space) rg_reciprocal	21.33 Å
I(0) (reciprocal space) i0_reciprocal	11020000.0000
Solution quality estimate total_estimate	0.8594
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.7 Å
Skewness Skewness skewness	0.433
Kurtosis Kurtosis kurtosis	-0.430
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4186000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.770; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.879; Smooth: 0.980

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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	High affinity nerve growth factor receptor
Molecular weight formula_weight	11221.6 kDa
EC 编号 ec_number	2.7.10.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	1864

NVSFPASVQLHTAVEMHHWCIPFSVDGQPAPSLRWLFNGSVLNETSFIFTEFLEPAANETVRHGCLRLNQPTHVNNGNYTLLAANPFGQASASIMAAFMDNP

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	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Macrocyclic Peptide
Molecular weight formula_weight	1620.9 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

GFFLYPHGFYGIVC

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 4 Entity 4 non-polymer

Description description	AMINOMETHYLAMIDE
Molecular weight formula_weight	74.1 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	91

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8. Citations (1)

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Unit-cell length a length_a	51.680 Å
Unit-cell length b length_b	66.972 Å
Unit-cell length c length_c	79.889 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.260 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1989
R_work r_work	0.1967
R_free r_free	0.2495

fit	/app/data/saxs_computation/yt/8yte/8yte.fit
pddf	/app/data/pr_computation/yt/8yte/8yte.pr.out
profile	/app/data/saxs_computation/yt/8yte/8yte.dat

Crystal Structure of TrkA D5 domain in complex with macrocyclic peptide

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

High affinity nerve growth factor receptor

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)