9d1x

Crystal structure of FGFR3 bound to indazole inhibitor

Method: X-RAY DIFFRACTION D_max: 63.6 Å Quality: GOOD

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

Fibroblast growth factor receptor 3

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 455–756	Fragment：kinase domain Mutation：P572S, P573G	A1A6M (3P)-N-(2,6-dimethylphenyl)-6-methoxy-3-(1-methyl-1H-pyrazol-4-yl)-1H-indazole-5-carboxamide × 1 CL CHLORIDE ION × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.1；293 K；0.2 M magnesium chloride, 0.3 M sodium chloride, 23% (w/v) PEG 3350, 0.1 M Tris-HCl pH 8.1	Resolution 1.60 Å R-free 0.190

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 9D1X	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1RY7 Crystal Structure of the 3 Ig form of FGFR3c in complex with FGF1 Deposited 2003-12-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 33–365（333 aa） Fragment：FGFR-3c	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Peg 4000, glycerol, MPD, cadmium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.20 Å R-free 0.341
2LZL FGFR3tm Deposited 2012-10-04	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 357–399（43 aa） Fragment：UNP residues 357-399 Chain B 357–399（43 aa） Fragment：UNP residues 357-399	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.7；313 K；Ionic strength (raw mmCIF value) 50；Pressure ambient NMR sample composition 0.75 mM [U-99% 13C; U-99% 15N] FGFR3tm, 0.75 mM FGFR3tm, 88 mM [U-99% 2H] DPC, 10 mM [U-99% 2H] SDS, 0.3 mM sodium azide, 6 mM TCEP, 5 mM citric acid, 15 mM Na2HPO4, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
4K33 Crystal Structure of FGF Receptor 3 (FGFR3) Kinase Domain Harboring the K650E Mutation, a Gain-of-Function Mutation Responsible for Thanatophoric Dysplasia Type II and Spermatocytic Seminoma Deposited 2013-04-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 449–759（311 aa） Fragment：Human FGF Receptor 3 Kinase Domain	Mutation：C482A, C582S, K650E	ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；100mM HEPES pH7.5, 19% PEG 4000, 4% C4H10O2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.34 Å R-free 0.228
6LVM Crystal structure of FGFR3 in complex with pyrimidine derivative Deposited 2020-02-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 472–759（288 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	EVR 2-[[5-[2-(3,5-dimethoxyphenyl)ethyl]-2-[[3-methoxy-4-[4-(4-methylpiperazin-1-yl)piperidin-1-yl]phenyl]amino]pyrimidin-4-yl]amino]-N-ethyl-benzenesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；296 K；Citric Acid, PEG 8000	Resolution 2.53 Å R-free 0.279
6PNX Crystal Structure of an Asymmetric Dimer of FGF Receptor 3 Kinases Trapped in A-loop Tyrosine Transphosphorylation Reaction Deposited 2019-07-03	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 451–759（309 aa） Chain B 451–759（309 aa）	Mutation：C482A, C582S, R669E Mutation：C482A, C582S, R669E	ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；0.1 M Hepes, pH 7.5, and 1.8 M (NH4)2SO4	Resolution 2.20 Å R-free 0.230
7DHL Crystal structure of FGFR3 in complex with pyrimidine derivative Deposited 2020-11-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 472–759（288 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	H6X 5-[2-(3,5-dimethoxyphenyl)ethyl]-N-[3-methoxy-4-[4-(4-methylpiperazin-1-yl)piperidin-1-yl]phenyl]pyrimidin-2-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；Citric Acid, Ammonium dihydrogen phosphate, PEG 3350	Resolution 2.57 Å R-free 0.254
7YSU Cryo-EM Structure of FGF23-FGFR3c-aKlotho-HS Quaternary Complex Deposited 2022-08-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 148–358（211 aa） Chain E 148–358（211 aa）	Not recorded	ZN ZINC ION × 1 CU COPPER (II) ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8UDT The X-RAY co-crystal structure of human FGFR3 and KIN-3248 Deposited 2023-09-29	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 455–756（302 aa） Fragment：kinase domain	Mutation：residues 572-585 replaced by Ser-Gly	MLT D-MALATE × 2 WGF 3-[(1-cyclopropyl-4,6-difluoro-1H-benzimidazol-5-yl)ethynyl]-1-[(3R,5R)-5-(methoxymethyl)-1-propanoylpyrrolidin-3-yl]-5-(methylamino)-1H-pyrazole-4-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.20 M DL-Malic acid pH 5.00, 18.00 % (w/v) PEG 4000	Resolution 2.83 Å R-free 0.274
8UDT The X-RAY co-crystal structure of human FGFR3 and KIN-3248 Deposited 2023-09-29	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 455–756（302 aa） Fragment：kinase domain	Mutation：residues 572-585 replaced by Ser-Gly	WGF 3-[(1-cyclopropyl-4,6-difluoro-1H-benzimidazol-5-yl)ethynyl]-1-[(3R,5R)-5-(methoxymethyl)-1-propanoylpyrrolidin-3-yl]-5-(methylamino)-1H-pyrazole-4-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.20 M DL-Malic acid pH 5.00, 18.00 % (w/v) PEG 4000	Resolution 2.83 Å R-free 0.274
8UDT The X-RAY co-crystal structure of human FGFR3 and KIN-3248 Deposited 2023-09-29	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 455–756（302 aa） Fragment：kinase domain	Mutation：residues 572-585 replaced by Ser-Gly	WGF 3-[(1-cyclopropyl-4,6-difluoro-1H-benzimidazol-5-yl)ethynyl]-1-[(3R,5R)-5-(methoxymethyl)-1-propanoylpyrrolidin-3-yl]-5-(methylamino)-1H-pyrazole-4-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.20 M DL-Malic acid pH 5.00, 18.00 % (w/v) PEG 4000	Resolution 2.83 Å R-free 0.274
8UDU The X-RAY co-crystal structure of human FGFR3 and Compound 17 Deposited 2023-09-29	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 455–756（302 aa） Fragment：kinase domain	Mutation：residues 572-585 replaced by Ser-Gly	CL CHLORIDE ION × 1 WIQ 3-[(6-chloro-1-cyclopropyl-1H-benzimidazol-5-yl)ethynyl]-1-[(3S,5S)-5-(methoxymethyl)-1-(prop-2-enoyl)pyrrolidin-3-yl]-5-(methylamino)-1H-pyrazole-4-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.10 M Magnesium Chloride, 0.10 M TRIS/HCl pH 8.10, 0.20 M Sodium Chloride, 20.00 % (w/v) PEG 3350	Resolution 1.74 Å R-free 0.256
8UDU The X-RAY co-crystal structure of human FGFR3 and Compound 17 Deposited 2023-09-29	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 455–756（302 aa） Fragment：kinase domain	Mutation：residues 572-585 replaced by Ser-Gly	CL CHLORIDE ION × 1 WIQ 3-[(6-chloro-1-cyclopropyl-1H-benzimidazol-5-yl)ethynyl]-1-[(3S,5S)-5-(methoxymethyl)-1-(prop-2-enoyl)pyrrolidin-3-yl]-5-(methylamino)-1H-pyrazole-4-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.10 M Magnesium Chloride, 0.10 M TRIS/HCl pH 8.10, 0.20 M Sodium Chloride, 20.00 % (w/v) PEG 3350	Resolution 1.74 Å R-free 0.256
8UDV The X-RAY co-crystal structure of human FGFR3 V555M and Compound 17 Deposited 2023-09-29	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 455–756（302 aa） Fragment：kinase domain	Mutation：V555M and residues 572-585 (Uniprot numbering) replaced by Ser-Gly	SO4 SULFATE ION × 3 WIQ 3-[(6-chloro-1-cyclopropyl-1H-benzimidazol-5-yl)ethynyl]-1-[(3S,5S)-5-(methoxymethyl)-1-(prop-2-enoyl)pyrrolidin-3-yl]-5-(methylamino)-1H-pyrazole-4-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.10 M BIS-TRIS/HCl pH 6.50, 0.20 M (NH4)2SO4, 25.00 % (w/v) PEG 3350	Resolution 2.35 Å R-free 0.261
8UDV The X-RAY co-crystal structure of human FGFR3 V555M and Compound 17 Deposited 2023-09-29	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 455–756（302 aa） Fragment：kinase domain	Mutation：V555M and residues 572-585 (Uniprot numbering) replaced by Ser-Gly	SO4 SULFATE ION × 2 WIQ 3-[(6-chloro-1-cyclopropyl-1H-benzimidazol-5-yl)ethynyl]-1-[(3S,5S)-5-(methoxymethyl)-1-(prop-2-enoyl)pyrrolidin-3-yl]-5-(methylamino)-1H-pyrazole-4-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.10 M BIS-TRIS/HCl pH 6.50, 0.20 M (NH4)2SO4, 25.00 % (w/v) PEG 3350	Resolution 2.35 Å R-free 0.261
8UDV The X-RAY co-crystal structure of human FGFR3 V555M and Compound 17 Deposited 2023-09-29	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 455–756（302 aa） Fragment：kinase domain	Mutation：V555M and residues 572-585 (Uniprot numbering) replaced by Ser-Gly	SO4 SULFATE ION × 2 WIQ 3-[(6-chloro-1-cyclopropyl-1H-benzimidazol-5-yl)ethynyl]-1-[(3S,5S)-5-(methoxymethyl)-1-(prop-2-enoyl)pyrrolidin-3-yl]-5-(methylamino)-1H-pyrazole-4-carboxamide × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.10 M BIS-TRIS/HCl pH 6.50, 0.20 M (NH4)2SO4, 25.00 % (w/v) PEG 3350	Resolution 2.35 Å R-free 0.261
9CD7 FGFR3 Kinase Domain with Inhibitor TYRA-300 Deposited 2024-06-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 448–759（312 aa）	Mutation：C482A, C582S, K650E	A1AV2 (3P)-5-[(1R)-1-(3,5-dichloropyridin-4-yl)ethoxy]-3-{6-[6-(methanesulfonyl)-2,6-diazaspiro[3.3]heptan-2-yl]pyridin-3-yl}-1H-indazole × 1 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.25；291 K；17% PEG Smear Medium 10% Tacsimate pH 5.25 0.2M Ammonium Sulfate	Resolution 2.53 Å R-free 0.267
9CD7 FGFR3 Kinase Domain with Inhibitor TYRA-300 Deposited 2024-06-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 448–759（312 aa）	Mutation：C482A, C582S, K650E	A1AV2 (3P)-5-[(1R)-1-(3,5-dichloropyridin-4-yl)ethoxy]-3-{6-[6-(methanesulfonyl)-2,6-diazaspiro[3.3]heptan-2-yl]pyridin-3-yl}-1H-indazole × 1 GOL GLYCEROL × 6 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.25；291 K；17% PEG Smear Medium 10% Tacsimate pH 5.25 0.2M Ammonium Sulfate	Resolution 2.53 Å R-free 0.267
9CD7 FGFR3 Kinase Domain with Inhibitor TYRA-300 Deposited 2024-06-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 448–759（312 aa）	Mutation：C482A, C582S, K650E	A1AV2 (3P)-5-[(1R)-1-(3,5-dichloropyridin-4-yl)ethoxy]-3-{6-[6-(methanesulfonyl)-2,6-diazaspiro[3.3]heptan-2-yl]pyridin-3-yl}-1H-indazole × 1 GOL GLYCEROL × 6 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.25；291 K；17% PEG Smear Medium 10% Tacsimate pH 5.25 0.2M Ammonium Sulfate	Resolution 2.53 Å R-free 0.267
9EKO A chimeric hybrid protein fused with the FGFR3 Transmembrane Domain Deposited 2024-12-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 371–399（29 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.90 Å R-free 0.287
9KFU Human FGFR3 in complex with inhibitor F1 Deposited 2024-11-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 448–756（309 aa）	Not recorded	A1L5T (7~{S})-2-azanyl-7-(4-fluorophenyl)-6,7-dihydro-4~{H}-[1,3]thiazolo[4,5-b]pyridin-5-one × 1 SO4 SULFATE ION × 4 CO COBALT (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；25mM HEPES pH7.5, 1.8-2.0 M LiSO4, 10 Mm CoCl2	Resolution 1.40 Å R-free 0.251
9VM9 Crystal structure of FGFR3 in complex with 10s Deposited 2025-06-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 455–756（302 aa）	Not recorded	A1ESW ~{N}-[1-methyl-3-[2-[[5-methyl-1-(2-morpholin-4-ylethyl)pyrazol-4-yl]amino]pyrimidin-4-yl]indol-6-yl]propanamide × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；25% (w/v) PEG 3350, 0.2 M MgCl2, and 0.1 M HEPES, pH 7.5	Resolution 2.65 Å R-free 0.312
9VM9 Crystal structure of FGFR3 in complex with 10s Deposited 2025-06-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 455–756（302 aa）	Not recorded	A1ESW ~{N}-[1-methyl-3-[2-[[5-methyl-1-(2-morpholin-4-ylethyl)pyrazol-4-yl]amino]pyrimidin-4-yl]indol-6-yl]propanamide × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；25% (w/v) PEG 3350, 0.2 M MgCl2, and 0.1 M HEPES, pH 7.5	Resolution 2.65 Å R-free 0.312
9VM9 Crystal structure of FGFR3 in complex with 10s Deposited 2025-06-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 455–756（302 aa）	Not recorded	A1ESW ~{N}-[1-methyl-3-[2-[[5-methyl-1-(2-morpholin-4-ylethyl)pyrazol-4-yl]amino]pyrimidin-4-yl]indol-6-yl]propanamide × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；25% (w/v) PEG 3350, 0.2 M MgCl2, and 0.1 M HEPES, pH 7.5	Resolution 2.65 Å R-free 0.312
9VM9 Crystal structure of FGFR3 in complex with 10s Deposited 2025-06-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 455–756（302 aa）	Not recorded	A1ESW ~{N}-[1-methyl-3-[2-[[5-methyl-1-(2-morpholin-4-ylethyl)pyrazol-4-yl]amino]pyrimidin-4-yl]indol-6-yl]propanamide × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；25% (w/v) PEG 3350, 0.2 M MgCl2, and 0.1 M HEPES, pH 7.5	Resolution 2.65 Å R-free 0.312
9VMB The X-RAY co-crystal structure of human FGFR3 and Compound 10t Deposited 2025-06-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 455–756（302 aa）	Not recorded	A1ESX ~{N}-[1-methyl-3-[2-[[3-methyl-1-(2-morpholin-4-ylethyl)pyrazol-4-yl]amino]pyrimidin-4-yl]indol-6-yl]propanamide × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；25% (w/v) PEG 3350, 0.2 M MgCl2, and 0.1 M HEPES, pH 7.5	Resolution 1.97 Å R-free 0.237
9VMB The X-RAY co-crystal structure of human FGFR3 and Compound 10t Deposited 2025-06-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 455–756（302 aa）	Not recorded	A1ESX ~{N}-[1-methyl-3-[2-[[3-methyl-1-(2-morpholin-4-ylethyl)pyrazol-4-yl]amino]pyrimidin-4-yl]indol-6-yl]propanamide × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；25% (w/v) PEG 3350, 0.2 M MgCl2, and 0.1 M HEPES, pH 7.5	Resolution 1.97 Å R-free 0.237
9VMB The X-RAY co-crystal structure of human FGFR3 and Compound 10t Deposited 2025-06-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 455–756（302 aa）	Not recorded	A1ESX ~{N}-[1-methyl-3-[2-[[3-methyl-1-(2-morpholin-4-ylethyl)pyrazol-4-yl]amino]pyrimidin-4-yl]indol-6-yl]propanamide × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；25% (w/v) PEG 3350, 0.2 M MgCl2, and 0.1 M HEPES, pH 7.5	Resolution 1.97 Å R-free 0.237
9VMB The X-RAY co-crystal structure of human FGFR3 and Compound 10t Deposited 2025-06-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 455–756（302 aa）	Not recorded	A1ESX ~{N}-[1-methyl-3-[2-[[3-methyl-1-(2-morpholin-4-ylethyl)pyrazol-4-yl]amino]pyrimidin-4-yl]indol-6-yl]propanamide × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；25% (w/v) PEG 3350, 0.2 M MgCl2, and 0.1 M HEPES, pH 7.5	Resolution 1.97 Å R-free 0.237

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

View Construct and Data Evidence

UniProt name	FGFR3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–291； UniProt 455–756

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	9d1x
Deposition date deposition_date	2024-08-08
最后修订 last_revision	2025-06-25
Structure title title	Crystal structure of FGFR3 bound to indazole inhibitor
Keywords keywords	fibroblast growth factor receptor 3, inhibitor, CELL CYCLE; CELL CYCLE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	19.89 Å
Radius of gyration Rg (electron density) rg_electron	19.06 Å
Forward intensity I(0) i0	34039700.00
Molecular weight molecular_weight	30003.0 kDa
Excluded volume excluded_volume	28959 Å³
Envelope volume envelope_volume	47312 Å³
Hydration-shell volume shell_volume	20563 Å³
Envelope diameter envelope_diameter	66.8 Å
Shell Rg shell_rg	25.58 Å
Envelope Rg envelope_rg	19.45 Å
Shape Rg shape_rg	19.04 Å
Total Rg total_rg	19.75 Å
Total atoms total_atoms	2264
Residues n_residues	282
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	63.6 Å
Rg (real space) rg_real	19.81 Å
Rg uncertainty (real space) rg_real_error	0.37 Å
I(0) (real space) i0_real	3.4040e+07
I(0) uncertainty (real space) i0_real_error	4.6620e+05
Rg (reciprocal space) rg_reciprocal	19.82 Å
I(0) (reciprocal space) i0_reciprocal	34040000.0000
Solution quality estimate total_estimate	0.8123
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.2 Å
Skewness Skewness skewness	0.293
Kurtosis Kurtosis kurtosis	-0.323
Angular range angular_range	— – 0.4000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8479000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.853; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Fibroblast growth factor receptor 3
Molecular weight formula_weight	33742.0 kDa
EC 编号 ec_number	2.7.10.1
Mutation mutation	P572S, P573G
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2519

MSELELPADPKWELSRARLTLGKPLGEGCFGQVVMAEAIGIDKDRAAKPVTVAVKMLKDDATDKDLSDLVSEMEMMKMIGKHKNIINLLGACTQGGPLYVLVEYAAKGNLREFLRARRSGEEQLTFKDLVSCAYQVARGMEYLASQKCIHRDLAARNVLVTEDNVMKIADFGLARDVHNLDYYKKTTNGRLPVKWMAPEALFDRVYTHQSDVWSFGVLLWEIFTLGGSPYPGIPVEELFKLLKEGHRMDKPANCTHDLYMIMRECWHAAPSQRPTFKQLVEDLDRVLTVTSHHHHHH

来源 Source

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

Entity 2 Entity 2 non-polymer

Description description	(3P)-N-(2,6-dimethylphenyl)-6-methoxy-3-(1-methyl-1H-pyrazol-4-yl)-1H-indazole-5-carboxamide
Molecular weight formula_weight	375.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	209

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8. Citations (1)

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Unit-cell length a length_a	55.870 Å
Unit-cell length b length_b	55.870 Å
Unit-cell length c length_c	365.784 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	33.230 Å
R factor r_factor	—
R_work r_work	0.1801
R_free r_free	0.1903

fit	/app/data/saxs_computation/d1/9d1x/9d1x.fit
pddf	/app/data/pr_computation/d1/9d1x/9d1x.pr.out
profile	/app/data/saxs_computation/d1/9d1x/9d1x.dat