← Back to search
5wbm

Structure of human Ketohexokinase complexed with hits from fragment screening

Method: X-RAY DIFFRACTION Dmax: 101.7 Å Quality: GOOD
▼

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

Ketohexokinase

Homo sapiens

UniProt P50053

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 5–298 Chain B； UniProt 5–298 Not recorded A4G [(3R)-1-(5-methyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-3-yl]methanol × 3 SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；17% PEG 8k, 0.1M Na-Citrate, 0.2M Ammonium sulfate, pH 4.5 Resolution 2.16 Å R-free 0.227

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 5WBM Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2HLZ Crystal Structure of human ketohexokinase Deposited 2006-07-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 5–298（294 aa）
Chain B 5–298（294 aa）
Chain C 5–298（294 aa）
Chain D 5–298（294 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) Non-standard monomer：Yes (specific site not provided by mmCIF) UNX UNKNOWN LIGAND × 32 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；291 K；17% PEG8000, 5mM Cobalt Chloride, 200mM ammonium sulfate, 100mM NaCitrate, pH 4.2, vapor diffusion, sitting drop, temperature 291K
Resolution 1.85 Å R-free 0.249
2HQQ Crystal structure of human ketohexokinase complexed to different sugar molecules Deposited 2006-07-19 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–298（298 aa）
Not recorded SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；291 K；0.7M ammonium sulphate, 0.5M lithium sulphate, 0.1M sodium citrate, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.86 Å R-free 0.234
2HW1 Crystal structure of human ketohexokinase complexed to different sugar molecules Deposited 2006-07-31 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–298（298 aa）
Not recorded FRU beta-D-fructofuranose × 2 SO4 SULFATE ION × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；291 K；0.7M ammonium sulphate, 0.5M lithium sulphate, 0.1M sodium citrate, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.10 Å R-free 0.228
3B3L Crystal structures of alternatively-spliced isoforms of human ketohexokinase Deposited 2007-10-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–298（298 aa）
Chain B 1–298（298 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；291 K；20% PEG 3000, 0.1M sodium acetate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.90 Å R-free 0.281
3B3L Crystal structures of alternatively-spliced isoforms of human ketohexokinase Deposited 2007-10-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–298（298 aa）
Chain D 1–298（298 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；291 K；20% PEG 3000, 0.1M sodium acetate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.90 Å R-free 0.281
3RO4 X-ray Structure of Ketohexokinase in complex with an indazole compound derivative Deposited 2011-04-25 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 5–298（294 aa）
Chain B 5–298（294 aa）
Not recorded SO4 SULFATE ION × 2 LJ9 3-ethyl-6-[(3aR,6aS)-hexahydropyrrolo[3,4-c]pyrrol-2(1H)-yl]-1-phenyl-1H-indazole × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；295 K；17% PEG 8k, 0.1M Na-Citrate, 0.2M Ammonium sulfate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 2.60 Å R-free 0.297
5WBO Structure of human Ketohexokinase complexed with hits from fragment screening Deposited 2017-06-29 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 5–298（294 aa）
Chain B 5–298（294 aa）
Not recorded A1Y 4,6-dimethyl-2-(morpholin-4-yl)pyridine-3-carbonitrile × 2 SO4 SULFATE ION × 3 CIT CITRIC ACID × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；17% PEG 8k, 0.1M Na-Citrate, 0.2M Ammonium sulfate, pH 4.5
Resolution 2.25 Å R-free 0.223
5WBP Structure of human Ketohexokinase complexed with hits from fragment screening Deposited 2017-06-29 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 5–298（294 aa）
Chain B 5–298（294 aa）
Not recorded A2J 3-(trifluoromethyl)quinoxalin-2(1H)-one × 1 SO4 SULFATE ION × 5 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；17% PEG 8k, 0.1M Na-Citrate, 0.2M Ammonium sulfate, pH 4.5
Resolution 2.74 Å R-free 0.229
5WBQ Structure of human Ketohexokinase complexed with hits from fragment screening Deposited 2017-06-29 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 5–298（294 aa）
Chain B 5–298（294 aa）
Not recorded A3J 2-ethyl-7-[(3S)-3-hydroxy-3-methylpyrrolidin-1-yl]-5-(trifluoromethyl)-1H-pyrrolo[3,2-b]pyridine-6-carbonitrile × 2 SO4 SULFATE ION × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；17% PEG 8k, 0.1M Na-Citrate, 0.2M Ammonium sulfate, pH 4.5
Resolution 2.40 Å R-free 0.248
5WBR Structure of human Ketohexokinase complexed with hits from fragment screening Deposited 2017-06-29 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 5–298（294 aa）
Chain B 5–298（294 aa）
Not recorded A3Y 6-[4-(2-hydroxyethyl)piperazin-1-yl]-2-[(3S)-3-(hydroxymethyl)piperidin-1-yl]-4-(trifluoromethyl)pyridine-3-carbonitrile × 2 SO4 SULFATE ION × 5 CIT CITRIC ACID × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；17% PEG 8k, 0.1M Na-Citrate, 0.2M Ammonium sulfate, pH 4.5
Resolution 2.58 Å R-free 0.241
5WBZ Structure of human Ketohexokinase complexed with hits from fragment screening Deposited 2017-06-29 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 5–298（294 aa）
Chain B 5–298（294 aa）
Not recorded A4J 6-[(3S,4S)-3,4-dihydroxypyrrolidin-1-yl]-2-[(3S)-3-hydroxy-3-methylpyrrolidin-1-yl]-4-(trifluoromethyl)pyridine-3-carbonitrile × 2 SO4 SULFATE ION × 3 CIT CITRIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；17% PEG 8k, 0.1M Na-Citrate, 0.2M Ammonium sulfate, pH 4.5
Resolution 2.40 Å R-free 0.214
6UL7 Structure of human ketohexokinase-C in complex with fructose, NO3, and osthole Deposited 2019-10-07 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–298（298 aa）
Not recorded FRU beta-D-fructofuranose × 2 A0O 7-methoxy-8-(3-methylbut-2-enyl)chromen-2-one × 2 NO3 NITRATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；290.15 K；0.1 M Bis-Tris, pH 5.5, 2 M ammonium sulfate, 1.3 M potassium nitrate, 100 mM magnesium chloride, 220 mM fructose, 3.8 mM osthole
Resolution 2.30 Å R-free 0.278
6W0N Structure of KHK in complex with compound 2 Deposited 2020-03-02 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 5–298（294 aa）
Chain B 5–298（294 aa）
Not recorded RYS 6-[(3~{S},4~{R})-3,4-bis(oxidanyl)pyrrolidin-1-yl]-2-[(3~{S})-3-methyl-3-oxidanyl-pyrrolidin-1-yl]-4-(trifluoromethyl)pyridine-3-carbonitrile × 2 SO4 SULFATE ION × 3 CIT CITRIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；295 K；17% PEG 8000, 100 mM Na citrate, pH 4.5, and 0.2 M ammonium sulfate
Resolution 2.41 Å R-free 0.204
6W0W Structure of KHK in complex with compound 3 Deposited 2020-03-03 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 5–298（294 aa）
Chain B 5–298（294 aa）
Not recorded RZA 6-[(3~{R},4~{S})-3,4-bis(oxidanyl)pyrrolidin-1-yl]-2-[(2~{S},3~{R})-2-methyl-3-oxidanyl-azetidin-1-yl]-4-(trifluoromethyl)pyridine-3-carbonitrile × 2 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；17-20% PEG 8000, 100 mM sodium citrate, pH 4.4-4.7, and 0.2 M ammonium sulfate
Resolution 2.80 Å R-free 0.216
6W0X Structure of KHK in complex with compound 4 (6-[(1~{S},5~{R})-6-(hydroxymethyl)-3-azabicyclo[3.1.0]hexan-3-yl]-2-[(2~{S},3~{R})-2-methyl-3-oxidanyl-azetidin-1-yl]-4-(trifluoromethyl)pyridine-3-carbonitrile) Deposited 2020-03-03 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 5–298（294 aa）
Chain B 5–298（294 aa）
Not recorded S6J 6-[(1~{S},5~{R})-6-(hydroxymethyl)-3-azabicyclo[3.1.0]hexan-3-yl]-2-[(2~{S},3~{R})-2-methyl-3-oxidanyl-azetidin-1-yl]-4-(trifluoromethyl)pyridine-3-carbonitrile × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；17-20% PEG8000, 100 mM sodium citrate, pH 4.4-4.7, 0.2 M ammonium sulfate
Resolution 2.38 Å R-free 0.206
6W0Y Structure of KHK in complex with compound 6 (2-[(1~{R},5~{S})-3-[5-cyano-6-[(2~{S},3~{R})-2-methyl-3-oxidanyl-azetidin-1-yl]-4-(trifluoromethyl)pyridin-2-yl]-3-azabicyclo[3.1.0]hexan-6-yl]ethanoic acid) Deposited 2020-03-03 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 5–298（294 aa）
Chain B 5–298（294 aa）
Not recorded S6S 2-[(1~{R},5~{S})-3-[5-cyano-6-[(2~{S},3~{R})-2-methyl-3-oxidanyl-azetidin-1-yl]-4-(trifluoromethyl)pyridin-2-yl]-3-azabicyclo[3.1.0]hexan-6-yl]ethanoic acid × 2 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；17-20% PEG8000, 100 mM sodium citrate, pH 4.4-4.7, 0.2 M ammonium sulfate
Resolution 2.54 Å R-free 0.205
6W0Z Structure of KHK in complex with compound 8 (2-[(1~{S},5~{R})-3-[2-[(2~{S})-2-methylazetidin-1-yl]-6-(trifluoromethyl)pyrimidin-4-yl]-3-azabicyclo[3.1.0]hexan-6-yl]ethanoic acid) Deposited 2020-03-03 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 5–298（294 aa）
Chain B 5–298（294 aa）
Not recorded S6D 2-[(1~{S},5~{R})-3-[2-[(2~{S})-2-methylazetidin-1-yl]-6-(trifluoromethyl)pyrimidin-4-yl]-3-azabicyclo[3.1.0]hexan-6-yl]ethanoic acid × 2 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；17-20% PEG8000, 100 mM sodium citrate, pH 4.4-4.7, 0.2 M ammonium sulfate
Resolution 2.30 Å R-free 0.195
8OME Crystal structure of hKHK-A in complex with compound-4 Deposited 2023-03-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–298（298 aa）
Chain D 1–298（298 aa）
Not recorded VTJ compound × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；15 % PEG 3350, 0.1 M ammonium formate pH 4.5
Resolution 2.00 Å R-free 0.231
8OME Crystal structure of hKHK-A in complex with compound-4 Deposited 2023-03-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 1–298（298 aa）
Chain C 1–298（298 aa）
Not recorded VTJ compound × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；15 % PEG 3350, 0.1 M ammonium formate pH 4.5
Resolution 2.00 Å R-free 0.231
8OMF Crystal structure of hKHK-C in complex with compound-4 Deposited 2023-03-31 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 5–298（294 aa）
Chain B 5–298（294 aa）
Not recorded SO4 SULFATE ION × 4 VTJ compound × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；20% PEG 3350 and 0.1 mM BIS-TRIS Propane pH 7.5
Resolution 2.14 Å R-free 0.254
8OMJ hKHK-C in complex with compound 28 Deposited 2023-03-31 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 5–298（294 aa）
Chain B 5–298（294 aa）
Not recorded VTM [3-[[6-[(3~{a}~{R},6~{a}~{S})-2,3,3~{a},4,6,6~{a}-hexahydro-1~{H}-pyrrolo[3,4-c]pyrrol-5-yl]-3-cyano-4-(trifluoromethyl)pyridin-2-yl]amino]-4-methylsulfanyl-phenyl]methoxy-methyl-phosphinic acid × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；13% PEG 8000, 0.2 M ammonium sulfate, 0.1 M tri-sodium citrate pH 4.2
Resolution 1.98 Å R-free 0.252
8OMK hKHK-C in complex with ADP & fructose 1-phosphate Deposited 2023-03-31 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 5–298（294 aa）
Chain B 5–298（294 aa）
Not recorded F1X 1-O-phosphono-beta-D-fructofuranose × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；2 M ammonium sulphate
Resolution 2.48 Å R-free 0.219
8UG1 Crystal structure of KHK-C and compound 13 Deposited 2023-10-05 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 5–298（294 aa）
Chain B 5–298（294 aa）
Not recorded WNH {(2R)-1-[(4M)-4-[1-(piperidin-4-yl)-1H-pyrazol-4-yl]-6-(trifluoromethyl)pyrimidin-2-yl]azetidin-2-yl}methanol × 2 SO4 SULFATE ION × 8 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；Polyethylene glycol 8,000, Ammonium Sulfate, tri-Sodium citrate
Resolution 1.99 Å R-free 0.205
8UG3 Crystal structure of KHK-C and compound 23 Deposited 2023-10-05 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 5–298（294 aa）
Chain B 5–298（294 aa）
Not recorded WRE 2-[(4P)-4-{2-[(2S)-2-methylazetidin-1-yl]-6-(trifluoromethyl)pyrimidin-4-yl}-1H-pyrazol-1-yl]-1-(piperazin-1-yl)ethan-1-one × 2 SO4 SULFATE ION × 7 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；Polyethylene glycol 8,000, Ammonium Sulfate, tri-Sodium citrate
Resolution 2.02 Å R-free 0.216
9FHD hKHK-C in fomplex with BI-9787 Deposited 2024-05-27 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 5–298（294 aa）
Chain B 5–298（294 aa）
Not recorded SO4 SULFATE ION × 3 A1ICK (2~{S})-3-[3-[[4-[bis(fluoranyl)methyl]-3-cyano-6-[(3~{S})-3-(dimethylamino)pyrrolidin-1-yl]pyridin-2-yl]amino]-4-methylsulfanyl-phenyl]-2-methyl-propanoic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277.15 K；13% PEG 8000, 0.2 M ammonium sulfate, 0.1 M tri-sodium citrate pH 4.2
Resolution 1.84 Å R-free 0.204
9FHE hKHK-C in complex with BI-9787 (pH 5.5) Deposited 2024-05-27 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 5–298（294 aa）
Chain B 5–298（294 aa）
Not recorded A1ICK (2~{S})-3-[3-[[4-[bis(fluoranyl)methyl]-3-cyano-6-[(3~{S})-3-(dimethylamino)pyrrolidin-1-yl]pyridin-2-yl]amino]-4-methylsulfanyl-phenyl]-2-methyl-propanoic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；0.1 M ammonium acetate, 17% PEG 10,000, 0.1M BIS-TRIS pH 5.5
Resolution 2.31 Å R-free 0.235
9Z28 KHK Bound to Compound 7 Deposited 2025-11-04 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 5–298（294 aa）
Chain B 5–298（294 aa）
Not recorded A1C0G 4-methyl-2-[(2S)-2-methylazetidin-1-yl]-6,7-dihydro-5H-cyclopenta[d]pyrimidine × 2 SO4 SULFATE ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；100 mM NaCitrate pH 4.5, 200 mM Ammonium Sulfate, 10-15% PEG 8000
Resolution 2.15 Å R-free 0.225
9Z29 KHK Bound to Compound 9 Deposited 2025-11-04 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 5–298（294 aa）
Chain B 5–298（294 aa）
Not recorded A1C0I 4-{2-[(2S)-2-methylazetidin-1-yl]-6,7-dihydro-5H-cyclopenta[d]pyrimidin-4-yl}benzamide × 2 FRU beta-D-fructofuranose × 1 SO4 SULFATE ION × 3 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；100 mM NaCitrate pH 4.5, 200 mM Ammonium Sulfate, 10-15% PEG 8000
Resolution 1.97 Å R-free 0.249
9Z2A KHK Bound to Compound 12 Deposited 2025-11-04 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 5–298（294 aa）
Chain B 5–298（294 aa）
Not recorded A1C0K (3M)-3-{2-[(2S)-2-methylazetidin-1-yl]-6,7-dihydro-5H-cyclopenta[d]pyrimidin-4-yl}benzene-1-sulfonamide × 2 FRU beta-D-fructofuranose × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；100 mM NaCitrate pH 4.5, 200 mM Ammonium Sulfate, 10-15% PEG 8000
Resolution 2.00 Å R-free 0.237
9Z2B KHK Bound to Compound 18 Deposited 2025-11-04 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 5–298（294 aa）
Chain B 5–298（294 aa）
Not recorded A1C0J (2S,3R)-1-{4-[4-(3-aminooxetan-3-yl)phenyl]-7,7-difluoro-6,7-dihydro-5H-cyclopenta[d]pyrimidin-2-yl}-2-methylazetidin-3-ol × 2 SO4 SULFATE ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；100 mM NaCitrate pH 4.5, 200 mM Ammonium Sulfate, 10-15% PEG 8000
Resolution 2.11 Å R-free 0.250
9Z2C KHK Bound to GS-1291269 Deposited 2025-11-04 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 5–298（294 aa）
Chain B 5–298（294 aa）
Not recorded A1C0H 3-amino-3-(4-{7,7-difluoro-2-[(2R)-2-(trifluoromethyl)azetidin-1-yl]-6,7-dihydro-5H-cyclopenta[d]pyrimidin-4-yl}phenyl)-1lambda~6~-thietane-1,1-dione × 2 FRU beta-D-fructofuranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；100 mM NaCitrate pH 4.5, 200 mM Ammonium Sulfate, 10-15% PEG 8000
Resolution 2.02 Å R-free 0.231

29 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KHK_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 20–313； UniProt 5–298 Author chain B； PDBConstruct 20–313； UniProt 5–298

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

SAXS profile for 5wbm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5wbm
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id5wbm
Deposition date deposition_date2017-06-29
Structure title titleStructure of human Ketohexokinase complexed with hits from fragment screening
Keywords keywordsKetohexokinase, Fragment-based drug discovery, SBDD, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier29.66 Å
Radius of gyration Rg (electron density) rg_electron29.51 Å
Forward intensity I(0) i073193800.00
Molecular weight molecular_weight65748.0 kDa
Excluded volume excluded_volume81695 ų
Envelope volume envelope_volume102020 ų
Hydration-shell volume shell_volume30346 ų
Envelope diameter envelope_diameter104.0 Å
Shell Rg shell_rg35.21 Å
Envelope Rg envelope_rg29.43 Å
Shape Rg shape_rg29.54 Å
Total Rg total_rg29.95 Å
Total atoms total_atoms4619
Residues n_residues598
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

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

Maximum dimension Dmax dmax101.7 Å
Rg (real space) rg_real29.86 Å
Rg uncertainty (real space) rg_real_error0.70 Å
I(0) (real space) i0_real7.3190e+07
I(0) uncertainty (real space) i0_real_error9.5740e+05
Rg (reciprocal space) rg_reciprocal29.78 Å
I(0) (reciprocal space) i0_reciprocal73190000.0000
Solution quality estimate total_estimate0.8305
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.8 Å
Skewness Skewness skewness0.505
Kurtosis Kurtosis kurtosis-0.454
Angular range angular_range— – 0.2650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha22580000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.674; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.811; Smooth: 0.959
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

▼

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id5wbmA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
Homologous superfamily homologous superfamily20 — Ribokinase
Domain ID domain_id5wbmB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
Homologous superfamily homologous superfamily20 — Ribokinase
▶

8. Citations (1)

▶

9. Files and Curves (10)