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)

Method: X-RAY DIFFRACTION D_max: 98.3 Å Quality: GOOD

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

Ketohexokinase

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 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	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

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 6W0X	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
5WBM Structure of human Ketohexokinase complexed with hits from fragment screening Deposited 2017-06-29	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	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
5WBO Structure of human Ketohexokinase complexed with hits from fragment screening Deposited 2017-06-29	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	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 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	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 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	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 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	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 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	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
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 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 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

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	6w0x
Deposition date deposition_date	2020-03-03
Structure title title	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)
Keywords keywords	Ketohexokinase, TRANSFERASE; 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	29.36 Å
Radius of gyration Rg (electron density) rg_electron	29.19 Å
Forward intensity I(0) i0	73003700.00
Molecular weight molecular_weight	65625.0 kDa
Excluded volume excluded_volume	81488 Å³
Envelope volume envelope_volume	99940 Å³
Hydration-shell volume shell_volume	30029 Å³
Envelope diameter envelope_diameter	103.3 Å
Shell Rg shell_rg	34.98 Å
Envelope Rg envelope_rg	29.17 Å
Shape Rg shape_rg	29.22 Å
Total Rg total_rg	29.63 Å
Total atoms total_atoms	4609
Residues n_residues	597
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	98.3 Å
Rg (real space) rg_real	29.56 Å
Rg uncertainty (real space) rg_real_error	0.82 Å
I(0) (real space) i0_real	7.3000e+07
I(0) uncertainty (real space) i0_real_error	9.7850e+05
Rg (reciprocal space) rg_reciprocal	29.48 Å
I(0) (reciprocal space) i0_reciprocal	73000000.0000
Solution quality estimate total_estimate	0.7700
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.3 Å
Skewness Skewness skewness	0.507
Kurtosis Kurtosis kurtosis	-0.442
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	23210000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.711; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.881; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Ketohexokinase
Molecular weight formula_weight	34076.6 kDa
EC 编号 ec_number	2.7.1.3
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4902

MGSSHHHHHHSSGLVPRGSQILCVGLVVLDVISLVDKYPKEDSEIRCLSQRWQRGGNASNSCTVLSLLGAPCAFMGSMAPGHVADFLVADFRRRGVDVSQVAWQSKGDTPSSCCIINNSNGNRTIVLHDTSLPDVSATDFEKVDLTQFKWIHIEGRNASEQVKMLQRIDAHNTRQPPEQKIRVSVEVEKPREELFQLFGYGDVVFVSKDVAKHLGFQSAEEALRGLYGRVRKGAVLVCAWAEEGADALGPDGKLLHSDAFPPPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGFDGIV

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 non-polymer

Description description	;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 ;
Molecular weight formula_weight	368.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	293

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8. Citations (1)

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Unit-cell length a length_a	82.790 Å
Unit-cell length b length_b	85.820 Å
Unit-cell length c length_c	137.760 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	2.380 Å
Low-resolution limit resolution_low	20.940 Å
R factor r_factor	0.1870
R_work r_work	0.1860
R_free r_free	0.2060

fit	/app/data/saxs_computation/w0/6w0x/6w0x.fit
pddf	/app/data/pr_computation/w0/6w0x/6w0x.pr.out
profile	/app/data/saxs_computation/w0/6w0x/6w0x.dat