2y5l

orally active aminopyridines as inhibitors of tetrameric fructose 1,6- bisphosphatase

Method: X-RAY DIFFRACTION D_max: 167.2 Å Quality: GOOD

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

FRUCTOSE-1,6-BISPHOSPHATASE 1

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–338 Chain B； UniProt 1–338 Chain C； UniProt 1–338 Chain D； UniProt 1–338	Not recorded	RO8 N-{[(2Z)-5-bromo-1,3-thiazol-2(3H)-ylidene]carbamoyl}-3-chlorobenzenesulfonamide × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.20 Å R-free 0.254
2	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain E； UniProt 1–338 Chain F； UniProt 1–338 Chain G； UniProt 1–338 Chain H； UniProt 1–338	Not recorded	RO8 N-{[(2Z)-5-bromo-1,3-thiazol-2(3H)-ylidene]carbamoyl}-3-chlorobenzenesulfonamide × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.20 Å R-free 0.254

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 2Y5L	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1FTA FRUCTOSE-1,6-BISPHOSPHATASE(D-FRUCTOSE-1,6-BISPHOSPHATE, 1-PHOSPHOHYDROLASE) (E.C.3.1.3.11) COMPLEXED WITH THE ALLOSTERIC INHIBITOR AMP Deposited 1993-09-27	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–337（337 aa） Chain B 1–337（337 aa） Chain C 1–337（337 aa） Chain D 1–337（337 aa）	Not recorded	AMP ADENOSINE MONOPHOSPHATE × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
2JJK FRUCTOSE-1,6-BISPHOSPHATASE(D-FRUCTOSE-1,6-BISPHOSPHATE -1- PHOSPHOHYDROLASE) (E.C.3.1.3.11) COMPLEXED WITH A DUAL BINDING AMP SITE INHIBITOR Deposited 2008-04-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–338（338 aa） Chain B 1–338（338 aa） Chain C 1–338（338 aa） Chain D 1–338（338 aa）	Not recorded	R15 N,N'-(heptane-1,7-diyldicarbamoyl)bis(3-chlorobenzenesulfonamide) × 2	X-RAY DIFFRACTION X-ray crystallization conditions RESERVOIR = 0.1M HEPES PH7.0, 0.1M AMMONIUM ACETATE, 12% PEG 3350	Resolution 2.00 Å R-free 0.266
2VT5 FRUCTOSE-1,6-BISPHOSPHATASE(D-FRUCTOSE-1,6-BISPHOSPHATE -1- PHOSPHOHYDROLASE) (E.C.3.1.3.11) COMPLEXED WITH A DUAL BINDING AMP SITE INHIBITOR Deposited 2008-05-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–338（338 aa） Chain B 1–338（338 aa） Chain C 1–338（338 aa） Chain D 1–338（338 aa）	Not recorded	ROK 4-AMINO-N-[(2-SULFANYLETHYL)CARBAMOYL]BENZENESULFONAMIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions RESERVOIR = 0.1M HEPES, PH7.0, 0.1M AMMONIUM ACETATE, 12% PEG 3350	Resolution 2.20 Å R-free 0.247
2VT5 FRUCTOSE-1,6-BISPHOSPHATASE(D-FRUCTOSE-1,6-BISPHOSPHATE -1- PHOSPHOHYDROLASE) (E.C.3.1.3.11) COMPLEXED WITH A DUAL BINDING AMP SITE INHIBITOR Deposited 2008-05-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain E 1–338（338 aa） Chain F 1–338（338 aa） Chain G 1–338（338 aa） Chain H 1–338（338 aa）	Not recorded	ROK 4-AMINO-N-[(2-SULFANYLETHYL)CARBAMOYL]BENZENESULFONAMIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions RESERVOIR = 0.1M HEPES, PH7.0, 0.1M AMMONIUM ACETATE, 12% PEG 3350	Resolution 2.20 Å R-free 0.247
2WBB FRUCTOSE-1,6-BISPHOSPHATASE(D-FRUCTOSE-1,6-BISPHOSPHATE-1- PHOSPHOHYDROLASE) (E.C.3.1.3.11) COMPLEXED WITH AN AMP SITE INHIBITOR Deposited 2009-02-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–338（338 aa） Chain B 1–338（338 aa） Chain C 1–338（338 aa） Chain D 1–338（338 aa）	Not recorded	RO3 N-{[(2Z)-5-BROMO-1,3-THIAZOL-2(3H)-YLIDENE]CARBAMOYL}-4-METHYLBENZENESULFONAMIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions 0.1M AMMONIUM ACETATE 0.1M HEPES PH7 25% PEG 3350	Resolution 2.22 Å R-free 0.248
2WBB FRUCTOSE-1,6-BISPHOSPHATASE(D-FRUCTOSE-1,6-BISPHOSPHATE-1- PHOSPHOHYDROLASE) (E.C.3.1.3.11) COMPLEXED WITH AN AMP SITE INHIBITOR Deposited 2009-02-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain E 1–338（338 aa） Chain F 1–338（338 aa） Chain G 1–338（338 aa） Chain H 1–338（338 aa）	Not recorded	RO3 N-{[(2Z)-5-BROMO-1,3-THIAZOL-2(3H)-YLIDENE]CARBAMOYL}-4-METHYLBENZENESULFONAMIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions 0.1M AMMONIUM ACETATE 0.1M HEPES PH7 25% PEG 3350	Resolution 2.22 Å R-free 0.248
2WBD FRUCTOSE-1,6-BISPHOSPHATASE(D-FRUCTOSE-1,6-BISPHOSPHATE-1- PHOSPHOHYDROLASE) (E.C.3.1.3.11) COMPLEXED WITH AN AMP SITE INHIBITOR Deposited 2009-02-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–338（338 aa） Chain B 1–338（338 aa） Chain C 1–338（338 aa） Chain D 1–338（338 aa）	Not recorded	RO5 N-[(5-bromo-1,3-thiazol-2-yl)carbamoyl]-3-ethylbenzenesulfonamide × 4	X-RAY DIFFRACTION X-ray crystallization conditions 0.1M AMMONIUM ACETATE, 0.1M HEPES PH 7.0, 15% PEG 3350	Resolution 2.40 Å R-free 0.277
2WBD FRUCTOSE-1,6-BISPHOSPHATASE(D-FRUCTOSE-1,6-BISPHOSPHATE-1- PHOSPHOHYDROLASE) (E.C.3.1.3.11) COMPLEXED WITH AN AMP SITE INHIBITOR Deposited 2009-02-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain E 1–338（338 aa） Chain F 1–338（338 aa） Chain G 1–338（338 aa） Chain H 1–338（338 aa）	Not recorded	RO5 N-[(5-bromo-1,3-thiazol-2-yl)carbamoyl]-3-ethylbenzenesulfonamide × 4	X-RAY DIFFRACTION X-ray crystallization conditions 0.1M AMMONIUM ACETATE, 0.1M HEPES PH 7.0, 15% PEG 3350	Resolution 2.40 Å R-free 0.277
2Y5K Orally active aminopyridines as inhibitors of tetrameric fructose 1,6- bisphosphatase Deposited 2011-01-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–338（338 aa） Chain B 1–338（338 aa） Chain C 1–338（338 aa） Chain D 1–338（338 aa）	Not recorded	YCU 1-[5-(2-METHOXYETHYL)-4-METHYL-THIOPHEN-2-YL]SULFONYL-3-[4-METHOXY-6-(METHYLCARBAMOYLAMINO)PYRIDIN-2-YL]UREA × 4	X-RAY DIFFRACTION X-ray crystallization conditions RESERVOIR: 0.1M HEPES, PH 7.0, 0.1 M AMMONIUM ACETATE, 12% PEG 3350.	Resolution 2.10 Å R-free 0.296
3A29 Crystal structure of human liver FBPase in complex with tricyclic inhibitor Deposited 2009-05-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–338（337 aa） Chain B 2–338（337 aa） Chain C 2–338（337 aa） Chain D 2–338（337 aa）	Not recorded	2T0 2-amino-4,5-dihydronaphtho[1,2-d][1,3]thiazol-8-yl dihydrogen phosphate × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；8-10% PEG 3350, 0.15M NaCl, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.60 Å R-free 0.247
3A29 Crystal structure of human liver FBPase in complex with tricyclic inhibitor Deposited 2009-05-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–338（337 aa） Chain B 2–338（337 aa）	Not recorded	2T0 2-amino-4,5-dihydronaphtho[1,2-d][1,3]thiazol-8-yl dihydrogen phosphate × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；8-10% PEG 3350, 0.15M NaCl, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.60 Å R-free 0.247
3A29 Crystal structure of human liver FBPase in complex with tricyclic inhibitor Deposited 2009-05-08	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 A 2–338（337 aa） Chain C 2–338（337 aa）	Not recorded	2T0 2-amino-4,5-dihydronaphtho[1,2-d][1,3]thiazol-8-yl dihydrogen phosphate × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；8-10% PEG 3350, 0.15M NaCl, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.60 Å R-free 0.247
3A29 Crystal structure of human liver FBPase in complex with tricyclic inhibitor Deposited 2009-05-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 2–338（337 aa） Chain D 2–338（337 aa）	Not recorded	2T0 2-amino-4,5-dihydronaphtho[1,2-d][1,3]thiazol-8-yl dihydrogen phosphate × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；8-10% PEG 3350, 0.15M NaCl, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.60 Å R-free 0.247
3A29 Crystal structure of human liver FBPase in complex with tricyclic inhibitor Deposited 2009-05-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 2–338（337 aa） Chain D 2–338（337 aa）	Not recorded	2T0 2-amino-4,5-dihydronaphtho[1,2-d][1,3]thiazol-8-yl dihydrogen phosphate × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；8-10% PEG 3350, 0.15M NaCl, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.60 Å R-free 0.247
3KBZ Crystal structure of human liver FBPase in complex with tricyclic inhibitor 6 Deposited 2009-10-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–338（337 aa） Chain B 2–338（337 aa） Chain C 2–338（337 aa） Chain D 2–338（337 aa）	Not recorded	2T4 {[(2-amino-8H-indeno[1,2-d][1,3]thiazol-4-yl)oxy]methyl}phosphonic acid × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；8-10% PEG 3350, 0.15M NaCl, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.45 Å R-free 0.275
3KC0 Crystal structure of human liver FBPase in complex with tricyclic inhibitor 10b Deposited 2009-10-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–338（337 aa） Chain B 2–338（337 aa） Chain C 2–338（337 aa） Chain D 2–338（337 aa）	Not recorded	2T5 [(8H-indeno[1,2-d][1,3]thiazol-4-yloxy)methyl]phosphonic acid × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；8-10% PEG 3350, 0.15M NaCl, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.80 Å R-free 0.254
3KC1 Crystal structure of human liver FBPase in complex with tricyclic inhibitor 19a Deposited 2009-10-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–338（337 aa） Chain B 2–338（337 aa） Chain C 2–338（337 aa） Chain D 2–338（337 aa）	Not recorded	2T6 {[(7-carbamoyl-8H-indeno[1,2-d][1,3]thiazol-4-yl)oxy]methyl}phosphonic acid × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；8-10% PEG 3350, 0.15M NaCl, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.25 Å R-free 0.262
4MJO Human liver fructose-1,6-bisphosphatase(d-fructose-1,6-bisphosphate, 1-phosphohydrolase) (e.c.3.1.3.11) complexed with the allosteric inhibitor 3 Deposited 2013-09-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–338（338 aa） Chain B 1–338（338 aa） Chain C 1–338（338 aa） Chain D 1–338（338 aa）	Not recorded	2C1 N-({4-bromo-6-[(methylcarbamoyl)amino]pyridin-2-yl}carbamoyl)-5-(2-methoxyethyl)-4-methylthiophene-2-sulfonamide × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；300 K；0.1 M ammonium acetate and 12% polyethylenglycol 3350 in 0.1 M HEPES, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 300K	Resolution 2.40 Å R-free 0.236
4MJO Human liver fructose-1,6-bisphosphatase(d-fructose-1,6-bisphosphate, 1-phosphohydrolase) (e.c.3.1.3.11) complexed with the allosteric inhibitor 3 Deposited 2013-09-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain E 1–338（338 aa） Chain F 1–338（338 aa） Chain G 1–338（338 aa） Chain H 1–338（338 aa）	Not recorded	2C1 N-({4-bromo-6-[(methylcarbamoyl)amino]pyridin-2-yl}carbamoyl)-5-(2-methoxyethyl)-4-methylthiophene-2-sulfonamide × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；300 K；0.1 M ammonium acetate and 12% polyethylenglycol 3350 in 0.1 M HEPES, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 300K	Resolution 2.40 Å R-free 0.236
5LDZ Quadruple space group ambiguity due to rotational and translational non-crystallographic symmetry in human liver fructose-1,6-bisphosphatase Deposited 2016-06-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–338（338 aa） Chain B 1–338（338 aa） Chain C 1–338（338 aa） Chain D 1–338（338 aa）	Not recorded	ZN ZINC ION × 6 SO4 SULFATE ION × 20 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；0.1 M Tris-HCl pH 8.5, 2 M (NH4)2SO4	Resolution 2.20 Å R-free 0.239
5LDZ Quadruple space group ambiguity due to rotational and translational non-crystallographic symmetry in human liver fructose-1,6-bisphosphatase Deposited 2016-06-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain E 1–338（338 aa） Chain F 1–338（338 aa）	Not recorded	ZN ZINC ION × 6 SO4 SULFATE ION × 18 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；0.1 M Tris-HCl pH 8.5, 2 M (NH4)2SO4	Resolution 2.20 Å R-free 0.239
6LW2 The N-arylsulfonyl-indole-2-carboxamide-based inhibitors against fructose-1,6-bisphosphatase Deposited 2020-02-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–338（338 aa） Chain B 1–338（338 aa） Chain C 1–338（338 aa） Chain D 1–338（338 aa）	Not recorded	EW0 7-chloranyl-4-[(3-methoxyphenyl)amino]-N-(4-methoxyphenyl)sulfonyl-1-methyl-indole-2-carboxamide × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2M Ammonium acetate, 0.1M HEPES, 20% PEG 3350, pH 7.0	Resolution 2.40 Å R-free 0.290
7C9Q Crystal structure of Human liver fructose-1,6-bisphoaphatase complex with Mg2+ and AMP Deposited 2020-06-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–338（338 aa） Chain B 1–338（338 aa） Chain C 1–338（338 aa） Chain D 1–338（338 aa）	Not recorded	AMP ADENOSINE MONOPHOSPHATE × 4 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；50mM Hepes pH 7.2, 150mM Sodium chloride, 8% (w/v) PEG 8000	Resolution 1.88 Å R-free 0.219
7CVH Human Fructose-1,6-bisphosphatase 1 in complex with geranylgeranyl diphosphate Deposited 2020-08-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–338（338 aa） Chain B 1–338（338 aa） Chain C 1–338（338 aa） Chain D 1–338（338 aa）	Not recorded	FBP 1,6-di-O-phosphono-beta-D-fructofuranose × 4 MG MAGNESIUM ION × 8 AMP ADENOSINE MONOPHOSPHATE × 4 GRG GERANYLGERANYL DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；28% (v/v) polyethylene glycol 600, 0.1M HEPES	Resolution 2.09 Å R-free 0.218
7CVN The N-arylsulfonyl-indole-2-carboxamide-based inhibitors against fructose-1,6-bisphosphatase Deposited 2020-08-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–338（338 aa） Chain B 1–338（338 aa） Chain C 1–338（338 aa） Chain D 1–338（338 aa）	Not recorded	GJO 4-(3-acetamidophenyl)-N-(4-methoxyphenyl)sulfonyl-7-nitro-1H-indole-2-carboxamide × 4 FBP 1,6-di-O-phosphono-beta-D-fructofuranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2M Ammonium acetate, 0.1M HEPES, 20% PEG 3350, pH 7.0	Resolution 2.75 Å R-free 0.234
7CWE Human Fructose-1,6-bisphosphatase 1 in APO R-state Deposited 2020-08-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–338（338 aa） Chain B 1–338（338 aa）	Not recorded	MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；0.05 M cadmium sulfate, 0.1 M HEPES, pH 7.5, 1 M sodium acetate	Resolution 3.00 Å R-free 0.296
7EZF Indole-2-carboxylic acid derivatives as allosteric inhibitors of fructose-1,6-bisphosphatase Deposited 2021-06-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–338（338 aa） Chain B 1–338（338 aa） Chain C 1–338（338 aa） Chain D 1–338（338 aa）	Not recorded	0KI 7-chloranyl-5-ethyl-3-(3-hydroxy-3-oxopropyl)-1H-indole-2-carboxylic acid × 4 FBP 1,6-di-O-phosphono-beta-D-fructofuranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.2M Ammonium acetate, 0.1M HEPES, 20% PEG 3350, pH 7.0	Resolution 2.76 Å R-free 0.236
7EZP Indole-2-carboxylic acid derivatives as allosteric inhibitors of fructose-1,6-bisphosphatase Deposited 2021-06-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–338（338 aa） Chain B 1–338（338 aa） Chain C 1–338（338 aa） Chain D 1–338（338 aa）	Not recorded	FBP 1,6-di-O-phosphono-beta-D-fructofuranose × 4 0GI 3-(3-hydroxy-3-oxopropyl)-5-(2-methylpropyl)-7-nitro-1H-indole-2-carboxylic acid × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.2M Ammonium acetate, 0.1M HEPES, 20% PEG 3350, pH 7.0	Resolution 2.80 Å R-free 0.256
7EZR Indole-2-carboxylic acid derivatives as allosteric inhibitors of fructose-1,6-bisphosphatase Deposited 2021-06-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–338（338 aa） Chain B 1–338（338 aa） Chain C 1–338（338 aa） Chain D 1–338（338 aa）	Not recorded	0H1 5-ethyl-7-nitro-3-[3-oxidanylidene-3-(thiophen-2-ylsulfonylamino)propyl]-1H-indole-2-carboxylic acid × 4 FBP 1,6-di-O-phosphono-beta-D-fructofuranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.2M Ammonium acetate, 0.1M HEPES, 20% PEG 3350, pH 7.0	Resolution 3.27 Å R-free 0.253
7WVB Human Fructose-1,6-bisphosphatase 1 mutant R50A in APO R-state Deposited 2022-02-10	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–338（338 aa） Chain B 1–338（338 aa） Chain C 1–338（338 aa） Chain D 1–338（338 aa）	Mutation：R50A Mutation：R50A Mutation：R50A Mutation：R50A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；0.1M BIS-Tris(pH 6.5), 20% PEGMME 5000, 2.5% sucrose	Resolution 2.09 Å R-free 0.233
9XV1 Crystal Structure of Fructose-1,6-bisphosphatase Complexed with a Covalent Inhibitor Deposited 2025-11-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–336（336 aa） Chain B 1–336（336 aa） Chain C 1–336（336 aa） Chain D 1–336（336 aa）	Not recorded	A1E1G 2-bromanyl-~{N}-[2-[4-[(3-phenylphenyl)carbamoylsulfamoyl]phenyl]ethyl]ethanamide × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Tris (pH 8.8), 15% (v/v) EtOH	Resolution 1.96 Å R-free 0.213

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

View Construct and Data Evidence

UniProt name	F16P1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–338； UniProt 1–338 Author chain B； PDBConstruct 1–338； UniProt 1–338 Author chain C； PDBConstruct 1–338； UniProt 1–338 Author chain D； PDBConstruct 1–338； UniProt 1–338 Author chain E； PDBConstruct 1–338； UniProt 1–338 Author chain F； PDBConstruct 1–338； UniProt 1–338 Author chain G； PDBConstruct 1–338； UniProt 1–338 Author chain H； PDBConstruct 1–338； UniProt 1–338

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	2y5l
Deposition date deposition_date	2011-01-14
Structure title title	orally active aminopyridines as inhibitors of tetrameric fructose 1,6- bisphosphatase
Keywords keywords	HYDROLASE; HYDROLASE
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	51.82 Å
Radius of gyration Rg (electron density) rg_electron	51.79 Å
Forward intensity I(0) i0	1097170000.00
Molecular weight molecular_weight	280490.0 kDa
Excluded volume excluded_volume	352740 Å³
Envelope volume envelope_volume	470920 Å³
Hydration-shell volume shell_volume	75970 Å³
Envelope diameter envelope_diameter	176.1 Å
Shell Rg shell_rg	54.84 Å
Envelope Rg envelope_rg	50.97 Å
Shape Rg shape_rg	51.82 Å
Total Rg total_rg	51.75 Å
Total atoms total_atoms	19600
Residues n_residues	2548
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	167.2 Å
Rg (real space) rg_real	51.97 Å
Rg uncertainty (real space) rg_real_error	1.56 Å
I(0) (real space) i0_real	1.0970e+09
I(0) uncertainty (real space) i0_real_error	2.0180e+07
Rg (reciprocal space) rg_reciprocal	51.67 Å
I(0) (reciprocal space) i0_reciprocal	1097000000.0000
Solution quality estimate total_estimate	0.8415
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	50.1 Å
Skewness Skewness skewness	0.349
Kurtosis Kurtosis kurtosis	-0.644
Angular range angular_range	— – 0.1500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	56090000.0000
Real-space data points n_real_points	31
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.216

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	FRUCTOSE-1,6-BISPHOSPHATASE 1
Molecular weight formula_weight	36859.4 kDa
EC 编号 ec_number	3.1.3.11
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	20167

MADQAPFDTDVNTLTRFVMEEGRKARGTGELTQLLNSLCTAVKAISSAVRKAGIAHLYGIAGSTNVTGDQVKKLDVLSNDLVMNMLKSSFATCVLVSEEDKHAIIVEPEKRGKYVVCFDPLDGSSNIDCLVSVGTIFGIYRKKSTDEPSEKDALQPGRNLVAAGYALYGSATMLVLAMDCGVNCFMLDPAIGEFILVDKDVKIKKKGKIYSLNEGYAKDFDPAVTEYIQRKKFPPDNSAPYGARYVGSMVADVHRTLVYGGIFLYPANKKSPNGKLRLLYECNPMAYVMEKAGGMATTGKEAVLDVIPTDIHQRAPVILGSPDDVLEFLKVYEKHSAQ

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	N-{[(2Z)-5-bromo-1,3-thiazol-2(3H)-ylidene]carbamoyl}-3-chlorobenzenesulfonamide
Molecular weight formula_weight	396.7 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	534

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7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2y5la_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.7 — Carbohydrate phosphatase
Superfamily Superfamily superfamily	e.7.1 — Carbohydrate phosphatase
Family Family family	e.7.1.1 — Inositol monophosphatase/fructose-1,6-bisphosphatase-like

Domain ID domain_id	d2y5lb_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.7 — Carbohydrate phosphatase
Superfamily Superfamily superfamily	e.7.1 — Carbohydrate phosphatase
Family Family family	e.7.1.1 — Inositol monophosphatase/fructose-1,6-bisphosphatase-like

Domain ID domain_id	d2y5lc_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.7 — Carbohydrate phosphatase
Superfamily Superfamily superfamily	e.7.1 — Carbohydrate phosphatase
Family Family family	e.7.1.1 — Inositol monophosphatase/fructose-1,6-bisphosphatase-like

Domain ID domain_id	d2y5ld_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.7 — Carbohydrate phosphatase
Superfamily Superfamily superfamily	e.7.1 — Carbohydrate phosphatase
Family Family family	e.7.1.1 — Inositol monophosphatase/fructose-1,6-bisphosphatase-like

Domain ID domain_id	d2y5le_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.7 — Carbohydrate phosphatase
Superfamily Superfamily superfamily	e.7.1 — Carbohydrate phosphatase
Family Family family	e.7.1.1 — Inositol monophosphatase/fructose-1,6-bisphosphatase-like

Domain ID domain_id	d2y5lf_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.7 — Carbohydrate phosphatase
Superfamily Superfamily superfamily	e.7.1 — Carbohydrate phosphatase
Family Family family	e.7.1.1 — Inositol monophosphatase/fructose-1,6-bisphosphatase-like

Domain ID domain_id	d2y5lg_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.7 — Carbohydrate phosphatase
Superfamily Superfamily superfamily	e.7.1 — Carbohydrate phosphatase
Family Family family	e.7.1.1 — Inositol monophosphatase/fructose-1,6-bisphosphatase-like

Domain ID domain_id	d2y5lh_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.7 — Carbohydrate phosphatase
Superfamily Superfamily superfamily	e.7.1 — Carbohydrate phosphatase
Family Family family	e.7.1.1 — Inositol monophosphatase/fructose-1,6-bisphosphatase-like

CATH v4.4 (16 domains)

Domain ID domain_id	2y5lA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	540 — Fructose-1,6-Bisphosphatase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Fructose-1,6-Bisphosphatase, subunit A, domain 1

Domain ID domain_id	2y5lA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	80 —

Domain ID domain_id	2y5lB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	540 — Fructose-1,6-Bisphosphatase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Fructose-1,6-Bisphosphatase, subunit A, domain 1

Domain ID domain_id	2y5lB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	80 —

Domain ID domain_id	2y5lC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	540 — Fructose-1,6-Bisphosphatase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Fructose-1,6-Bisphosphatase, subunit A, domain 1

Domain ID domain_id	2y5lC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	80 —

Domain ID domain_id	2y5lD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	540 — Fructose-1,6-Bisphosphatase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Fructose-1,6-Bisphosphatase, subunit A, domain 1

Domain ID domain_id	2y5lD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	80 —

Domain ID domain_id	2y5lE01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	540 — Fructose-1,6-Bisphosphatase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Fructose-1,6-Bisphosphatase, subunit A, domain 1

Domain ID domain_id	2y5lE02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	80 —

Domain ID domain_id	2y5lF01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	540 — Fructose-1,6-Bisphosphatase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Fructose-1,6-Bisphosphatase, subunit A, domain 1

Domain ID domain_id	2y5lF02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	80 —

Domain ID domain_id	2y5lG01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	540 — Fructose-1,6-Bisphosphatase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Fructose-1,6-Bisphosphatase, subunit A, domain 1

Domain ID domain_id	2y5lG02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	80 —

Domain ID domain_id	2y5lH01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	540 — Fructose-1,6-Bisphosphatase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Fructose-1,6-Bisphosphatase, subunit A, domain 1

Domain ID domain_id	2y5lH02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	80 —

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8. Citations (1)

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Unit-cell length a length_a	66.791 Å
Unit-cell length b length_b	285.084 Å
Unit-cell length c length_c	83.687 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.30 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	142.860 Å
R factor r_factor	0.2074
R_work r_work	0.2050
R_free r_free	0.2537

fit	/app/data/saxs_computation/y5/2y5l/2y5l.fit
pddf	/app/data/pr_computation/y5/2y5l/2y5l.pr.out
profile	/app/data/saxs_computation/y5/2y5l/2y5l.dat