2y5k

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

Method: X-RAY DIFFRACTION

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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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	1-[5-(2-METHOXYETHYL)-4-METHYL-THIOPHEN-2-YL]SULFONYL-3-[4-METHOXY-6-(METHYLCARBAMOYLAMINO)PYRIDIN-2-YL]UREA × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

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

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2y5k
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. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

2y5k__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2y5k__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2y5k__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	34.20 Å
Rg (electron density)	33.43 Å
Total Rg	33.82 Å
Atom count	9849
Residues	1275
Excluded volume	177270 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2y5k__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. 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	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	10852

MADQAPFDTDVNTLTRFVMEEGRKARGTGELTQLLNSLCTAVKAISSAVRKAGIAHLYGIAGSTNVTGDQVKKLDVLSNDLVMNMLKSSFATCVLVSEEDKHAIIVEPEKRGKYVVCFDPLDGSSNIDCLVSVGTIFGIYRKKSTDEPSEKDALQPGRNLVAAGYALYGSATMLVLAMDCGVNCFMLDPAIGEFILVDKDVKIKKKGKIYSLNEGYAKDFDPAVTEYIQRKKFPPDNSAPYGARYVGSMVADVHRTLVYGGIFLYPANKKSPNGKLRLLYECNPMAYVMEKAGGMATTGKEAVLDVIPTDIHQRAPVILGSPDDVLEFLKVYEKHSAQ

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	1-[5-(2-METHOXYETHYL)-4-METHYL-THIOPHEN-2-YL]SULFONYL-3-[4-METHOXY-6-(METHYLCARBAMOYLAMINO)PYRIDIN-2-YL]UREA
Molecular weight formula_weight	457.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1003

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2y5ka_
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	d2y5kb_
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	d2y5kc_
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	d2y5kd_
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 (8 domains)

Domain ID domain_id	2y5kA01
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	2y5kA02
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	2y5kB01
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	2y5kB02
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	2y5kC01
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	2y5kC02
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	2y5kD01
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	2y5kD02
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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Unit-cell length a length_a	67.136 Å
Unit-cell length b length_b	82.784 Å
Unit-cell length c length_c	276.604 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	16

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

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	29.480 Å
R factor r_factor	0.2466
R_work r_work	0.2440
R_free r_free	0.2963

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

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

FRUCTOSE-1,6-BISPHOSPHATASE 1

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2y5k__assembly_1__model_1

2y5k__assembly_1__model_1 | I(q)

2y5k__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

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

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

FRUCTOSE-1,6-BISPHOSPHATASE 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2y5k__assembly_1__model_1

2y5k__assembly_1__model_1 | I(q)

2y5k__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)