SAXSdb — 9wp3

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

;cGMP-dependent 3',5'-cyclic phosphodiesterase ;

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	ZINC ION × 4 MAGNESIUM ION × 4 7-oxidanylidene-~{N}-[(1~{S})-1-[4-(trifluoromethyl)phenyl]propyl]-2,4,5,6-tetrahydropyrazolo[3,4-c]pyridine-3-carboxamide × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PDE2A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–340； UniProt 580–919 Author chain B； PDBConstruct 1–340； UniProt 580–919 Author chain C； PDBConstruct 1–340； UniProt 580–919 Author chain D； PDBConstruct 1–340； UniProt 580–919

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	9wp3
Deposition date deposition_date	2025-09-08
Last revision last_revision	2026-02-18
Structure title title	The crystal structure of PDE2A complexed with inhibitor 13j
Keywords keywords	PDE2A inhibitor, 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.

9wp3__assembly_1__model_1

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

Download this curve (.dat)

9wp3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9wp3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.55 Å
Rg (electron density)	34.82 Å
Total Rg	35.21 Å
Atom count	10032
Residues	1243
Excluded volume	178410 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9wp3__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 (5)

Entity 1 Entity 1 polymer

Description description	;cGMP-dependent 3',5'-cyclic phosphodiesterase ;
Molecular weight formula_weight	39763.6 kDa
EC 编号 ec_number	3.1.4.17
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	10150

DEYTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFLDEE

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 BL21

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	7-oxidanylidene-~{N}-[(1~{S})-1-[4-(trifluoromethyl)phenyl]propyl]-2,4,5,6-tetrahydropyrazolo[3,4-c]pyridine-3-carboxamide
Molecular weight formula_weight	366.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	94

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Unit-cell length a length_a	55.782 Å
Unit-cell length b length_b	73.080 Å
Unit-cell length c length_c	91.114 Å
Unit-cell angle α angle_alpha	109.62 °
Unit-cell angle β angle_beta	91.18 °
Unit-cell angle γ angle_gamma	90.85 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	2.502 Å
Low-resolution limit resolution_low	23.732 Å
R factor r_factor	0.2591
R_work r_work	0.2562
R_free r_free	0.3109

The crystal structure of PDE2A complexed with inhibitor 13j

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

;cGMP-dependent 3',5'-cyclic phosphodiesterase ;

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

9wp3__assembly_1__model_1

9wp3__assembly_1__model_1 | I(q)

9wp3__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)

The crystal structure of PDE2A complexed with inhibitor 13j

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

;cGMP-dependent 3',5'-cyclic phosphodiesterase ;

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

9wp3__assembly_1__model_1

9wp3__assembly_1__model_1 | I(q)

9wp3__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)