SAXSdb — 9i9q

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

5-hydroxymethyl-dUMP N-hydrolase

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ETHANOL × 1 1,2-ETHANEDIOL × 1 2-[1-methyl-5-[[1-[2-(methylamino)phenyl]carbonylpiperidin-4-yl]amino]-1,2,4-triazol-3-yl]-1~{H}-indole-6-carbonitrile × 2 CHLORIDE ION × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	2-[1-methyl-5-[[1-[2-(methylamino)phenyl]carbonylpiperidin-4-yl]amino]-1,2,4-triazol-3-yl]-1~{H}-indole-6-carbonitrile × 2 CHLORIDE ION × 3 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DNPH1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–144； UniProt 20–162 Author chain B； PDBConstruct 2–144； UniProt 20–162 Author chain C； PDBConstruct 2–144； UniProt 20–162 Author chain D； PDBConstruct 2–144； UniProt 20–162

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	9i9q
Deposition date deposition_date	2025-02-06
Structure title title	Crystal structure of DNPH1 bound by compound 2.
Keywords keywords	DNPH1, inhibitor, small molecule, drug discovery, DDR, DNA damage response, 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.

9i9q__assembly_1__model_1

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

Download this curve (.dat)

9i9q__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9i9q__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.36 Å
Rg (electron density)	18.29 Å
Total Rg	19.17 Å
Atom count	2057
Residues	253
Excluded volume	36145 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9i9q__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9i9q__assembly_2__model_1`	dimeric （2）	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 (6)

Entity 1 Entity 1 polymer

Description description	5-hydroxymethyl-dUMP N-hydrolase
Molecular weight formula_weight	17174.3 kDa
EC 编号 ec_number	3.2.2.-
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	4412

MRPALYFCGSIRGGREDRTLYERIVSRLRRFGTVLTEHVAAAELGARGEEAAGGDRLIHEQDLEWLQQADVVVAEVTQPSLGVGYELGRAVAFNKRILCLFRPQSGRVLSAMIRGAADGSRFQVWDYEEGEVEALLDRYFEADPLEENLYFQ

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	ETHANOL
Molecular weight formula_weight	46.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	2-[1-methyl-5-[[1-[2-(methylamino)phenyl]carbonylpiperidin-4-yl]amino]-1,2,4-triazol-3-yl]-1~{H}-indole-6-carbonitrile
Molecular weight formula_weight	454.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	249

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Unit-cell length a length_a	74.887 Å
Unit-cell length b length_b	74.887 Å
Unit-cell length c length_c	253.173 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	32

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.721 Å
Low-resolution limit resolution_low	34.230 Å
R factor r_factor	0.2262
R_work r_work	0.2255
R_free r_free	0.2404

Crystal structure of DNPH1 bound by compound 2.

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

5-hydroxymethyl-dUMP N-hydrolase

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

9i9q__assembly_1__model_1

9i9q__assembly_1__model_1 | I(q)

9i9q__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 (6)

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 non-polymer

Entity 6 Entity 6 water

7. Citations (1)

Crystal structure of DNPH1 bound by compound 2.

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

5-hydroxymethyl-dUMP N-hydrolase

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

9i9q__assembly_1__model_1

9i9q__assembly_1__model_1 | I(q)

9i9q__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 (6)

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 non-polymer

Entity 6 Entity 6 water

7. Citations (1)