7z5n

Crystal structure of DYRK1A in complex with CX-4945

Method: X-RAY DIFFRACTION

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

Dual specificity tyrosine-phosphorylation-regulated kinase 1A

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid × 1 SULFATE ION × 5 TETRAETHYLENE GLYCOL × 2 DI(HYDROXYETHYL)ETHER × 1 1,2-ETHANEDIOL × 3 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid × 1 SULFATE ION × 5 TETRAETHYLENE GLYCOL × 2 1,2-ETHANEDIOL × 3 TRIETHYLENE GLYCOL × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid × 1 SULFATE ION × 3 TETRAETHYLENE GLYCOL × 1 1,2-ETHANEDIOL × 3 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid × 1 SULFATE ION × 3 TETRAETHYLENE GLYCOL × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid × 1 SULFATE ION × 2 TETRAETHYLENE GLYCOL × 1 DI(HYDROXYETHYL)ETHER × 1 1,2-ETHANEDIOL × 1 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid × 1 SULFATE ION × 1 1,2-ETHANEDIOL × 1 water × 1	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid × 1 SULFATE ION × 2 DI(HYDROXYETHYL)ETHER × 2 1,2-ETHANEDIOL × 2 water × 1	Consistent with protein count
8	Protein monomer	Monomer	Protein 1	5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid × 1 SULFATE ION × 1 TETRAETHYLENE GLYCOL × 1 TRIETHYLENE GLYCOL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DYR1A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–364； UniProt 126–489 Author chain B； PDBConstruct 1–364； UniProt 126–489 Author chain C； PDBConstruct 1–364； UniProt 126–489 Author chain D； PDBConstruct 1–364； UniProt 126–489 Author chain E； PDBConstruct 1–364； UniProt 126–489 Author chain F； PDBConstruct 1–364； UniProt 126–489 Author chain G； PDBConstruct 1–364； UniProt 126–489 Author chain H； PDBConstruct 1–364； UniProt 126–489

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	7z5n
Deposition date deposition_date	2022-03-09
Structure title title	Crystal structure of DYRK1A in complex with CX-4945
Keywords keywords	Kinase, diabetes, kinase inhibitor, TRANSFERASE; TRANSFERASE
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.

7z5n__assembly_5__model_1

Assembly 5 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7z5n__assembly_5__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7z5n__assembly_5__model_1 | P(r) · Pending

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

Rg（Guinier）	22.69 Å
Rg (electron density)	21.55 Å
Total Rg	22.31 Å
Atom count	2773
Residues	339
Excluded volume	49465 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7z5n__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7z5n__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`7z5n__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`7z5n__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`7z5n__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`7z5n__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`7z5n__assembly_7__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`7z5n__assembly_8__model_1`	monomeric （1）	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 (8)

Entity 1 Entity 1 polymer

Description description	Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Molecular weight formula_weight	43180.6 kDa
EC 编号 ec_number	2.7.12.1
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	21926

DSSHKKERKVYNDGYDDDNYDYIVKNGEKWMDRYEIDSLIGKGSFGQVVKAYDRVEQEWVAIKIIKNKKAFLNQAQIEVRLLELMNKHDTEMKYYIVHLKRHFMFRNHLCLVFEMLSYNLYDLLRNTNFRGVSLNLTRKFAQQMCTALLFLATPELSIIHCDLKPENILLCNPKRSAIKIVDFGSSCQLGQRIYQYIQSRFYRSPEVLLGMPYDLAIDMWSLGCILVEMHTGEPLFSGANEVDQMNKIVEVLGIPPAHILDQAPKARKFFEKLPDGTWNLKKTKDGKREYKPPGTRKLHNILGVETGGPGGRRAGESGHTVADYLKFKDLILRMLDYDPKTRIQPYYALQHSFFKKTADEGTNTHHHHHH

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	5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid
Molecular weight formula_weight	349.8 kDa
Source method src_method	syn
Copy count entity_count	8

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	22

Entity 4 Entity 4 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 7 Entity 7 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	206

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Unit-cell length a length_a	247.682 Å
Unit-cell length b length_b	134.317 Å
Unit-cell length c length_c	121.717 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.48 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.770 Å
Low-resolution limit resolution_low	26.140 Å
R factor r_factor	0.2073
R_work r_work	0.2050
R_free r_free	0.2516

Crystal structure of DYRK1A in complex with CX-4945

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

Dual specificity tyrosine-phosphorylation-regulated kinase 1A

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

7z5n__assembly_5__model_1

7z5n__assembly_5__model_1 | I(q)

7z5n__assembly_5__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 (8)

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 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)

Crystal structure of DYRK1A in complex with CX-4945

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

Dual specificity tyrosine-phosphorylation-regulated kinase 1A

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

7z5n__assembly_5__model_1

7z5n__assembly_5__model_1 | I(q)

7z5n__assembly_5__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 (8)

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 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)