8r8e

DYRK1a in Complex with 2-Cyclopentyl-7-iodo-1H-indole-3-carbonitrile

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	2-cyclopentyl-7-iodanyl-1~{H}-indole-3-carbonitrile × 1 PENTAETHYLENE GLYCOL × 2 TETRAETHYLENE GLYCOL × 1 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 DI(HYDROXYETHYL)ETHER × 2 GLYCEROL × 3 1,2-ETHANEDIOL × 2 SULFATE ION × 8 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	2-cyclopentyl-7-iodanyl-1~{H}-indole-3-carbonitrile × 1 PENTAETHYLENE GLYCOL × 1 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 DI(HYDROXYETHYL)ETHER × 1 GLYCEROL × 3 1,2-ETHANEDIOL × 3 SULFATE ION × 5 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	2-cyclopentyl-7-iodanyl-1~{H}-indole-3-carbonitrile × 1 PENTAETHYLENE GLYCOL × 1 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 GLYCEROL × 3 1,2-ETHANEDIOL × 1 SULFATE ION × 5 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	2-cyclopentyl-7-iodanyl-1~{H}-indole-3-carbonitrile × 1 PENTAETHYLENE GLYCOL × 1 GLYCEROL × 2 SULFATE ION × 7 PHOSPHATE ION × 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, 2
Chains and sequence ranges	Author chain A； PDBConstruct 3–361； UniProt 127–485 Author chain B； PDBConstruct 3–361； UniProt 127–485 Author chain C； PDBConstruct 3–361； UniProt 127–485 Author chain D； PDBConstruct 3–361； UniProt 118–476

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	8r8e
Deposition date deposition_date	2023-11-29
Structure title title	DYRK1a in Complex with 2-Cyclopentyl-7-iodo-1H-indole-3-carbonitrile
Keywords keywords	Small Molecule, Kinase, Halogen Bond, Water interaction, 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.

8r8e__assembly_1__model_1

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

Download this curve (.dat)

8r8e__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8r8e__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.02 Å
Rg (electron density)	21.69 Å
Total Rg	22.50 Å
Atom count	2962
Residues	346
Excluded volume	52881 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8r8e__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8r8e__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`8r8e__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`8r8e__assembly_4__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 (12)

Entity 1 Entity 1 polymer

Description description	Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Molecular weight formula_weight	42081.5 kDa
EC 编号 ec_number	2.7.12.1
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	12068

SMSSHKKERKVYNDGYDDDNYDYIVKNGEKWMDRYEIDSLIGKGSFGQVVKAYDRVEQEWVAIKIIKNKKAFLNQAQIEVRLLELMNKHDTEMKYYIVHLKRHFMFRNHLCLVFEMLSYNLYDLLRNTNFRGVSLNLTRKFAQQMCTALLFLATPELSIIHCDLKPENILLCNPKRSAIKIVDFGSSCQLGQRIYQYIQSRFYRSPEVLLGMPYDLAIDMWSLGCILVEMHTGEPLFSGANEVDQMNKIVEVLGIPPAHILDQAPKARKFFEKLPDGTWNLKKTKDGKREYKPPGTRKLHNILGVETGGPGGRRAGESGHTVADYLKFKDLILRMLDYDPKTRIQPYYALQHSFFKKTADE

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(DE3)

Entity 2 Entity 2 polymer

Description description	Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Molecular weight formula_weight	42001.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

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(DE3)

Entity 3 Entity 3 non-polymer

Description description	2-cyclopentyl-7-iodanyl-1~{H}-indole-3-carbonitrile
Molecular weight formula_weight	336.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	PENTAETHYLENE GLYCOL
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 8 Entity 8 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 9 Entity 9 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 10 Entity 10 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	25

Entity 11 Entity 11 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 12 Entity 12 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	518

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Unit-cell length a length_a	244.236 Å
Unit-cell length b length_b	64.473 Å
Unit-cell length c length_c	147.332 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	115.58 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	2.220 Å
Low-resolution limit resolution_low	49.080 Å
R factor r_factor	0.1999
R_work r_work	0.1994
R_free r_free	0.2338

DYRK1a in Complex with 2-Cyclopentyl-7-iodo-1H-indole-3-carbonitrile

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

8r8e__assembly_1__model_1

8r8e__assembly_1__model_1 | I(q)

8r8e__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 (12)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

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 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 water

7. Citations (1)

DYRK1a in Complex with 2-Cyclopentyl-7-iodo-1H-indole-3-carbonitrile

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

8r8e__assembly_1__model_1

8r8e__assembly_1__model_1 | I(q)

8r8e__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 (12)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

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 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 water

7. Citations (1)