9vir

Crystal Structure of the NUAK1-MARK3 kinase domain chimera bound with small molecule inhibitor N-(5-((5-chloro-4-(((3aS,6R,6aR)-6-methoxy-3a,5,6,6a-tetrahydrofuro[3,2-b]furan-3-yl)oxy)pyrimidin-2-yl)amino)-2-(((2R,7aR)-2-fluorotetrahydro-1H-pyrrolizin-7a(5H)-yl)methoxy)phenyl)-1-methyl-1H-pyrazole-4-carboxamide

Method: X-RAY DIFFRACTION

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

MAP/microtubule affinity-regulating kinase 3

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	;~{N}-[5-[[4-[[(3~{R},3~{a}~{R},6~{a}~{S})-3-methoxy-2,3,3~{a},6~{a}-tetrahydrofuro[3,2-b]furan-6-yl]oxy]-5-chloranyl-pyrimidin-2-yl]amino]-2-[[(2~{R},8~{R})-2-fluoranyl-1,2,3,5,6,7-hexahydropyrrolizin-8-yl]methoxy]phenyl]-1-methyl-pyrazole-4-carboxamide ; × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MARK3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–326； UniProt 48–370

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	9vir
Deposition date deposition_date	2025-06-18
Last revision last_revision	2026-04-22
Structure title title	Crystal Structure of the NUAK1-MARK3 kinase domain chimera bound with small molecule inhibitor N-(5-((5-chloro-4-(((3aS,6R,6aR)-6-methoxy-3a,5,6,6a-tetrahydrofuro[3,2-b]furan-3-yl)oxy)pyrimidin-2-yl)amino)-2-(((2R,7aR)-2-fluorotetrahydro-1H-pyrrolizin-7a(5H)-yl)methoxy)phenyl)-1-methyl-1H-pyrazole-4-carboxamide
Keywords keywords	protein kinase, complex, CYTOSOLIC PROTEIN; CYTOSOLIC PROTEIN
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.

9vir__assembly_1__model_1

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

Download this curve (.dat)

9vir__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9vir__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.78 Å
Rg (electron density)	20.75 Å
Total Rg	21.74 Å
Atom count	2607
Residues	318
Excluded volume	46653 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9vir__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9vir__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	MAP/microtubule affinity-regulating kinase 3
Molecular weight formula_weight	37744.7 kDa
EC 编号 ec_number	2.7.11.1
Mutation mutation	I62L/L72R/V116I/G137K/F141Y/A146E
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3232

MGSDEQPHIGNYRLLKTLGKGNFAKVKRARHILTGREVAIKIIDKTQLNPTSLQKLFREVRIMKILNHPNIIKLFEVIETEKTLYLIMEYASKGEVYDYLVEHGRMKEKEARSKFRQIVSAVQYCHQKRIVHRDLKAENLLLDADMNIKIADFGFSNEFTVGGKLDTFCGSPPYAAPELFQGKKYDGPEVDVWSLGVILYTLVSGSLPFDGQNLKELRERVLRGKYRIPFYMSTDCENLLKRFLVLNPIKRGTLEQIMKDRWINAGHEEDELKPFVEPELDISDQKRIDIMVGMGYSQEEIQESLSKMKYDEITATYLLLGRKSSE

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 polymer

Description description	MAP/microtubule affinity-regulating kinase 3
Molecular weight formula_weight	27762.1 kDa
EC 编号 ec_number	2.7.11.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

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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 3 Entity 3 non-polymer

Description description	;~{N}-[5-[[4-[[(3~{R},3~{a}~{R},6~{a}~{S})-3-methoxy-2,3,3~{a},6~{a}-tetrahydrofuro[3,2-b]furan-6-yl]oxy]-5-chloranyl-pyrimidin-2-yl]amino]-2-[[(2~{R},8~{R})-2-fluoranyl-1,2,3,5,6,7-hexahydropyrrolizin-8-yl]methoxy]phenyl]-1-methyl-pyrazole-4-carboxamide ;
Molecular weight formula_weight	642.1 kDa
Source method src_method	man
Copy count entity_count	1

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Unit-cell length a length_a	84.360 Å
Unit-cell length b length_b	45.320 Å
Unit-cell length c length_c	165.677 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.30 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	46.314 Å
R factor r_factor	0.2694
R_work r_work	0.2672
R_free r_free	0.3158

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

MAP/microtubule affinity-regulating kinase 3

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

9vir__assembly_1__model_1

9vir__assembly_1__model_1 | I(q)

9vir__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

7. Citations (1)

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

MAP/microtubule affinity-regulating kinase 3

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

9vir__assembly_1__model_1

9vir__assembly_1__model_1 | I(q)

9vir__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

7. Citations (1)