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6bp0

Crystal Structure of the Human vaccinia-related kinase 1 bound to (R)-2-phenylaminopteridinone inhibitor

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Serine/threonine-protein kinase VRK1

Homo sapiens

UniProt Q99986

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein monomer Monomer Protein 1 CHLORIDE ION × 2 water × 1 Consistent with protein count
2 Protein monomer Monomer Protein 1 CHLORIDE ION × 3 (7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-5,7,8-trimethyl-7,8-dihydropteridin-6(5H)-one × 1 1,2-ETHANEDIOL × 1 water × 1 Consistent with protein count
3 Protein monomer Monomer Protein 1 CHLORIDE ION × 1 SULFATE ION × 1 GLYCEROL × 1 water × 1 Consistent with protein count
4 Protein monomer Monomer Protein 1 CHLORIDE ION × 1 (7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-5,7,8-trimethyl-7,8-dihydropteridin-6(5H)-one × 1 SULFATE ION × 4 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2kty 2kul 2lav 2rsv 3op5 3op5 3op5 3op5 5ukf 5ukf 5ukf 5ukf

80 assemblies; showing the first 12

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
7m10 7tan 8f8y 8f8y

4 assemblies

View Construct and Data Evidence
UniProt name VRK1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–364； UniProt 3–364 Author chain B； PDBConstruct 3–364； UniProt 3–364 Author chain C； PDBConstruct 3–364； UniProt 3–364 Author chain D； PDBConstruct 3–364； UniProt 3–364

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_id6bp0
Deposition date deposition_date2017-11-21
Structure title titleCrystal Structure of the Human vaccinia-related kinase 1 bound to (R)-2-phenylaminopteridinone inhibitor
Keywords keywords;transferase, protein kinase domain, Structural Genomics, Structural Genomics Consortium, SGC, Transferase-Transferase Inhibitor Complex ;; transferase/transferase inhibitor
Experimental Method methodX-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.

6bp0__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6bp0__assembly_2__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

6bp0__assembly_2__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）20.72 Å
Rg (electron density)19.46 Å
Total Rg20.41 Å
Atom count2432
Residues304
Excluded volume43232 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6bp0__assembly_1__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 6bp0__assembly_2__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 6bp0__assembly_3__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 6bp0__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 (7)

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd6bp0a_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.0 — automated matches
Domain ID domain_idd6bp0b_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.0 — automated matches
Domain ID domain_idd6bp0c_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.0 — automated matches
Domain ID domain_idd6bp0d_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id6bp0A02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id6bp0B02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id6bp0C02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id6bp0D02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
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7. Citations (1)