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6bp0

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

Method: X-RAY DIFFRACTION Dmax: 115.7 Å Quality: GOOD
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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 Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 3–364 Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A CL CHLORIDE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；22% PEG3350; 0.02M Lithium Sulfate; 0.1M Buffer system SBG pH 7.0 Resolution 1.90 Å R-free 0.226
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 3–364 Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A CL CHLORIDE ION × 3 E1D (7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-5,7,8-trimethyl-7,8-dihydropteridin-6(5H)-one × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；22% PEG3350; 0.02M Lithium Sulfate; 0.1M Buffer system SBG pH 7.0 Resolution 1.90 Å R-free 0.226
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 3–364 Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A CL CHLORIDE ION × 1 SO4 SULFATE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；22% PEG3350; 0.02M Lithium Sulfate; 0.1M Buffer system SBG pH 7.0 Resolution 1.90 Å R-free 0.226
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain D； UniProt 3–364 Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A CL CHLORIDE ION × 1 E1D (7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-5,7,8-trimethyl-7,8-dihydropteridin-6(5H)-one × 1 SO4 SULFATE ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；22% PEG3350; 0.02M Lithium Sulfate; 0.1M Buffer system SBG pH 7.0 Resolution 1.90 Å R-free 0.226

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6BP0 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2KTY Solution Structure of human Vaccinia Related Kinase-1 Deposited 2010-02-10 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–360（360 aa） Fragment：residues 1-360
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 20
NMR sample composition 0.3-0.5mM [U-100% 13C; U-100% 15N; U-80% 2H] Vaccinia Related-Kinase 1; 0.3-0.5mM [U-100% 15N; U-50% 2H] Vaccinia Related-Kinase 1; 0.1-0.2mM [U-100% 15N] Vaccinia Related-Kinase 1; 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.3-0.5mM [U-100% 13C; U-100% 15N; U-70% 2H] Vaccinia Related-Kinase 1; 0.3-0.5mM [13C;15N]-Val,Ile,Leu; [U-100% 2H] Vaccinia Related-Kinase 1; 100% D2O | 100% D2O
Resolution not provided
2KUL Solution structure of human vaccinia related kinase 1(VRK1) Deposited 2010-02-19 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–360（360 aa） Fragment：residues 1-360
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 20
NMR sample composition 0.3-0.5mM [U-100% 13C; U-100% 15N; U-80% 2H] Vaccinia Related-Kinase 1; 0.3-0.5mM [U-100% 15N; U-50% 2H] Vaccinia Related-Kinase 1; 0.1-0.2mM [U-100% 15N] Vaccinia Related-Kinase 1; 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.3-0.5mM [U-100% 13C; U-100% 15N; U-70% 2H] Vaccinia Related-Kinase 1; 0.3-0.5mM [13C;15N]-Val,Ile,Leu; [U-100% 2H] Vaccinia Related-Kinase 1; 100% D2O | 100% D2O
Resolution not provided
2LAV NMR solution structure of human Vaccinia-Related Kinase 1 Deposited 2011-03-21 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–361（361 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 20
NMR sample composition 0.3-0.5 mM [U-100% 13C; U-100% 15N; U-80% 2H] Vaccinia Related-Kinase 1, 0.3-0.5 mM [U-100% 15N; U-50% 2H] Vaccinia Related-Kinase 1, 0.1-0.2 mM [U-100% 15N] Vaccinia Related-Kinase 1, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.3-0.5 mM [U-100% 13C; U-100% 15N; U-70% 2H] Vaccinia Related-Kinase 1, 0.3-0.5 mM [13C;15N]-Val,Ile,Leu; [U-100% 2H] Vaccinia Related-Kinase 1, 100% D2O | 100% D2O
Resolution not provided
2RSV Solution structure of human full-length vaccinia related kinase 1 (VRK1) Deposited 2012-07-12 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–396（396 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120；Pressure ambient
NMR sample composition 0.4 MM [U-13C; U-15N; U-2H; 1H ILE, LEU, VAL, ALA METHYL; 1H MET METHYL,GAMMA; 1H PHE EPSILON] VRK1, 20 MM [U-2H] TRIS,100 MM SODIUM CHLORIDE, 50 MM GLUTAMIC ACID, 50 MM ARGININE, 1 MM [U-2H] DTT, 0.02 % SODIUM AZIDE, 90% H2O/10% D2O; 0.4 MM [U-13C; U-15N; U-2H; 1H ILE, LEU, VAL METHYL; 1H PHE, TYR EPSILON] VRK1, 20 MM [U-2H] TRIS,100 MM SODIUM CHLORIDE, 50 MM GLUTAMIC ACID, 50 MM ARGININE, 1 MM [U-2H] DTT, 0.02 % SODIUM AZIDE, 90% H2O/10% D2O; 0.4 MM [U-15N; U-2H; 13C,1H ILE, LEU, VAL METHYL; 13C,1H PHE DELTA/EPSILON/ZETA] VRK1, 20 MM [U-2H] TRIS,100 MM SODIUM CHLORIDE, 50 MM GLUTAMIC ACID, 50 MM ARGININE, 1 MM [U-2H] DTT, 0.02 % SODIUM AZIDE, 90% H2O/10% D2O; 0.4 MM SAIL-VRK1, 20 MM [U-2H] TRIS, 100 MM SODIUM CHLORIDE, 50 MM GLUTAMIC ACID, 50 MM ARGININE, 1 MM [U-2H] DTT, 0.02 % SODIUM AZIDE, 90% H2O/10% D2O; | 90% H2O/10% D2O
Resolution not provided
3OP5 Human vaccinia-related kinase 1 Deposited 2010-08-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3–364（362 aa） Fragment：KINASE DOMAIN, RESIDUES 3-369
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A REB [4-({4-[(5-cyclopropyl-1H-pyrazol-3-yl)amino]pyrimidin-2-yl}amino)phenyl]acetonitrile × 1 EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.2m K/Na(tartrate), 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.40 Å R-free 0.213
3OP5 Human vaccinia-related kinase 1 Deposited 2010-08-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 3–364（362 aa） Fragment：KINASE DOMAIN, RESIDUES 3-369
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A REB [4-({4-[(5-cyclopropyl-1H-pyrazol-3-yl)amino]pyrimidin-2-yl}amino)phenyl]acetonitrile × 1 EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.2m K/Na(tartrate), 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.40 Å R-free 0.213
3OP5 Human vaccinia-related kinase 1 Deposited 2010-08-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 3–364（362 aa） Fragment：KINASE DOMAIN, RESIDUES 3-369
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A REB [4-({4-[(5-cyclopropyl-1H-pyrazol-3-yl)amino]pyrimidin-2-yl}amino)phenyl]acetonitrile × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.2m K/Na(tartrate), 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.40 Å R-free 0.213
3OP5 Human vaccinia-related kinase 1 Deposited 2010-08-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 3–364（362 aa） Fragment：KINASE DOMAIN, RESIDUES 3-369
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A REB [4-({4-[(5-cyclopropyl-1H-pyrazol-3-yl)amino]pyrimidin-2-yl}amino)phenyl]acetonitrile × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.2m K/Na(tartrate), 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.40 Å R-free 0.213
5UKF Crystal Structure of the Human Vaccinia-related Kinase 1 Bound to an Oxindole Inhibitor Deposited 2017-01-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3–364（362 aa） Fragment：UNP residues 3-364
Not recorded 8E1 4-{[(Z)-(7-oxo-6,7-dihydro-8H-[1,3]thiazolo[5,4-e]indol-8-ylidene)methyl]amino}benzene-1-sulfonamide × 1 PO4 PHOSPHATE ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；27.5% PEG 3350; 0.3M AmSO4; 0.1M HEPES pH 7.0
Resolution 2.40 Å R-free 0.214
5UKF Crystal Structure of the Human Vaccinia-related Kinase 1 Bound to an Oxindole Inhibitor Deposited 2017-01-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 3–364（362 aa） Fragment：UNP residues 3-364
Not recorded 8E1 4-{[(Z)-(7-oxo-6,7-dihydro-8H-[1,3]thiazolo[5,4-e]indol-8-ylidene)methyl]amino}benzene-1-sulfonamide × 1 PO4 PHOSPHATE ION × 4 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；27.5% PEG 3350; 0.3M AmSO4; 0.1M HEPES pH 7.0
Resolution 2.40 Å R-free 0.214
5UKF Crystal Structure of the Human Vaccinia-related Kinase 1 Bound to an Oxindole Inhibitor Deposited 2017-01-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 3–364（362 aa） Fragment：UNP residues 3-364
Not recorded 8E1 4-{[(Z)-(7-oxo-6,7-dihydro-8H-[1,3]thiazolo[5,4-e]indol-8-ylidene)methyl]amino}benzene-1-sulfonamide × 1 PO4 PHOSPHATE ION × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；27.5% PEG 3350; 0.3M AmSO4; 0.1M HEPES pH 7.0
Resolution 2.40 Å R-free 0.214
5UKF Crystal Structure of the Human Vaccinia-related Kinase 1 Bound to an Oxindole Inhibitor Deposited 2017-01-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 3–364（362 aa） Fragment：UNP residues 3-364
Not recorded 8E1 4-{[(Z)-(7-oxo-6,7-dihydro-8H-[1,3]thiazolo[5,4-e]indol-8-ylidene)methyl]amino}benzene-1-sulfonamide × 1 CL CHLORIDE ION × 4 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；27.5% PEG 3350; 0.3M AmSO4; 0.1M HEPES pH 7.0
Resolution 2.40 Å R-free 0.214
5UVF Crystal Structure of the Human vaccinia-related kinase bound to BI-D1870 Deposited 2017-02-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3–364（362 aa） Fragment：UNP RESIDUES 3-364
Mutation：YES 7DZ (7S)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-5,7-dimethyl-8-(3-methylbutyl)-7,8-dihydropteridin-6(5H)-one × 1 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；25% PEG3350, 0.1M BISTRIS, 0.2M, LITHIUM SULFATE, PH 6.5
Resolution 2.00 Å R-free 0.204
5UVF Crystal Structure of the Human vaccinia-related kinase bound to BI-D1870 Deposited 2017-02-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 3–364（362 aa） Fragment：UNP RESIDUES 3-364
Mutation：YES 7DZ (7S)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-5,7-dimethyl-8-(3-methylbutyl)-7,8-dihydropteridin-6(5H)-one × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；25% PEG3350, 0.1M BISTRIS, 0.2M, LITHIUM SULFATE, PH 6.5
Resolution 2.00 Å R-free 0.204
5UVF Crystal Structure of the Human vaccinia-related kinase bound to BI-D1870 Deposited 2017-02-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 3–364（362 aa） Fragment：UNP RESIDUES 3-364
Mutation：YES 7DZ (7S)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-5,7-dimethyl-8-(3-methylbutyl)-7,8-dihydropteridin-6(5H)-one × 1 PO4 PHOSPHATE ION × 4 PEG DI(HYDROXYETHYL)ETHER × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；25% PEG3350, 0.1M BISTRIS, 0.2M, LITHIUM SULFATE, PH 6.5
Resolution 2.00 Å R-free 0.204
5UVF Crystal Structure of the Human vaccinia-related kinase bound to BI-D1870 Deposited 2017-02-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 3–364（362 aa） Fragment：UNP RESIDUES 3-364
Mutation：YES 7DZ (7S)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-5,7-dimethyl-8-(3-methylbutyl)-7,8-dihydropteridin-6(5H)-one × 1 PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；25% PEG3350, 0.1M BISTRIS, 0.2M, LITHIUM SULFATE, PH 6.5
Resolution 2.00 Å R-free 0.204
6AC9 Crystal structure of human Vaccinia-related kinase 1 (VRK1) in complex with AMP-PNP Deposited 2018-07-25 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–364（364 aa）
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 2 CL CHLORIDE ION × 1 PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；27.5 % w/v PEG 3350, 0.2 M of ammonium sulfate, 0.1 M of HEPES (pH 7.0)
Resolution 2.07 Å R-free 0.223
6AC9 Crystal structure of human Vaccinia-related kinase 1 (VRK1) in complex with AMP-PNP Deposited 2018-07-25 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–364（364 aa）
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 3 CL CHLORIDE ION × 1 PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；27.5 % w/v PEG 3350, 0.2 M of ammonium sulfate, 0.1 M of HEPES (pH 7.0)
Resolution 2.07 Å R-free 0.223
6AC9 Crystal structure of human Vaccinia-related kinase 1 (VRK1) in complex with AMP-PNP Deposited 2018-07-25 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–364（364 aa）
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 1 CL CHLORIDE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；27.5 % w/v PEG 3350, 0.2 M of ammonium sulfate, 0.1 M of HEPES (pH 7.0)
Resolution 2.07 Å R-free 0.223
6AC9 Crystal structure of human Vaccinia-related kinase 1 (VRK1) in complex with AMP-PNP Deposited 2018-07-25 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–364（364 aa）
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 1 CL CHLORIDE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；27.5 % w/v PEG 3350, 0.2 M of ammonium sulfate, 0.1 M of HEPES (pH 7.0)
Resolution 2.07 Å R-free 0.223
6BRU Crystal Structure of the Human vaccinia-related kinase bound to a (S)-2-phenylaminopteridinone inhibitor Deposited 2017-12-01 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3–364（362 aa）
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；22% PEG3350, 0.02M Lithium Sulfate, 0.1M Buffer system SBG pH 7.0
Resolution 1.80 Å R-free 0.214
6BRU Crystal Structure of the Human vaccinia-related kinase bound to a (S)-2-phenylaminopteridinone inhibitor Deposited 2017-12-01 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 3–364（362 aa）
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A SO4 SULFATE ION × 3 E5M (7S)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-5,7,8-trimethyl-7,8-dihydropteridin-6(5H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；22% PEG3350, 0.02M Lithium Sulfate, 0.1M Buffer system SBG pH 7.0
Resolution 1.80 Å R-free 0.214
6BRU Crystal Structure of the Human vaccinia-related kinase bound to a (S)-2-phenylaminopteridinone inhibitor Deposited 2017-12-01 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 3–364（362 aa）
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；22% PEG3350, 0.02M Lithium Sulfate, 0.1M Buffer system SBG pH 7.0
Resolution 1.80 Å R-free 0.214
6BRU Crystal Structure of the Human vaccinia-related kinase bound to a (S)-2-phenylaminopteridinone inhibitor Deposited 2017-12-01 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 3–364（362 aa）
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A SO4 SULFATE ION × 2 E5M (7S)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-5,7,8-trimethyl-7,8-dihydropteridin-6(5H)-one × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；22% PEG3350, 0.02M Lithium Sulfate, 0.1M Buffer system SBG pH 7.0
Resolution 1.80 Å R-free 0.214
6BTW Crystal Structure of the Human vaccinia-related kinase bound to a phenyl-pteridinone inhibitor Deposited 2017-12-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3–364（362 aa） Fragment：residues 3-364
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A CL CHLORIDE ION × 2 E8D 2-[(3,5-difluoro-4-hydroxyphenyl)amino]-8-phenyl-7,8-dihydropteridin-6(5H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；22% PEG3350, 0.02M Lithium Sulfate, 0.1M Buffer system SBG pH 7.0
Resolution 1.90 Å R-free 0.215
6BTW Crystal Structure of the Human vaccinia-related kinase bound to a phenyl-pteridinone inhibitor Deposited 2017-12-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 3–364（362 aa） Fragment：residues 3-364
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A CL CHLORIDE ION × 3 E8D 2-[(3,5-difluoro-4-hydroxyphenyl)amino]-8-phenyl-7,8-dihydropteridin-6(5H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；22% PEG3350, 0.02M Lithium Sulfate, 0.1M Buffer system SBG pH 7.0
Resolution 1.90 Å R-free 0.215
6BTW Crystal Structure of the Human vaccinia-related kinase bound to a phenyl-pteridinone inhibitor Deposited 2017-12-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 3–364（362 aa） Fragment：residues 3-364
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A CL CHLORIDE ION × 1 SO4 SULFATE ION × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；22% PEG3350, 0.02M Lithium Sulfate, 0.1M Buffer system SBG pH 7.0
Resolution 1.90 Å R-free 0.215
6BTW Crystal Structure of the Human vaccinia-related kinase bound to a phenyl-pteridinone inhibitor Deposited 2017-12-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 3–364（362 aa） Fragment：residues 3-364
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A CL CHLORIDE ION × 3 E8D 2-[(3,5-difluoro-4-hydroxyphenyl)amino]-8-phenyl-7,8-dihydropteridin-6(5H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；22% PEG3350, 0.02M Lithium Sulfate, 0.1M Buffer system SBG pH 7.0
Resolution 1.90 Å R-free 0.215
6BU6 Crystal Structure of the Human vaccinia-related kinase bound to a bis-difluorophenol-aminopyridine inhibitor Deposited 2017-12-08 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3–364（362 aa） Fragment：residues 3-364
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A E8V 4,4'-(2-aminopyridine-3,5-diyl)bis(2,6-difluorophenol) × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；22% PEG3350; 0.02M Lithium Sulfate; 0.1M Buffer system SBG pH 7.0
Resolution 1.80 Å R-free 0.212
6BU6 Crystal Structure of the Human vaccinia-related kinase bound to a bis-difluorophenol-aminopyridine inhibitor Deposited 2017-12-08 Different construct Different ligand/ion Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 3–364（362 aa） Fragment：residues 3-364
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A E8V 4,4'-(2-aminopyridine-3,5-diyl)bis(2,6-difluorophenol) × 1 CL CHLORIDE ION × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；22% PEG3350; 0.02M Lithium Sulfate; 0.1M Buffer system SBG pH 7.0
Resolution 1.80 Å R-free 0.212
6BU6 Crystal Structure of the Human vaccinia-related kinase bound to a bis-difluorophenol-aminopyridine inhibitor Deposited 2017-12-08 Different construct Different ligand/ion Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 3–364（362 aa） Fragment：residues 3-364
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A CL CHLORIDE ION × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；22% PEG3350; 0.02M Lithium Sulfate; 0.1M Buffer system SBG pH 7.0
Resolution 1.80 Å R-free 0.212
6BU6 Crystal Structure of the Human vaccinia-related kinase bound to a bis-difluorophenol-aminopyridine inhibitor Deposited 2017-12-08 Different construct Different ligand/ion Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 3–364（362 aa） Fragment：residues 3-364
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A E8V 4,4'-(2-aminopyridine-3,5-diyl)bis(2,6-difluorophenol) × 1 CL CHLORIDE ION × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；22% PEG3350; 0.02M Lithium Sulfate; 0.1M Buffer system SBG pH 7.0
Resolution 1.80 Å R-free 0.212
6CFM Crystal Structure of the Human vaccinia-related kinase bound to a propynyl-pteridinone inhibitor Deposited 2018-02-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3–364（362 aa） Fragment：residues 3-364
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A CL CHLORIDE ION × 1 EA7 (7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7,8-dimethyl-5-(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；22% PEG3350, 0.02M Lithium Sulfate, 0.1M Buffer system SBG pH 7.0
Resolution 2.45 Å R-free 0.245
6CFM Crystal Structure of the Human vaccinia-related kinase bound to a propynyl-pteridinone inhibitor Deposited 2018-02-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 3–364（362 aa） Fragment：residues 3-364
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A CL CHLORIDE ION × 2 EA7 (7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7,8-dimethyl-5-(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；22% PEG3350, 0.02M Lithium Sulfate, 0.1M Buffer system SBG pH 7.0
Resolution 2.45 Å R-free 0.245
6CFM Crystal Structure of the Human vaccinia-related kinase bound to a propynyl-pteridinone inhibitor Deposited 2018-02-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 3–364（362 aa） Fragment：residues 3-364
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；22% PEG3350, 0.02M Lithium Sulfate, 0.1M Buffer system SBG pH 7.0
Resolution 2.45 Å R-free 0.245
6CFM Crystal Structure of the Human vaccinia-related kinase bound to a propynyl-pteridinone inhibitor Deposited 2018-02-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 3–364（362 aa） Fragment：residues 3-364
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A CL CHLORIDE ION × 3 EA7 (7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7,8-dimethyl-5-(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；22% PEG3350, 0.02M Lithium Sulfate, 0.1M Buffer system SBG pH 7.0
Resolution 2.45 Å R-free 0.245
6CMM Crystal Structure of the Human vaccinia-related kinase bound to a N,N-dipropynyl-dihydropteridine inhibitor Deposited 2018-03-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3–364（362 aa） Fragment：residues 3-364
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A ACT ACETATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；30.25% PEG3350, 200 mM LiSO4, 0.1M SBG buffer pH 6.5
Resolution 2.10 Å R-free 0.222
6CMM Crystal Structure of the Human vaccinia-related kinase bound to a N,N-dipropynyl-dihydropteridine inhibitor Deposited 2018-03-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 3–364（362 aa） Fragment：residues 3-364
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A ACT ACETATE ION × 3 F7D (7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7-methyl-5,8-di(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one × 1 SO4 SULFATE ION × 2 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；30.25% PEG3350, 200 mM LiSO4, 0.1M SBG buffer pH 6.5
Resolution 2.10 Å R-free 0.222
6CMM Crystal Structure of the Human vaccinia-related kinase bound to a N,N-dipropynyl-dihydropteridine inhibitor Deposited 2018-03-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 3–364（362 aa） Fragment：residues 3-364
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A ACT ACETATE ION × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；30.25% PEG3350, 200 mM LiSO4, 0.1M SBG buffer pH 6.5
Resolution 2.10 Å R-free 0.222
6CMM Crystal Structure of the Human vaccinia-related kinase bound to a N,N-dipropynyl-dihydropteridine inhibitor Deposited 2018-03-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 3–364（362 aa） Fragment：residues 3-364
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A ACT ACETATE ION × 1 F7D (7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7-methyl-5,8-di(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；30.25% PEG3350, 200 mM LiSO4, 0.1M SBG buffer pH 6.5
Resolution 2.10 Å R-free 0.222
6CNX Crystal Structure of the Human vaccinia-related kinase 1 (VRK1) bound to an N-propynyl-N-isopentyl-dihydropteridin inhibitor Deposited 2018-03-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3–364（362 aa） Fragment：residues 3-364
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A F87 (7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7-methyl-8-(3-methylbutyl)-5-(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one × 1 SO4 SULFATE ION × 1 ACT ACETATE ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；30.25% PEG3350, 30mM LiSO4, 0.1M SBG (Sodium-tartrate, Bis-Tris, Glycylglycine)
Resolution 2.00 Å R-free 0.211
6CNX Crystal Structure of the Human vaccinia-related kinase 1 (VRK1) bound to an N-propynyl-N-isopentyl-dihydropteridin inhibitor Deposited 2018-03-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 3–364（362 aa） Fragment：residues 3-364
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A F87 (7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7-methyl-8-(3-methylbutyl)-5-(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one × 1 ACT ACETATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；30.25% PEG3350, 30mM LiSO4, 0.1M SBG (Sodium-tartrate, Bis-Tris, Glycylglycine)
Resolution 2.00 Å R-free 0.211
6CNX Crystal Structure of the Human vaccinia-related kinase 1 (VRK1) bound to an N-propynyl-N-isopentyl-dihydropteridin inhibitor Deposited 2018-03-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 3–364（362 aa） Fragment：residues 3-364
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A SO4 SULFATE ION × 1 ACT ACETATE ION × 4 FCS (7S)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7-methyl-8-(3-methylbutyl)-5-(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；30.25% PEG3350, 30mM LiSO4, 0.1M SBG (Sodium-tartrate, Bis-Tris, Glycylglycine)
Resolution 2.00 Å R-free 0.211
6CNX Crystal Structure of the Human vaccinia-related kinase 1 (VRK1) bound to an N-propynyl-N-isopentyl-dihydropteridin inhibitor Deposited 2018-03-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 3–364（362 aa） Fragment：residues 3-364
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A F87 (7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7-methyl-8-(3-methylbutyl)-5-(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one × 1 SO4 SULFATE ION × 2 ACT ACETATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；30.25% PEG3350, 30mM LiSO4, 0.1M SBG (Sodium-tartrate, Bis-Tris, Glycylglycine)
Resolution 2.00 Å R-free 0.211
6CQH Crystal Structure of the Human vaccinia-related kinase bound to a N-propynyl-N-ethyl-dihydropteridine inhibitor Deposited 2018-03-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3–364（362 aa） Fragment：residues 3-364
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A F8Y (7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-8-ethyl-7-methyl-5-(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one × 1 SO4 SULFATE ION × 2 ACT ACETATE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；25% PEG3350, 300 mM LiSO4, 0.1M SBG, pH 6.0, 30% glycerol
Resolution 2.15 Å R-free 0.239
6CQH Crystal Structure of the Human vaccinia-related kinase bound to a N-propynyl-N-ethyl-dihydropteridine inhibitor Deposited 2018-03-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 3–364（362 aa） Fragment：residues 3-364
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A F8Y (7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-8-ethyl-7-methyl-5-(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one × 1 SO4 SULFATE ION × 3 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；25% PEG3350, 300 mM LiSO4, 0.1M SBG, pH 6.0, 30% glycerol
Resolution 2.15 Å R-free 0.239
6CQH Crystal Structure of the Human vaccinia-related kinase bound to a N-propynyl-N-ethyl-dihydropteridine inhibitor Deposited 2018-03-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 3–364（362 aa） Fragment：residues 3-364
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；25% PEG3350, 300 mM LiSO4, 0.1M SBG, pH 6.0, 30% glycerol
Resolution 2.15 Å R-free 0.239
6CQH Crystal Structure of the Human vaccinia-related kinase bound to a N-propynyl-N-ethyl-dihydropteridine inhibitor Deposited 2018-03-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 3–364（362 aa） Fragment：residues 3-364
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A F8Y (7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-8-ethyl-7-methyl-5-(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one × 1 SO4 SULFATE ION × 2 ACT ACETATE ION × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；25% PEG3350, 300 mM LiSO4, 0.1M SBG, pH 6.0, 30% glycerol
Resolution 2.15 Å R-free 0.239
6CSW Crystal Structure of the Human vaccinia-related kinase bound to a N-methyl-N-propyl-dihydropteridine inhibitor Deposited 2018-03-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3–364（362 aa） Fragment：residues 3-364
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A SO4 SULFATE ION × 2 ACT ACETATE ION × 1 PG4 TETRAETHYLENE GLYCOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；27.5% PEG3350; 300 mM LiSO4; 0.1M SBG pH 7.0
Resolution 2.25 Å R-free 0.233
6CSW Crystal Structure of the Human vaccinia-related kinase bound to a N-methyl-N-propyl-dihydropteridine inhibitor Deposited 2018-03-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 3–364（362 aa） Fragment：residues 3-364
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A SO4 SULFATE ION × 3 FBY (7R)-5-butyl-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7,8-dimethyl-7,8-dihydropteridin-6(5H)-one × 1 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；27.5% PEG3350; 300 mM LiSO4; 0.1M SBG pH 7.0
Resolution 2.25 Å R-free 0.233
6CSW Crystal Structure of the Human vaccinia-related kinase bound to a N-methyl-N-propyl-dihydropteridine inhibitor Deposited 2018-03-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 3–364（362 aa） Fragment：residues 3-364
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A SO4 SULFATE ION × 3 GOL GLYCEROL × 4 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；27.5% PEG3350; 300 mM LiSO4; 0.1M SBG pH 7.0
Resolution 2.25 Å R-free 0.233
6CSW Crystal Structure of the Human vaccinia-related kinase bound to a N-methyl-N-propyl-dihydropteridine inhibitor Deposited 2018-03-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 3–364（362 aa） Fragment：residues 3-364
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A SO4 SULFATE ION × 6 ACT ACETATE ION × 1 FBY (7R)-5-butyl-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7,8-dimethyl-7,8-dihydropteridin-6(5H)-one × 1 GOL GLYCEROL × 7 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；27.5% PEG3350; 300 mM LiSO4; 0.1M SBG pH 7.0
Resolution 2.25 Å R-free 0.233
6DD4 Crystal Structure of the Human vaccinia-related kinase bound to a N,N-dipropyl-dihydropteridine inhibitor Deposited 2018-05-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3–364（362 aa） Fragment：residues 3-364
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A CL CHLORIDE ION × 5 ACT ACETATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；27.5% PEG3350, 200 mM LiSO4, 0.1M SBG, pH 7.0
Resolution 2.10 Å R-free 0.226
6DD4 Crystal Structure of the Human vaccinia-related kinase bound to a N,N-dipropyl-dihydropteridine inhibitor Deposited 2018-05-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 3–364（362 aa） Fragment：residues 3-364
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A ACT ACETATE ION × 2 G6J (7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7-methyl-5,8-dipropyl-7,8-dihydropteridin-6(5H)-one × 1 SO4 SULFATE ION × 3 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；27.5% PEG3350, 200 mM LiSO4, 0.1M SBG, pH 7.0
Resolution 2.10 Å R-free 0.226
6DD4 Crystal Structure of the Human vaccinia-related kinase bound to a N,N-dipropyl-dihydropteridine inhibitor Deposited 2018-05-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 3–364（362 aa） Fragment：residues 3-364
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A CL CHLORIDE ION × 2 ACT ACETATE ION × 1 SO4 SULFATE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；27.5% PEG3350, 200 mM LiSO4, 0.1M SBG, pH 7.0
Resolution 2.10 Å R-free 0.226
6DD4 Crystal Structure of the Human vaccinia-related kinase bound to a N,N-dipropyl-dihydropteridine inhibitor Deposited 2018-05-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 3–364（362 aa） Fragment：residues 3-364
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A CL CHLORIDE ION × 1 ACT ACETATE ION × 1 G6J (7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7-methyl-5,8-dipropyl-7,8-dihydropteridin-6(5H)-one × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；27.5% PEG3350, 200 mM LiSO4, 0.1M SBG, pH 7.0
Resolution 2.10 Å R-free 0.226
6NPN Crystal Structure of the Human vaccinia-related kinase bound to a N,N-dipropynyl-dihydropteridine-3-hydroxyindazole inhibitor Deposited 2019-01-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3–364（362 aa） Fragment：residues 3-364
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A KWJ (7R)-7-methyl-2-[(3-oxo-2,3-dihydro-1H-indazol-6-yl)amino]-5,8-di(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one × 1 SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；27.5% PEG 3350, 20 mM Li2SO4, 0.1M SBG, pH 6.0
Resolution 2.20 Å R-free 0.218
6NPN Crystal Structure of the Human vaccinia-related kinase bound to a N,N-dipropynyl-dihydropteridine-3-hydroxyindazole inhibitor Deposited 2019-01-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 3–364（362 aa） Fragment：residues 3-364
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A KWJ (7R)-7-methyl-2-[(3-oxo-2,3-dihydro-1H-indazol-6-yl)amino]-5,8-di(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one × 1 SO4 SULFATE ION × 3 EDO 1,2-ETHANEDIOL × 5 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；27.5% PEG 3350, 20 mM Li2SO4, 0.1M SBG, pH 6.0
Resolution 2.20 Å R-free 0.218
6NPN Crystal Structure of the Human vaccinia-related kinase bound to a N,N-dipropynyl-dihydropteridine-3-hydroxyindazole inhibitor Deposited 2019-01-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 3–364（362 aa） Fragment：residues 3-364
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A KWJ (7R)-7-methyl-2-[(3-oxo-2,3-dihydro-1H-indazol-6-yl)amino]-5,8-di(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one × 1 SO4 SULFATE ION × 4 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；27.5% PEG 3350, 20 mM Li2SO4, 0.1M SBG, pH 6.0
Resolution 2.20 Å R-free 0.218
6NPN Crystal Structure of the Human vaccinia-related kinase bound to a N,N-dipropynyl-dihydropteridine-3-hydroxyindazole inhibitor Deposited 2019-01-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 3–364（362 aa） Fragment：residues 3-364
Mutation：K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A KWJ (7R)-7-methyl-2-[(3-oxo-2,3-dihydro-1H-indazol-6-yl)amino]-5,8-di(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one × 1 SO4 SULFATE ION × 4 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；27.5% PEG 3350, 20 mM Li2SO4, 0.1M SBG, pH 6.0
Resolution 2.20 Å R-free 0.218
6VXU Structure of Human Vaccinia-related Kinase 1 (VRK1) bound to ACH471 Deposited 2020-02-24 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3–364（362 aa）
Mutation：K34A,K35A,E36A,E212A,K214A,E215A,E292A,K293A,K295A,K359A,K360A RTJ (7R)-8-(cyclopropylmethyl)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7-methyl-5-(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；27.5% PEG3350; 300 mM LiSO4; 0.1 M SBG (each Sodium-tartrate + Bis-Tris + Glycylglycine) pH 6.5
Resolution 2.00 Å R-free 0.203
6VXU Structure of Human Vaccinia-related Kinase 1 (VRK1) bound to ACH471 Deposited 2020-02-24 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 3–364（362 aa）
Mutation：K34A,K35A,E36A,E212A,K214A,E215A,E292A,K293A,K295A,K359A,K360A RTJ (7R)-8-(cyclopropylmethyl)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7-methyl-5-(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；27.5% PEG3350; 300 mM LiSO4; 0.1 M SBG (each Sodium-tartrate + Bis-Tris + Glycylglycine) pH 6.5
Resolution 2.00 Å R-free 0.203
6VXU Structure of Human Vaccinia-related Kinase 1 (VRK1) bound to ACH471 Deposited 2020-02-24 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 3–364（362 aa）
Mutation：K34A,K35A,E36A,E212A,K214A,E215A,E292A,K293A,K295A,K359A,K360A SO4 SULFATE ION × 3 VBD (7S)-8-(cyclopropylmethyl)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7-methyl-5-(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；27.5% PEG3350; 300 mM LiSO4; 0.1 M SBG (each Sodium-tartrate + Bis-Tris + Glycylglycine) pH 6.5
Resolution 2.00 Å R-free 0.203
6VXU Structure of Human Vaccinia-related Kinase 1 (VRK1) bound to ACH471 Deposited 2020-02-24 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 3–364（362 aa）
Mutation：K34A,K35A,E36A,E212A,K214A,E215A,E292A,K293A,K295A,K359A,K360A RTJ (7R)-8-(cyclopropylmethyl)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7-methyl-5-(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one × 1 SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；27.5% PEG3350; 300 mM LiSO4; 0.1 M SBG (each Sodium-tartrate + Bis-Tris + Glycylglycine) pH 6.5
Resolution 2.00 Å R-free 0.203
6VZH Structure of Human Vaccinia-related Kinase 1 (VRK1) Bound to LDSM311 Deposited 2020-02-28 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3–364（362 aa）
Mutation：K34A,K35A,E36A,E212A,K214A,E215A,E292A,K293A,K295A,K359A,K360A SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；27.5% PEG3350, 300 mM lithium sulfate, 0.1 M sodium tartrate, 0.1 M Bis-Tris, 0.1 M glycylglycine, cryoprotectant: 30% glycerol
Resolution 2.55 Å R-free 0.251
6VZH Structure of Human Vaccinia-related Kinase 1 (VRK1) Bound to LDSM311 Deposited 2020-02-28 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 3–364（362 aa）
Mutation：K34A,K35A,E36A,E212A,K214A,E215A,E292A,K293A,K295A,K359A,K360A SO4 SULFATE ION × 3 RYA (7~{R})-2-[[3,5-bis(fluoranyl)-4-oxidanyl-phenyl]amino]-5,7-dimethyl-8-prop-2-ynyl-7~{H}-pteridin-6-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；27.5% PEG3350, 300 mM lithium sulfate, 0.1 M sodium tartrate, 0.1 M Bis-Tris, 0.1 M glycylglycine, cryoprotectant: 30% glycerol
Resolution 2.55 Å R-free 0.251
6VZH Structure of Human Vaccinia-related Kinase 1 (VRK1) Bound to LDSM311 Deposited 2020-02-28 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 3–364（362 aa）
Mutation：K34A,K35A,E36A,E212A,K214A,E215A,E292A,K293A,K295A,K359A,K360A SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；27.5% PEG3350, 300 mM lithium sulfate, 0.1 M sodium tartrate, 0.1 M Bis-Tris, 0.1 M glycylglycine, cryoprotectant: 30% glycerol
Resolution 2.55 Å R-free 0.251
6VZH Structure of Human Vaccinia-related Kinase 1 (VRK1) Bound to LDSM311 Deposited 2020-02-28 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 3–364（362 aa）
Mutation：K34A,K35A,E36A,E212A,K214A,E215A,E292A,K293A,K295A,K359A,K360A SO4 SULFATE ION × 2 RYA (7~{R})-2-[[3,5-bis(fluoranyl)-4-oxidanyl-phenyl]amino]-5,7-dimethyl-8-prop-2-ynyl-7~{H}-pteridin-6-one × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；27.5% PEG3350, 300 mM lithium sulfate, 0.1 M sodium tartrate, 0.1 M Bis-Tris, 0.1 M glycylglycine, cryoprotectant: 30% glycerol
Resolution 2.55 Å R-free 0.251
7M10 PHF2 PHD Domain Complexed with Peptide From N-terminus of VRK1 Deposited 2021-03-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–13（12 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 FMT FORMIC ACID × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；292 K；3.5M Sodium Formate,100mM TRIS pH 8.2
Resolution 1.15 Å R-free 0.165
7TAN Structure of VRK1 C-terminal tail bound to nucleosome core particle Deposited 2021-12-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain K 1–396（396 aa）
Chain L 1–396（396 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.00 Å
8F8Y PHF2 (PHD+JMJ) in Complex with VRK1 N-Terminal Peptide Deposited 2022-11-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 2–13（12 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 SO4 SULFATE ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.3；292 K；2.5M Ammonium Sulfate 90mM Bis-Tris Propane, pH 6.3 4% Pentaerythritol ethoxylate (3/4 EO/OH)
Resolution 3.06 Å R-free 0.249
8F8Y PHF2 (PHD+JMJ) in Complex with VRK1 N-Terminal Peptide Deposited 2022-11-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 2–13（12 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 SO4 SULFATE ION × 10 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.3；292 K；2.5M Ammonium Sulfate 90mM Bis-Tris Propane, pH 6.3 4% Pentaerythritol ethoxylate (3/4 EO/OH)
Resolution 3.06 Å R-free 0.249
8V42 Structure of Human Vaccinia-related Kinase 1 (VRK1) Bound to ACH000400 Deposited 2023-11-28 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3–364（362 aa）
Mutation：K34A,K35A,E36A,E212A,K214A,E215A,E292A,K293A,K295A PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；22% PEG3350, 20 mM Li2SO4, 0.1 M Buffer system SBG pH 7.0
Resolution 2.30 Å R-free 0.231
8V42 Structure of Human Vaccinia-related Kinase 1 (VRK1) Bound to ACH000400 Deposited 2023-11-28 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 3–364（362 aa）
Mutation：K34A,K35A,E36A,E212A,K214A,E215A,E292A,K293A,K295A YD9 (7S)-2-(3,5-difluoro-4-hydroxyanilino)-7-methyl-5-[(1,2-oxazol-5-yl)methyl]-8-(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；22% PEG3350, 20 mM Li2SO4, 0.1 M Buffer system SBG pH 7.0
Resolution 2.30 Å R-free 0.231
8V42 Structure of Human Vaccinia-related Kinase 1 (VRK1) Bound to ACH000400 Deposited 2023-11-28 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 3–364（362 aa）
Mutation：K34A,K35A,E36A,E212A,K214A,E215A,E292A,K293A,K295A SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；22% PEG3350, 20 mM Li2SO4, 0.1 M Buffer system SBG pH 7.0
Resolution 2.30 Å R-free 0.231
8V42 Structure of Human Vaccinia-related Kinase 1 (VRK1) Bound to ACH000400 Deposited 2023-11-28 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 3–364（362 aa）
Mutation：K34A,K35A,E36A,E212A,K214A,E215A,E292A,K293A,K295A YD9 (7S)-2-(3,5-difluoro-4-hydroxyanilino)-7-methyl-5-[(1,2-oxazol-5-yl)methyl]-8-(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；22% PEG3350, 20 mM Li2SO4, 0.1 M Buffer system SBG pH 7.0
Resolution 2.30 Å R-free 0.231
9ZKG VRK1 in complex with the inhibitor MP-60 Deposited 2025-12-06 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3–364（362 aa）
Mutation：M1A, M2P, K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；303 K；30,25% PEG3350, 0.2 M LiSO4, 0.1M SBG pH 6,5
Resolution 2.06 Å R-free 0.216
9ZKG VRK1 in complex with the inhibitor MP-60 Deposited 2025-12-06 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 3–364（362 aa）
Mutation：M1A, M2P, K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A EDO 1,2-ETHANEDIOL × 2 PEG DI(HYDROXYETHYL)ETHER × 1 ACN ACETONE × 1 GG0 2-(2-azanylethanoylamino)ethanoic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；303 K；30,25% PEG3350, 0.2 M LiSO4, 0.1M SBG pH 6,5
Resolution 2.06 Å R-free 0.216
9ZKG VRK1 in complex with the inhibitor MP-60 Deposited 2025-12-06 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 3–364（362 aa）
Mutation：M1A, M2P, K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A GOL GLYCEROL × 2 EDO 1,2-ETHANEDIOL × 3 CL CHLORIDE ION × 2 A1C2O (5Z)-3-butyl-5-[(3,5-dichloro-4-hydroxyphenyl)methylidene]-1,3-thiazolidine-2,4-dione × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；303 K；30,25% PEG3350, 0.2 M LiSO4, 0.1M SBG pH 6,5
Resolution 2.06 Å R-free 0.216
9ZKG VRK1 in complex with the inhibitor MP-60 Deposited 2025-12-06 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 3–364（362 aa）
Mutation：M1A, M2P, K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 2 CL CHLORIDE ION × 4 PEG DI(HYDROXYETHYL)ETHER × 1 A1C2O (5Z)-3-butyl-5-[(3,5-dichloro-4-hydroxyphenyl)methylidene]-1,3-thiazolidine-2,4-dione × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；303 K；30,25% PEG3350, 0.2 M LiSO4, 0.1M SBG pH 6,5
Resolution 2.06 Å R-free 0.216

25 other PDB entries and 80 assemblies. Open the comparison page and filter oligomeric states

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.

SAXS scattering curve SAXS Profile

SAXS profile for 6bp0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6bp0
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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. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier39.90 Å
Radius of gyration Rg (electron density) rg_electron38.87 Å
Forward intensity I(0) i0294983000.00
Molecular weight molecular_weight140610.0 kDa
Excluded volume excluded_volume176010 ų
Envelope volume envelope_volume244180 ų
Hydration-shell volume shell_volume51155 ų
Envelope diameter envelope_diameter119.0 Å
Shell Rg shell_rg46.42 Å
Envelope Rg envelope_rg37.53 Å
Shape Rg shape_rg38.86 Å
Total Rg total_rg39.32 Å
Total atoms total_atoms9902
Residues n_residues1247
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax115.7 Å
Rg (real space) rg_real39.54 Å
Rg uncertainty (real space) rg_real_error0.69 Å
I(0) (real space) i0_real2.9500e+08
I(0) uncertainty (real space) i0_real_error3.9390e+06
Rg (reciprocal space) rg_reciprocal39.77 Å
I(0) (reciprocal space) i0_reciprocal295100000.0000
Solution quality estimate total_estimate0.8337
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary60.7 Å
Skewness Skewness skewness-0.105
Kurtosis Kurtosis kurtosis-0.746
Angular range angular_range— – 0.2000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha31700000.0000
Real-space data points n_real_points41
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.947; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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7. 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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8. Citations (1)

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9. Files and Curves (10)