8V42: Human Vaccinia-related Kinase 1

Structure of Human Vaccinia-related Kinase 1 (VRK1) Bound to ACH000400. Determined by X-ray diffraction at 2.3 Å resolution. Released 4 Sept 2024.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 4
Atoms: 9,908
Mol. weight: 165.9 kDa
Ligands: YD9
Released: 4 Sept 2024

Explore 8V42 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8V42 contains 68 α-helices and 48 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 15 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	28-30	3	1
β-strand	36-42	7	1
β-strand	52-56	5	1
β-strand	68-74	7	1
α-helix	78-90	13
α-helix	93-103	11
α-helix	111-112	2
β-strand	113-121	9	1
β-strand	124-132	9	1
β-strand	134-137	4	2
α-helix	138-144	7
α-helix	151-170	20
β-strand	173-174	2	3
α-helix	180-182	3
β-strand	183-186	4	2
β-strand	189-195	7	2
β-strand	202-203	2	3
α-helix	206-208	3
α-helix	210-212	3
α-helix	230-233	4
α-helix	240-256	17
α-helix	268-280	13
α-helix	282-289	8
α-helix	297-307	11
α-helix	313-315	3
α-helix	317-330	14

Chain B: 17 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	29-30	2	4
β-strand	36-42	7	4
β-strand	51-56	6	4
β-strand	68-73	6	4
α-helix	79-90	12
α-helix	93-102	10
α-helix	111-112	2
β-strand	113-118	6	4
β-strand	127-132	6	4
β-strand	134-137	4	5
α-helix	138-144	7
α-helix	151-170	20
β-strand	173-174	2	6
α-helix	180-182	3
β-strand	183-186	4	5
β-strand	189-195	7	5
β-strand	202-203	2	6
α-helix	206-208	3
α-helix	210-213	4
β-strand	215	1	7
α-helix	230-233	4
β-strand	236	1	7
α-helix	237-238	2
α-helix	240-256	17
α-helix	262-264	3
α-helix	268-280	13
α-helix	282-289	8
α-helix	297-307	11
α-helix	313-315	3
α-helix	317-330	14

Chain C: 18 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	28-30	3	8
β-strand	36-42	7	8
β-strand	51-56	6	8
α-helix	61-62	2
β-strand	68-74	7	8
α-helix	78-90	13
α-helix	93-102	10
α-helix	111-112	2
β-strand	113-120	8	8
β-strand	125-132	8	8
β-strand	134-137	4	9
α-helix	138-144	7
α-helix	151-170	20
β-strand	173-174	2	10
α-helix	180-182	3
β-strand	183-186	4	9
β-strand	189-195	7	9
β-strand	202-203	2	10
α-helix	206-208	3
α-helix	210-212	3
α-helix	230-233	4
α-helix	236-238	3
α-helix	240-256	17
α-helix	262-264	3
α-helix	268-280	13
α-helix	282-289	8
α-helix	297-307	11
α-helix	313-315	3
α-helix	317-330	14

Chain D: 18 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	28-31	4	11
β-strand	36-42	7	11
β-strand	51-55	5	11
β-strand	68-74	7	11
α-helix	78-90	13
α-helix	93-102	10
α-helix	110-112	3
β-strand	113-120	8	11
β-strand	125-132	8	11
β-strand	137	1	12
α-helix	138-144	7
α-helix	151-170	20
β-strand	173-174	2	13
α-helix	180-182	3
β-strand	183-186	4	12
β-strand	189-195	7	12
β-strand	202-203	2	13
α-helix	206-208	3
α-helix	210-213	4
β-strand	215	1	14
α-helix	217-219	3
α-helix	230-233	4
β-strand	236	1	14
α-helix	237-238	2
α-helix	240-256	17
α-helix	260-263	4
α-helix	268-280	13
α-helix	282-289	8
α-helix	297-307	11
α-helix	313-315	3
α-helix	317-329	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine/threonine-protein kinase VRK1	A, B, C, D	protein	364	Homo sapiens	Q99986 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>8V42_1 Serine/threonine-protein kinase VRK1 (chains A, B, C, D)
SMRVKAAQAGRQSSAKRHLAEQFAVGEIITDMAAAAWKVGLPIGQGGFGCIYLADMNSSE
SVGSDAPCVVKVEPSDNGPLFTELKFYQRAAKPEQIQKWIRTRKLKYLGVPKYWGSGLHD
KNGKSYRFMIMDRFGSDLQKIYEANAKRFSRKTVLQLSLRILDILEYIHEHEYVHGDIKA
SNLLLNYKNPDQVYLVDYGLAYRYCPEGVHKAYAADPKRCHDGTIEFTSIDAHNGVAPSR
RGDLEILGYCMIQWLTGHLPWEDNLKDPKYVRDSKIRYRENIASLMDKCFPAANAPGEIA
KYMETVKLLDYTEKPLYENLRDILLQGLKAIGSKDDGKLDLSVVENGGLKAKTITKKRAA
EIEE

Ligands and cofactors

ID	Name	Formula	Copies
YD9	(7S)-2-(3,5-difluoro-4-hydroxyanilino)-7-methyl-5-[(1,2-oxazol-5-yl)methyl]-8-(…	C20 H16 F2 N6 O3	2

Water and common crystallization additives (PEG, SO4) are not listed.

Primary citation

Novel Dihydropteridinone Derivatives As Potent Inhibitors of the Understudied Human Kinases Vaccinia-Related Kinase 1 and Casein Kinase 1 delta / epsilon. de Souza Gama, F.H., Dutra, L.A., Hawgood, M. et al. J Med Chem (2024) 67:8609-8629. DOI 10.1021/acs.jmedchem.3c02250 · PubMed

Other PDB entries of the same protein (UniProt Q99986 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7M10 1.15 Å, PHF2 PHD Domain Complexed with Peptide From N-terminus of VRK1
6BRU 1.8 Å, Crystal Structure of the Human vaccinia-related kinase bound to a…
6BU6 1.8 Å, Crystal Structure of the Human vaccinia-related kinase bound to a…
6BP0 1.9 Å, Crystal Structure of the Human vaccinia-related kinase 1 bound to…
6BTW 1.9 Å, Crystal Structure of the Human vaccinia-related kinase bound to a phenyl-pteridinone…
5UVF 2.0 Å, Crystal Structure of the Human vaccinia-related kinase bound to BI-D1870
6CNX 2.0 Å, Crystal Structure of the Human vaccinia-related kinase 1 (VRK1) bound to an…
6VXU 2.0 Å, Structure of Human Vaccinia-related Kinase 1 (VRK1) bound to ACH471
9ZKG 2.06 Å, VRK1 in complex with the inhibitor MP-60
6AC9 2.07 Å, Crystal structure of human Vaccinia-related kinase 1 (VRK1) in complex with AMP-PNP
6CMM 2.1 Å, Crystal Structure of the Human vaccinia-related kinase bound to a…
6DD4 2.1 Å, Crystal Structure of the Human vaccinia-related kinase bound to a…

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