6NPN: Human vaccinia-related kinase

Crystal Structure of the Human vaccinia-related kinase bound to a N,N-dipropynyl-dihydropteridine-3-hydroxyindazole inhibitor. Determined by X-ray diffraction at 2.2 Å resolution. Released 20 Feb 2019.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 4
Atoms: 10,564
Mol. weight: 167.98 kDa
Ligands: KWJ
Released: 20 Feb 2019

Explore 6NPN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6NPN contains 67 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: 16 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	28-30	3	1
β-strand	36-42	7	1
β-strand	51-56	6	1
α-helix	61-63	3
β-strand	68-74	7	1
α-helix	78-90	13
α-helix	93-102	10
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	193-195	3	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: 18 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	28-30	3	4
β-strand	36-39	4	4
β-strand	51-56	6	4
β-strand	68-73	6	4
α-helix	78-90	13
α-helix	93-103	11
α-helix	110-112	3
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	193-195	3	5
β-strand	202-203	2	6
α-helix	206-208	3
α-helix	210-213	4
β-strand	215	1	7
α-helix	217-219	3
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: 16 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
β-strand	68-74	7	8
α-helix	78-90	13
α-helix	93-102	10
α-helix	111-112	2
β-strand	113-121	9	8
β-strand	124-132	9	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	193-195	3	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	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: 17 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	23-24	2
β-strand	28-30	3	11
β-strand	36-42	7	11
β-strand	51-56	6	11
β-strand	68-74	7	11
α-helix	78-90	13
α-helix	93-102	10
α-helix	111-112	2
β-strand	113-121	9	11
β-strand	124-132	9	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	183-185	3	12
β-strand	193-195	3	12
β-strand	202-203	2	13
α-helix	206-208	3
α-helix	210-213	4
β-strand	215	1	14
α-helix	230-233	4
β-strand	236	1	14
α-helix	237-238	2
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

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

>6NPN_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
KWJ	(7R)-7-methyl-2-[(3-oxo-2,3-dihydro-1H-indazol-6-yl)amino]-5,8-di(prop-2-yn-1-y…	C20 H17 N7 O2	4

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

Primary citation

Crystal Structure of the Human vaccinia-related kinase bound to a N,N-dipropynyl-dihydropteridine-3-hydroxyindazole inhibitor. Counago, R.M., dos Reis, C.V., Takarada, J.E. et al. To be published.

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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