7NZY: Human Casein Kinase I delta

Crystal structure of human Casein Kinase I delta in complex with CGS-15943. Determined by X-ray diffraction at 1.85 Å resolution. Released 5 Oct 2022.

Method: X-ray diffraction
Resolution: 1.85 Å
Organism: Homo sapiens
Chains: 4
Atoms: 10,173
Mol. weight: 147.76 kDa
Ligands: MLI, PO4, UX2
Released: 5 Oct 2022

Explore 7NZY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7NZY contains 67 α-helices and 50 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: 17 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	1
β-strand	9-17	9	1
β-strand	22-28	7	1
β-strand	33-41	9	1
α-helix	49-58	10
α-helix	65-67	3
β-strand	68-74	7	1
β-strand	77-83	7	1
β-strand	88	1	2
α-helix	89-95	7
α-helix	102-121	20
β-strand	124-125	2	3
α-helix	131-133	3
β-strand	134-136	3	2
α-helix	139-141	3
α-helix	144	1
β-strand	145-147	3	2
β-strand	154-155	2	3
α-helix	164-167	4
α-helix	182-185	4
α-helix	188-190	3
α-helix	192-208	17
α-helix	221-234	14
α-helix	237-240	4
α-helix	246-257	12
α-helix	262-264	3
α-helix	266-279	14
α-helix	289-292	4

Chain B: 17 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	4
β-strand	9-17	9	4
β-strand	22-28	7	4
β-strand	33-41	9	4
α-helix	49-58	10
α-helix	65-67	3
β-strand	68-74	7	4
β-strand	77-83	7	4
β-strand	88	1	5
α-helix	89-95	7
α-helix	102-121	20
β-strand	124-125	2	6
α-helix	131-133	3
β-strand	134-136	3	5
α-helix	139-141	3
α-helix	144	1
β-strand	145-147	3	5
β-strand	154-155	2	6
α-helix	164-167	4
β-strand	169	1	7
α-helix	182-185	4
β-strand	188	1	7
α-helix	189-190	2
α-helix	192-208	17
α-helix	221-234	14
α-helix	237-240	4
α-helix	246-257	12
α-helix	262-264	3
α-helix	266-279	14
α-helix	289-292	4

Chain C: 17 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	8
β-strand	9-17	9	8
β-strand	22-28	7	8
β-strand	33-41	9	8
α-helix	49-59	11
α-helix	66-67	2
β-strand	68-74	7	8
β-strand	77-83	7	8
β-strand	88	1	9
α-helix	89-95	7
α-helix	102-121	20
β-strand	124-125	2	10
α-helix	131-133	3
β-strand	134-136	3	9
α-helix	139-141	3
β-strand	145-147	3	9
β-strand	154-155	2	10
β-strand	157	1	11
β-strand	164	1	11
α-helix	165-167	3
α-helix	171-173	3
α-helix	182-185	4
α-helix	188-190	3
α-helix	192-208	17
α-helix	225-233	9
α-helix	237-240	4
α-helix	246-257	12
α-helix	262-264	3
α-helix	266-279	14
α-helix	289-292	4

Chain D: 16 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	12
β-strand	9-17	9	12
β-strand	22-28	7	12
β-strand	33-41	9	12
α-helix	49-59	11
α-helix	66-67	2
β-strand	68-74	7	12
β-strand	77-83	7	12
β-strand	88	1	13
α-helix	89-95	7
α-helix	102-121	20
β-strand	124-125	2	14
α-helix	131-133	3
β-strand	134-136	3	13
α-helix	139-141	3
β-strand	145-147	3	13
β-strand	154-155	2	14
β-strand	157	1	15
β-strand	164	1	15
α-helix	165-167	3
α-helix	182-185	4
α-helix	188-190	3
α-helix	192-208	17
α-helix	223-233	11
α-helix	237-240	4
α-helix	247-257	11
α-helix	262-264	3
α-helix	266-279	14
α-helix	289-292	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Casein kinase I isoform delta	A, B, C, D	protein	314	Homo sapiens	P48730 (AlphaFold model)

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

>7NZY_1 Casein kinase I isoform delta (chains A, B, C, D)
MGSSHHHHHHSSGLVPRGSHMELRVGNRYRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLE
CVKTKHPQLHIESKIYKMMQGGVGIPTIRWCGAEGDYNVMVMELLGPSLEDLFNFCSRKF
SLKTVLLLADQMISRIEYIHSKNFIHRDVKPDNFLMGLGKKGNLVYIIDFGLAKKYRDAR
THQHIPYRENKNLTGTARYASINTHLGIEQSRRDDLESLGYVLMYFNLGSLPWQGLKAAT
KRQKYERISEKKMSTPIEVLCKGYPSEFATYLNFCRSLRFDDKPDYSYLRQLFRNLFHRQ
GFSYDYVFDWNMLK

Ligands and cofactors

ID	Name	Formula	Copies
MLI	Malonate ion	C3 H2 O4	4
PO4	Phosphate ion	O4 P	4
UX2	9-chloranyl-2-(furan-2-yl)-[1,2,4]triazolo[1,5-c]quinazolin-5-amine	C13 H8 Cl N5 O	4

Primary citation

Phenotypic Discovery of Triazolo[1,5- c ]quinazolines as a First-In-Class Bone Morphogenetic Protein Amplifier Chemotype. Wesseler, F., Lohmann, S., Riege, D. et al. J Med Chem (2022) 65:15263-15281. DOI 10.1021/acs.jmedchem.2c01199 · PubMed

Other PDB entries of the same protein (UniProt P48730 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9SIX 1.23 Å, CK1d in complex with IG130
6RCG 1.4 Å, Crystal structure of Casein kinase 1 delta (CK1 delta) complexed with SR3029 inhibitor
6RCH 1.45 Å, Crystal structure of Casein kinase I isoform delta (CK1 delta) complexed with SR4133…
8IZC 1.45 Å, Human CK1 Delta Kinase structure bound to Inhibitor
9SIV 1.5 Å, Phosphorylated CK1d in complex with IG84
9SIZ 1.5 Å, CK1d in complex with IG138
9SIW 1.55 Å, CK1d in complex with IG111
6PXN 1.55 Å, Human Casein Kinase 1 delta Tau mutant (R178C)
6GZM 1.59 Å, Crystal Structure of Human CKIdelta with A86
9SJ1 1.6 Å, CK1d in complex with IG84
8D7O 1.65 Å, Human Casein kinase 1 delta in complex with phosphorylated human PERIOD2 FASP peptide
8D7N 1.66 Å, Human Casein kinase 1 delta in complex with phosphorylated human PERIOD2 FASP peptide

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