4KBA: CK1d

CK1d in complex with 9-[3-(4-fluorophenyl)-1-methyl-1H-pyrazol-4-yl]-2,3,4,5-tetrahydropyrido[2,3-f][1,4]oxazepine inhibitor. Determined by X-ray diffraction at 1.98 Å resolution. Released 18 Sept 2013.

Method: X-ray diffraction
Resolution: 1.98 Å
Organism: Homo sapiens
Chains: 4
Atoms: 9,278
Mol. weight: 156.31 kDa
Ligands: 1QM
Released: 18 Sept 2013

Explore 4KBA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4KBA contains 56 α-helices and 45 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: 14 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	1
β-strand	9-18	10	1
β-strand	21-28	8	1
β-strand	33-39	7	1
α-helix	49-59	11
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	182-185	4
α-helix	188-190	3
α-helix	192-208	17
α-helix	228-234	7
α-helix	237-240	4
α-helix	247-257	11
α-helix	266-279	14
α-helix	289-292	4

Chain B: 15 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	4
β-strand	9-16	8	4
β-strand	23-28	6	4
β-strand	33-40	8	4
α-helix	49-59	11
α-helix	66-67	2
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
β-strand	145-147	3	5
β-strand	154-155	2	6
β-strand	157	1	7
β-strand	164	1	7
α-helix	165-167	3
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	247-257	11
α-helix	266-279	14
α-helix	289-292	4

Chain C: 13 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	9-17	9	8
β-strand	22-28	7	8
β-strand	33-39	7	8
α-helix	49-59	11
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
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	247-257	11
α-helix	266-279	14
α-helix	289-292	4

Chain D: 14 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	11
β-strand	9-14	6	11
β-strand	23-28	6	11
β-strand	33-40	8	11
α-helix	49-59	11
β-strand	68-73	6	11
β-strand	78-83	6	11
β-strand	88	1	12
α-helix	89-95	7
α-helix	102-121	20
β-strand	124-125	2	13
α-helix	131-133	3
β-strand	134-136	3	12
α-helix	139-141	3
β-strand	145-147	3	12
β-strand	154-155	2	13
α-helix	165-167	3
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	247-257	11
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	331	Homo sapiens	P48730 (AlphaFold model)

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

>4KBA_1 Casein kinase I isoform delta (chains A, B, C, D)
MHHHHHHSSGLVPRGSLRVGNRYRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLECVKTKH
PQLHIESKIYKMMQGGVGIPTIRWCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVL
LLADQMISRIEYIHSKNFIHRDVKPDNFLMGLGKKGNLVYIIDFGLAKKYRDARTHQHIP
YRENKNLTGTARYASINTHLGIEQSRRDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYE
RISEKKMSTPIEVLCKGYPSEFATYLNFCRSLRFDDKPDYSYLRQLFRNLFHRQGFSYDY
VFDWNMLKFGASRAADDAERERRDREERLRH

Ligands and cofactors

ID	Name	Formula	Copies
1QM	9-[3-(4-fluorophenyl)-1-methyl-1H-pyrazol-4-yl]-2,3,4,5-tetrahydropyrido[2,3-f]…	C18 H17 F N4 O	4

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

Primary citation

Ligand-protein interactions of selective casein kinase 1 delta inhibitors. Mente, S., Arnold, E., Butler, T. et al. J Med Chem (2013) 56:6819-6828. DOI 10.1021/jm4006324 · 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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