9CSK: CDK4 cyclin D1

Crystal structure of CDK4 cyclin D1 in complex with atirmociclib. Determined by X-ray diffraction at 2.25 Å resolution. Released 26 Mar 2025.

Method: X-ray diffraction
Resolution: 2.25 Å
Organism: Homo sapiens
Chains: 4
Atoms: 8,626
Mol. weight: 130.56 kDa
Ligands: A1AZ4
Released: 26 Mar 2025

Explore 9CSK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9CSK contains 68 α-helices and 22 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, 0 β-strands

Element	Residues	Length
α-helix	26-37	12
α-helix	39-41	3
α-helix	44-47	4
α-helix	54-71	18
α-helix	77-89	13
α-helix	96-98	3
α-helix	99-114	16
α-helix	118-120	3
α-helix	121-126	6
α-helix	134-147	14
α-helix	157-167	11
α-helix	172-191	20
α-helix	194-197	4
α-helix	200-218	19
α-helix	224-226	3
α-helix	229-237	9
α-helix	241-256	16

Chain B: 17 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	6	1
β-strand	7-13	7	1
β-strand	20-24	5	1
β-strand	31-40	10	1
β-strand	42	1	2
β-strand	48	1	2
α-helix	51-62	12
α-helix	63-66	4
β-strand	71	1	3
β-strand	74-82	9	1
β-strand	86-94	9	1
β-strand	98-99	2	3
α-helix	100-106	7
α-helix	108	1
α-helix	114-133	20
β-strand	146-148	3	3
β-strand	154-156	3	3
α-helix	162-166	5
α-helix	183-187	5
α-helix	195-209	15
α-helix	219-230	12
α-helix	232-234	3
α-helix	246-248	3
α-helix	253-256	4
α-helix	257-260	4
α-helix	266-275	10
α-helix	284-285	2
α-helix	286-290	5

Chain C: 17 helices, 0 β-strands

Element	Residues	Length
α-helix	25-37	13
α-helix	39-41	3
α-helix	44-47	4
α-helix	54-70	17
α-helix	77-91	15
α-helix	96-98	3
α-helix	99-114	16
α-helix	118-120	3
α-helix	121-126	6
α-helix	134-147	14
α-helix	157-167	11
α-helix	172-190	19
α-helix	194-197	4
α-helix	200-218	19
α-helix	224-226	3
α-helix	229-237	9
α-helix	241-257	17

Chain D: 17 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	7-14	8	4
β-strand	19-24	6	4
β-strand	31-40	10	4
β-strand	42	1	5
β-strand	48	1	5
α-helix	51-61	11
α-helix	62-66	5
β-strand	71	1	6
β-strand	74-82	9	4
β-strand	86-94	9	4
β-strand	98-99	2	6
α-helix	100-106	7
α-helix	108	1
α-helix	114-133	20
β-strand	146-148	3	6
β-strand	154-156	3	6
α-helix	162-165	4
α-helix	183-187	5
α-helix	195-209	15
α-helix	219-230	12
α-helix	232-234	3
α-helix	235-237	3
α-helix	246-248	3
α-helix	254-256	3
α-helix	257-260	4
α-helix	266-275	10
α-helix	284-285	2
α-helix	286-290	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
G1/S-specific cyclin-D1	A, C	protein	257	Homo sapiens	P24385 (AlphaFold model)
Cyclin-dependent kinase 4	B, D	protein	314	Homo sapiens	P11802 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>9CSK_1 G1/S-specific cyclin-D1 (chains A, C)
MAYPDANLLNDRVLRAMLKAEETCAPSVSYFKCVQKEVLPSMRKIVATWMLEVCEEQKCE
EEVFPLAMNYLDRFLSLEPVKKSRLQLLGATCMFVASKMKETIPLTAEKLCIYTDNSIRP
EELLQMELLLVNKLKWNLAAMTPHDFIEHFLSKMPEAEENKQIIRKHAQTFVALCATDVK
FISNPPSMVAAGSVVAAVQGLNLRSPNNFLSYYRLTRFLSRVIKCDPDCLRACQEQIEAL
LESSLRQAQQNMDPKAA

Sequence of entity 2 (B, D), FASTA

>9CSK_2 Cyclin-dependent kinase 4 (chains B, D)
MATSRYEPVAEIGVGAYGTVYKARDPHSGHFVALKSVRVPNGEEGLPISTVREVALLRRL
EAFEHPNVVRLMDVCATSRTDREIKVTLVFEHVDQDLRTYLDKAPPPGLPAETIKDLMRQ
FLRGLDFLHANCIVHRDLKPENILVTSGGTVKLADFGLARIYSYQMALTPVVVTLWYRAP
EVLLQSTYATPVDMWSVGCIFAEMFRRKPLFCGNSEADQLGKIFDLIGLPPEDDWPRDVS
LPRGAFPPRGPRPVQSVVPEMEESGAQLLLEMLTFNPHKRISAFRALQHSYLHKDEGNPE
LENLYFQGHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
A1AZ4	Atirmociclib	C22 H27 Cl F N5 O3	2

Primary citation

CDK4 selective inhibition improves preclinical anti-tumor efficacy and safety. Palmer, C.L., Boras, B., Pascual, B. et al. Cancer Cell (2025) 43:464-481.e14. DOI 10.1016/j.ccell.2025.02.006 · PubMed

Other PDB entries of the same protein (UniProt P24385 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2W96 2.3 Å, Crystal Structure of CDK4 in complex with a D-type cyclin
6P8E 2.3 Å, Crystal structure of CDK4 in complex with CyclinD1 and P27
2W9Z 2.45 Å, Crystal Structure of CDK4 in complex with a D-type cyclin
5VZU 2.7 Å, Crystal structure of the Skp1-FBXO31-cyclin D1 complex
2W99 2.8 Å, Crystal Structure of CDK4 in complex with a D-type cyclin
6P8G 2.8 Å, Crystal structure of CDK4 in complex with CyclinD1 and P27
2W9F 2.85 Å, Crystal Structure of CDK4 in complex with a D-type cyclin
6P8F 2.89 Å, Crystal structure of CDK4 in complex with CyclinD1 and P27
6P8H 3.19 Å, Crystal structure of CDK4 in complex with CyclinD1 and P21
9IVD 3.55 Å, Cryo-EM structure of CyclinD1 bound AMBRA1-DDB1

Browse structure collections

About this viewer

MolViewer shows 9CSK directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.