SAXSdb — 4tth

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cyclin homolog

Saimiriine herpesvirus 2

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–254	Not recorded	Cyclin-dependent kinase 6 × 1 （Q00534） 24V 9-cyclopentyl-N-(5-piperazin-1-ylpyridin-2-yl)pyrido[4,5]pyrrolo[1,2-d]pyrimidin-2-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；10 mM TRIS pH 7.9, 100 mM calcium acetate, 10 mM DTT, 8-12% PEG 3350, 100 mM NDSB-201	Resolution 2.90 Å R-free 0.337

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 4TTH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BU2 X-RAY STRUCTURE OF A VIRAL CYCLIN FROM HERPESVIRUS SAIMIRI Deposited 1998-09-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–250（229 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 3.00 Å R-free 0.325
1JOW Crystal structure of a complex of human CDK6 and a viral cyclin Deposited 2001-07-31	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–254（254 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；Tris/HCL, sodium chloride, PEG 3350, calcium acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K	Resolution 3.10 Å R-free 0.323
1XO2 Crystal structure of a human cyclin-dependent kinase 6 complex with a flavonol inhibitor, fisetin Deposited 2004-10-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–254（254 aa）	Not recorded	FSE 3,7,3',4'-TETRAHYDROXYFLAVONE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.90 Å R-free 0.313
2EUF X-ray structure of human CDK6-Vcyclin in complex with the inhibitor PD0332991 Deposited 2005-10-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–254（254 aa）	Not recorded	CA CALCIUM ION × 1 ACT ACETATE ION × 1 LQQ 6-ACETYL-8-CYCLOPENTYL-5-METHYL-2-[(5-PIPERAZIN-1-YLPYRIDIN-2-YL)AMINO]PYRIDO[2,3-D]PYRIMIDIN-7(8H)-ONE × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；50 mM Tris/HCl pH 8.0, 0.1 M CaAcetate, 10% PEG3350, 10 mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 3.00 Å R-free 0.306
2F2C X-ray structure of human CDK6-Vcyclinwith the inhibitor aminopurvalanol Deposited 2005-11-16	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–254（254 aa）	Not recorded	SO4 SULFATE ION × 1 AP9 (2S)-2-({6-[(3-AMINO-5-CHLOROPHENYL)AMINO]-9-ISOPROPYL-9H-PURIN-2-YL}AMINO)-3-METHYLBUTAN-1-OL × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；50 mM Tris/HCl pH 8.0, 0.1 M CaOAc, 13% PEG 3350, 10 mM DTT, 0.1M sulfobetaine, 1mM inhibitor, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.301

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CGH2_SHV21
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–254； UniProt 1–254

Cyclin-dependent kinase 6

Homo sapiens

UniProt Q00534

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–326	Not recorded	Cyclin homolog × 1 （Q01043） 24V 9-cyclopentyl-N-(5-piperazin-1-ylpyridin-2-yl)pyrido[4,5]pyrrolo[1,2-d]pyrimidin-2-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；10 mM TRIS pH 7.9, 100 mM calcium acetate, 10 mM DTT, 8-12% PEG 3350, 100 mM NDSB-201	Resolution 2.90 Å R-free 0.337

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 4TTH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BI7 MECHANISM OF G1 CYCLIN DEPENDENT KINASE INHIBITION FROM THE STRUCTURE OF THE CDK6-P16INK4A TUMOR SUPPRESSOR COMPLEX Deposited 1998-06-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–326（326 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.40 Å R-free 0.330
1BI8 MECHANISM OF G1 CYCLIN DEPENDENT KINASE INHIBITION FROM THE STRUCTURES CDK6-P19INK4D INHIBITOR COMPLEX Deposited 1998-06-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–326（326 aa） Chain C 1–326（326 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å R-free 0.308
1BLX P19INK4D/CDK6 COMPLEX Deposited 1998-07-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–326（326 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 1.90 Å R-free 0.253
1G3N STRUCTURE OF A P18(INK4C)-CDK6-K-CYCLIN TERNARY COMPLEX Deposited 2000-10-24	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–326（326 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；(NH4)2SO4, Dioxane, Tris-HCl, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.90 Å R-free 0.262
1G3N STRUCTURE OF A P18(INK4C)-CDK6-K-CYCLIN TERNARY COMPLEX Deposited 2000-10-24	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 1–326（326 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；(NH4)2SO4, Dioxane, Tris-HCl, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.90 Å R-free 0.262
1G3N STRUCTURE OF A P18(INK4C)-CDK6-K-CYCLIN TERNARY COMPLEX Deposited 2000-10-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–326（326 aa） Chain E 1–326（326 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；(NH4)2SO4, Dioxane, Tris-HCl, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.90 Å R-free 0.262
1G3N STRUCTURE OF A P18(INK4C)-CDK6-K-CYCLIN TERNARY COMPLEX Deposited 2000-10-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–326（326 aa） Chain E 1–326（326 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；(NH4)2SO4, Dioxane, Tris-HCl, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.90 Å R-free 0.262
1JOW Crystal structure of a complex of human CDK6 and a viral cyclin Deposited 2001-07-31	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–308（308 aa） Fragment：residues 1-308	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；Tris/HCL, sodium chloride, PEG 3350, calcium acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K	Resolution 3.10 Å R-free 0.323
1XO2 Crystal structure of a human cyclin-dependent kinase 6 complex with a flavonol inhibitor, fisetin Deposited 2004-10-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–308（308 aa）	Not recorded	FSE 3,7,3',4'-TETRAHYDROXYFLAVONE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.90 Å R-free 0.313
2EUF X-ray structure of human CDK6-Vcyclin in complex with the inhibitor PD0332991 Deposited 2005-10-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–308（308 aa） Fragment：fragment 1-308	Not recorded	CA CALCIUM ION × 1 ACT ACETATE ION × 1 LQQ 6-ACETYL-8-CYCLOPENTYL-5-METHYL-2-[(5-PIPERAZIN-1-YLPYRIDIN-2-YL)AMINO]PYRIDO[2,3-D]PYRIMIDIN-7(8H)-ONE × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；50 mM Tris/HCl pH 8.0, 0.1 M CaAcetate, 10% PEG3350, 10 mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 3.00 Å R-free 0.306
2F2C X-ray structure of human CDK6-Vcyclinwith the inhibitor aminopurvalanol Deposited 2005-11-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–308（308 aa） Fragment：fragment 1-308	Not recorded	SO4 SULFATE ION × 1 AP9 (2S)-2-({6-[(3-AMINO-5-CHLOROPHENYL)AMINO]-9-ISOPROPYL-9H-PURIN-2-YL}AMINO)-3-METHYLBUTAN-1-OL × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；50 mM Tris/HCl pH 8.0, 0.1 M CaOAc, 13% PEG 3350, 10 mM DTT, 0.1M sulfobetaine, 1mM inhibitor, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.301
3NUP CDK6 (monomeric) in complex with inhibitor Deposited 2010-07-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–301（301 aa） Fragment：UNP residues 1-301	Not recorded	3NU 4-[3-(1-methylethyl)-1H-pyrazol-4-yl]-N-(1-methylpiperidin-4-yl)pyrimidin-2-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6；298 K；0.1M MES pH 6.0, 12% PEG3350, 0.1M NH4NO3, EVAPORATION, temperature 298K	Resolution 2.60 Å R-free 0.264
3NUX CDK6 (monomeric) in complex with inhibitor Deposited 2010-07-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–301（301 aa） Fragment：UNP residues 1-301	Not recorded	3NV 4-[5-chloro-3-(1-methylethyl)-1H-pyrazol-4-yl]-N-(5-piperazin-1-ylpyridin-2-yl)pyrimidin-2-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.1M MES pH 6.0, 12% PEG3350, 0.1M NH4NO3 , VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.266
4AUA Liganded X-ray crystal structure of cyclin dependent kinase 6 (CDK6) Deposited 2012-05-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–301（301 aa） Fragment：KINASE DOMAIN, RESIDUES 1-301	Not recorded	4AU 1H-benzimidazol-2-yl(1H-pyrrol-2-yl)methanone × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.7；287 K；5MG/ML 0.1 M MES/NAOH PH 5.7,, 4.5% W/V PEG 3350, 25 MM SODIUM NITRATE, 10% V/V GLYCEROL, 10 DEGREES CELSIUS	Resolution 2.31 Å R-free 0.277
4EZ5 CDK6 (monomeric) in complex with inhibitor Deposited 2012-05-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–301（301 aa） Fragment：UNP residues 1-301	Not recorded	0RS {5-[4-(dimethylamino)piperidin-1-yl]-1H-imidazo[4,5-b]pyridin-2-yl}[2-(isoquinolin-4-yl)pyridin-4-yl]methanone × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.1M MES pH 6.0, 12% PEG-3350, 0.1M NH4NO3, EVAPORATION, temperature 298K, VAPOR DIFFUSION, HANGING DROP	Resolution 2.70 Å R-free 0.287
5L2I The X-ray co-crystal structure of human CDK6 and Palbociclib. Deposited 2016-08-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–301（301 aa） Fragment：UNP residues 1-301	Not recorded	LQQ 6-ACETYL-8-CYCLOPENTYL-5-METHYL-2-[(5-PIPERAZIN-1-YLPYRIDIN-2-YL)AMINO]PYRIDO[2,3-D]PYRIMIDIN-7(8H)-ONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；286.15 K；1:1 (protein to well buffer) with well buffer containing: 0.1 M MES pH 6.0, 70 - 80 mM NH4NO3, 10 - 15% polyethyleneglycol 3350.	Resolution 2.75 Å R-free 0.304
5L2S The X-ray co-crystal structure of human CDK6 and Abemaciclib. Deposited 2016-08-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–301（301 aa） Fragment：UNP residues 1-301	Not recorded	6ZV N-{5-[(4-ethylpiperazin-1-yl)methyl]pyridin-2-yl}-5-fluoro-4-[4-fluoro-2-methyl-1-(propan-2-yl)-1H-benzimidazol-6-yl]py rimidin-2-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；286.15 K；1:1 (protein to well buffer) with well buffer containing: 0.1 M MES pH 6.0, 70 - 80 mM NH4NO3, 10 - 15% polyethyleneglycol 3350	Resolution 2.27 Å R-free 0.249
5L2T The X-ray co-crystal structure of human CDK6 and Ribociclib. Deposited 2016-08-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–301（301 aa） Fragment：UNP residues 1-301	Not recorded	6ZZ 7-cyclopentyl-N,N-dimethyl-2-{[5-(piperazin-1-yl)pyridin-2-yl]amino}-7H-pyrrolo[2,3-d]pyrimidine-6-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；286.15 K；1:1 (protein to well buffer) with well buffer containing: 0.1 M MES pH 6.0, 70 - 80 mM NH4NO3, 10 - 15% polyethyleneglycol 3350	Resolution 2.37 Å R-free 0.258
6OQL CDK6 in complex with Cpd13 (R)-5-fluoro-4-(4-methyl-5,6,7,8-tetrahydro-4H-pyrazolo[1,5-a]azepin-3-yl)-N-(5-(4-methylpiperazin-1-yl)pyridin-2-yl)pyrimidin-2-amine Deposited 2019-04-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 11–301（291 aa） Fragment：kinase domain	Not recorded	N1A 5-fluoro-N-[5-(4-methylpiperazin-1-yl)pyridin-2-yl]-4-[(4R)-4-methyl-5,6,7,8-tetrahydro-4H-pyrazolo[1,5-a]azepin-3-yl]pyrimidin-2-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6；292 K；13-17% PEG 3350, 80 mM NH4NO3, 100 mM MES pH 6.0	Resolution 2.71 Å R-free 0.253
6OQO CDK6 in complex with Cpd24 N-(5-(6-ethyl-2,6-diazaspiro[3.3]heptan-2-yl)pyridin-2-yl)-5-fluoro-4-(4-methyl-5,6,7,8-tetrahydro-4H-pyrazolo[1,5-a]azepin-3-yl)pyrimidin-2-amine Deposited 2019-04-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 11–301（291 aa） Fragment：kinase domain	Not recorded	N1J N-[5-(6-ethyl-2,6-diazaspiro[3.3]heptan-2-yl)pyridin-2-yl]-5-fluoro-4-[(4R)-4-methyl-5,6,7,8-tetrahydro-4H-pyrazolo[1,5-a]azepin-3-yl]pyrimidin-2-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7.5；292 K；17 % w/v PEG 3,350, 100 mM HEPES, pH 7.5, 200 mM NaCl, 20 mM L-Glutathione	Resolution 1.98 Å R-free 0.264
8I0M Structure of CDK6 in complex with inhibitor Deposited 2023-01-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–301（301 aa）	Not recorded	NJ6 2-[(4-azanylcyclohexyl)amino]-7-cyclopentyl-~{N},~{N}-dimethyl-pyrrolo[2,3-d]pyrimidine-6-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；0.2 M BIS-TRIS pH 7.0, 20% PEG 4,000	Resolution 2.78 Å R-free 0.282
9D8U Crystal structure of CDK6 in complex with atirmociclib Deposited 2024-08-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–301（301 aa）	Not recorded	A1AZ4 Atirmociclib × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；286.15 K；Well Ingredients: Salt: 0.133 M Ammonium Nitrate Precipitant: 5.09 %w/v PEG 3350 Buffer: 0.1 M MES (pH 6.00) Plate setup temperature: 21 C Plate incubation temperature: 13 C Drop volume from well: 0.3 uL Drop protein volume: 0.3 uL	Resolution 2.00 Å R-free 0.253
9PE7 CDK6 to CDK4 active site surrogate in complex with compound 6 Deposited 2025-07-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–301（301 aa）	Mutation：E21V, K26T, T106R, Q149E	A1CIF (3R,4R)-4-({(4M)-5-fluoro-4-[4-fluoro-2-methyl-1-(propan-2-yl)-1H-1,3-benzimidazol-6-yl]pyrimidin-2-yl}amino)-1-(methanesulfonyl)piperidin-3-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；286.15 K；Well volume: 100.0 uL Well Ingredients: Precipitant: 4.0 %w/v (8.0 uL of stock 50.0 %w/v) PEG 3350 Salt: 5.0 mM (5.0 uL of stock 100.0 mM) Calcium chloride dihydrate Salt: 0.0928571429 M (9.2857142857 uL of stock 1.0 M) Ammonium Nitrate Plate setup temperature: 21 C Plate incubation temperature: 13 C Drop volume from well: 1.0 uL Drop protein volume: 1.0 uL Protein formulation name: LJIC-3730A1 + PF-6825089 b Protein Formulation Composition: Protein: CDK6 mutated to look like CDK4 (6.87 mg/mL) Compound: PF-6825089 (1.00 mM)	Resolution 2.05 Å R-free 0.267
9PE8 CDK6 to CDK4 active site surrogate in complex with PF-07220060 Deposited 2025-07-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–301（301 aa）	Mutation：E21V, K26T, T106R, Q149E	A1AZ4 Atirmociclib × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；286.15 K；Well volume: 50.0 uL Well Ingredients: Salt: 0.2714285714 M (1.357142857 uL of stock 10.0 M) Ammonium Nitrate Precipitant: 9.4545454545 %w/v (9.4545454545 uL of stock 50.0 %w/v) PEG 3350 Buffer: 0.1 M (5.0 uL of stock 1.0 M) MES (pH 6.00) Plate setup temperature: 21 C Plate incubation temperature: 13 C Drop volume from well: 0.3 uL Drop protein volume: 0.3 uL Protein Formulation Composition: Protein: quad mutant (6.80 mg/mL) (0.20 mM) Ligand: PF-7220060 (1.00 mM)	Resolution 1.80 Å R-free 0.252

21 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CDK6_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–326； UniProt 1–326

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4tth
Deposition date deposition_date	2014-06-20
Structure title title	Crystal structure of a CDK6/Vcyclin complex with inhibitor bound
Keywords keywords	Kinase, TRANSFERASE-CELL CYCLE-INHIBITOR complex; TRANSFERASE/CELL CYCLE/INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	24.87 Å
Radius of gyration Rg (electron density) rg_electron	23.78 Å
Forward intensity I(0) i0	46451900.00
Molecular weight molecular_weight	55307.0 kDa
Excluded volume excluded_volume	70396 Å³
Envelope volume envelope_volume	82723 Å³
Hydration-shell volume shell_volume	28650 Å³
Envelope diameter envelope_diameter	79.0 Å
Shell Rg shell_rg	31.34 Å
Envelope Rg envelope_rg	24.02 Å
Shape Rg shape_rg	23.79 Å
Total Rg total_rg	24.65 Å
Total atoms total_atoms	3896
Residues n_residues	500
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	83.7 Å
Rg (real space) rg_real	24.79 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	4.6450e+07
I(0) uncertainty (real space) i0_real_error	6.7330e+05
Rg (reciprocal space) rg_reciprocal	24.81 Å
I(0) (reciprocal space) i0_reciprocal	46450000.0000
Solution quality estimate total_estimate	0.8065
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.9 Å
Skewness Skewness skewness	0.263
Kurtosis Kurtosis kurtosis	-0.472
Angular range angular_range	— – 0.3200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	18430000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.833; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Cyclin homolog
Molecular weight formula_weight	28665.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3906

MADSPNRLNRAKIDSTTMKDPRVLNNLKLRELLLPKFTSLWEIQTEVTVDNRTILLTWMHLLCESFELDKSVFPLSVSILDRYLCKKQGTKKTLQKIGAACVLIGSKIRTVKPMTVSKLTYLSCDCFTNLELINQEKDILEALKWDTEAVLATDFLIPLCNALKIPEDLWPQLYEAASTTICKALIQPNIALLSPGLICAGGLLTTIETDNTNCRPWTCYLEDLSSILNFSTNTVRTVKDQVSEAFSLYDLEIL

来源 Source

来源生物 organism	Saimiriine herpesvirus 2
通用名 common_name	SaHV-2
NCBI Class编号 ncbi_taxonomy_id	10383
宿主生物 host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Cyclin-dependent kinase 6
Molecular weight formula_weight	36987.3 kDa
EC 编号 ec_number	2.7.11.22
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MEKDGLCRADQQYECVAEIGEGAYGKVFKARDLKNGGRFVALKRVRVQTGEEGMPLSTIREVAVLRHLETFEHPNVVRLFDVCTVSRTDRETKLTLVFEHVDQDLTTYLDKVPEPGVPTETIKDMMFQLLRGLDFLHSHRVVHRDLKPQNILVTSSGQIKLADFGLARIYSFQMALTSVVVTLWYRAPEVLLQSSYATPVDLWSVGCIFAEMFRRKPLFRGSSDVDQLGKILDVIGLPGEEDWPRDVALPRQAFHSKSAQPIEKFVTDIDELGKDLLLKCLTFNPAKRISAYSALSHPYFQDLERCKENLDSHLPPSQNTSELNTA

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Trichoplusia ni

Entity 3 Entity 3 non-polymer

Description description	9-cyclopentyl-N-(5-piperazin-1-ylpyridin-2-yl)pyrido[4,5]pyrrolo[1,2-d]pyrimidin-2-amine
Molecular weight formula_weight	414.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	10

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7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d4ttha1
Class class	a — All alpha proteins
Fold Fold fold	a.74 — Cyclin-like
Superfamily Superfamily superfamily	a.74.1 — Cyclin-like
Family Family family	a.74.1.1 — Cyclin

Domain ID domain_id	d4ttha2
Class class	a — All alpha proteins
Fold Fold fold	a.74 — Cyclin-like
Superfamily Superfamily superfamily	a.74.1 — Cyclin-like
Family Family family	a.74.1.1 — Cyclin

Domain ID domain_id	d4tthb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.7 — Protein kinases, catalytic subunit

CATH v4.4 (4 domains)

Domain ID domain_id	4tthA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily	10 — Cyclin-like

Domain ID domain_id	4tthA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily	10 — Cyclin-like

Domain ID domain_id	4tthB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	4tthB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

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8. Citations (1)

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Unit-cell length a length_a	71.100 Å
Unit-cell length b length_b	71.100 Å
Unit-cell length c length_c	448.995 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	19.680 Å
R factor r_factor	0.2396
R_work r_work	0.2346
R_free r_free	0.3366

fit	/app/data/saxs_computation/tt/4tth/4tth.fit
pddf	/app/data/pr_computation/tt/4tth/4tth.pr.out
profile	/app/data/saxs_computation/tt/4tth/4tth.dat

Crystal structure of a CDK6/Vcyclin complex with inhibitor bound

1. Protein Identity and Related Structures Protein Identity & Related Structures

Cyclin homolog

State in the Current Structure

Other States of the Same Protein in the Database

Cyclin-dependent kinase 6

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)