6gu7

CDK1/Cks2 in complex with AZD5438

Method: X-RAY DIFFRACTION D_max: 107.0 Å Quality: EXCELLENT

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

Cyclin-dependent kinase 1

Homo sapiens

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 1–297	Not recorded	Cyclin-dependent kinases regulatory subunit 2 × 1 （P33552） FB8 4-(2-methyl-3-propan-2-yl-imidazol-4-yl)-~{N}-(4-methylsulfonylphenyl)pyrimidin-2-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；CONDITIONS AROUND 0.1M TRIS/BICINE (PH8.5), 10% PEG8K, 20% ETHYLENE GLYCOL PROTEIN AT 10-12 MG/ML, 0.5mM INHIBITOR	Resolution 2.75 Å R-free 0.274
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–297	Not recorded	Cyclin-dependent kinases regulatory subunit 2 × 1 （P33552）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；CONDITIONS AROUND 0.1M TRIS/BICINE (PH8.5), 10% PEG8K, 20% ETHYLENE GLYCOL PROTEIN AT 10-12 MG/ML, 0.5mM INHIBITOR	Resolution 2.75 Å R-free 0.274
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 1–297	Not recorded	Cyclin-dependent kinases regulatory subunit 2 × 1 （P33552）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；CONDITIONS AROUND 0.1M TRIS/BICINE (PH8.5), 10% PEG8K, 20% ETHYLENE GLYCOL PROTEIN AT 10-12 MG/ML, 0.5mM INHIBITOR	Resolution 2.75 Å R-free 0.274
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain G； UniProt 1–297	Not recorded	Cyclin-dependent kinases regulatory subunit 2 × 1 （P33552）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；CONDITIONS AROUND 0.1M TRIS/BICINE (PH8.5), 10% PEG8K, 20% ETHYLENE GLYCOL PROTEIN AT 10-12 MG/ML, 0.5mM INHIBITOR	Resolution 2.75 Å R-free 0.274

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 6GU7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4Y72 Human CDK1/CyclinB1/CKS2 With Inhibitor Deposited 2015-02-13	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 1–297（297 aa）	Not recorded	LZ9 {[(2,6-difluorophenyl)carbonyl]amino}-N-(4-fluorophenyl)-1H-pyrazole-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.7；277 K；Conditions around 0.1M MES/imidazole buffer (pH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K Protein at 10-12 mg/ml	Resolution 2.30 Å R-free 0.252
4YC3 CDK1/CyclinB1/CKS2 Apo Deposited 2015-02-19	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 1–297（297 aa）	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.7；277 K；0.1M MES/imidazole buffer (pH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K Protein at 10-12 mg/ml	Resolution 2.70 Å R-free 0.260
4YC6 CDK1/CKS1 Deposited 2015-02-19	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–297（297 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.3；277 K；16-18% PEG 10 000, 0.1M imidazole pH 8.2 -8.4	Resolution 2.60 Å R-free 0.267
4YC6 CDK1/CKS1 Deposited 2015-02-19	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–297（297 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.3；277 K；16-18% PEG 10 000, 0.1M imidazole pH 8.2 -8.4	Resolution 2.60 Å R-free 0.267
4YC6 CDK1/CKS1 Deposited 2015-02-19	Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1–297（297 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.3；277 K；16-18% PEG 10 000, 0.1M imidazole pH 8.2 -8.4	Resolution 2.60 Å R-free 0.267
4YC6 CDK1/CKS1 Deposited 2015-02-19	Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 1–297（297 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.3；277 K；16-18% PEG 10 000, 0.1M imidazole pH 8.2 -8.4	Resolution 2.60 Å R-free 0.267
5HQ0 Ternary complex of human proteins CDK1, Cyclin B and CKS2, bound to an inhibitor Deposited 2016-01-21	Different construct 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 1–297（297 aa） Fragment：Fall Armyworm	Not recorded	LZ9 {[(2,6-difluorophenyl)carbonyl]amino}-N-(4-fluorophenyl)-1H-pyrazole-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.7；277 K；0.1 M MES pH6.7, 6.55 MPD, 5% PEG4K, 10% PEG 1K	Resolution 2.30 Å R-free 0.252
5LQF CDK1/CyclinB1/CKS2 in complex with NU6102 Deposited 2016-08-17	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 1–297（297 aa）	Not recorded	4SP O6-CYCLOHEXYLMETHOXY-2-(4'-SULPHAMOYLANILINO) PURINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.7；277 K；0.1M MES/IMIDAZOLE BUFFER (PH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K PROTEIN AT 10-12 MG/ML	Resolution 2.06 Å R-free 0.254
5LQF CDK1/CyclinB1/CKS2 in complex with NU6102 Deposited 2016-08-17	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–297（297 aa）	Not recorded	4SP O6-CYCLOHEXYLMETHOXY-2-(4'-SULPHAMOYLANILINO) PURINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.7；277 K；0.1M MES/IMIDAZOLE BUFFER (PH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K PROTEIN AT 10-12 MG/ML	Resolution 2.06 Å R-free 0.254
6GU2 CDK1/CyclinB/Cks2 in complex with Flavopiridol Deposited 2018-06-19	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 1–297（297 aa）	Not recorded	F9Z 2-(2-chlorophenyl)-8-[(3~{R},4~{R})-1-methyl-3-oxidanyl-piperidin-4-yl]-5,7-bis(oxidanyl)chromen-4-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1M MES/IMIDAZOLE BUFFER (PH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K PROTEIN AT 10-12 MG/ML + 0.5mM Inhibitor	Resolution 2.00 Å R-free 0.239
6GU3 CDK1/CyclinB/Cks2 in complex with AZD5438 Deposited 2018-06-19	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–297（297 aa）	Not recorded	FB8 4-(2-methyl-3-propan-2-yl-imidazol-4-yl)-~{N}-(4-methylsulfonylphenyl)pyrimidin-2-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1M MES/IMIDAZOLE BUFFER (PH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K PROTEIN AT 10-12 MG/ML + 0.5mM Inhibitor	Resolution 2.65 Å R-free 0.258
6GU4 CDK1/CyclinB/Cks2 in complex with CGP74514A Deposited 2018-06-19	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 1–297（297 aa）	Not recorded	FC8 ~{N}2-[(1~{R},2~{S})-2-azanylcyclohexyl]-~{N}6-(3-chlorophenyl)-9-ethyl-purine-2,6-diamine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1M MES/IMIDAZOLE BUFFER (PH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K PROTEIN AT 10-12 MG/ML + 0.5mM Inhibitor	Resolution 2.73 Å R-free 0.253
6GU6 CDK1/Cks2 in complex with Dinaciclib Deposited 2018-06-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–297（297 aa）	Not recorded	1QK 3-[({3-ethyl-5-[(2S)-2-(2-hydroxyethyl)piperidin-1-yl]pyrazolo[1,5-a]pyrimidin-7-yl}amino)methyl]-1-hydroxypyridinium × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；CONDITIONS AROUND 0.1M BIS-TRIS(PH6.5), 0.2M SODIUM NITRATE 20% PEG3350, PROTEIN AT 10-12 MG/ML, 0.5Mm INHIBITOR	Resolution 2.33 Å R-free 0.246
6TWN Crystal structure of Talin1 R7R8 in complex with CDK1 (206-223) Deposited 2020-01-13	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 207–223（17 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；0.1M Na citrate pH 5.6, 20% Isopropanol and 20% PEG4K	Resolution 2.28 Å R-free 0.262
6TWN Crystal structure of Talin1 R7R8 in complex with CDK1 (206-223) Deposited 2020-01-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 207–223（17 aa）	Not recorded	GOL GLYCEROL × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；0.1M Na citrate pH 5.6, 20% Isopropanol and 20% PEG4K	Resolution 2.28 Å R-free 0.262
7NJ0 CryoEM structure of the human Separase-Cdk1-cyclin B1-Cks1 complex Deposited 2021-02-14	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–297（297 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	PO4 PHOSPHATE ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9SKQ Cryo-EM structure of CAK-CDK1-cyclin B1 Deposited 2025-09-02	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–297（297 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å

12 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CDK1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–302； UniProt 1–297 Author chain C； PDBConstruct 6–302； UniProt 1–297 Author chain E； PDBConstruct 6–302； UniProt 1–297 Author chain G； PDBConstruct 6–302； UniProt 1–297

Cyclin-dependent kinases regulatory subunit 2

Homo sapiens

UniProt P33552

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 1–79	Not recorded	Cyclin-dependent kinase 1 × 1 （P06493） FB8 4-(2-methyl-3-propan-2-yl-imidazol-4-yl)-~{N}-(4-methylsulfonylphenyl)pyrimidin-2-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；CONDITIONS AROUND 0.1M TRIS/BICINE (PH8.5), 10% PEG8K, 20% ETHYLENE GLYCOL PROTEIN AT 10-12 MG/ML, 0.5mM INHIBITOR	Resolution 2.75 Å R-free 0.274
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 1–79	Not recorded	Cyclin-dependent kinase 1 × 1 （P06493）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；CONDITIONS AROUND 0.1M TRIS/BICINE (PH8.5), 10% PEG8K, 20% ETHYLENE GLYCOL PROTEIN AT 10-12 MG/ML, 0.5mM INHIBITOR	Resolution 2.75 Å R-free 0.274
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain F； UniProt 1–79	Not recorded	Cyclin-dependent kinase 1 × 1 （P06493）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；CONDITIONS AROUND 0.1M TRIS/BICINE (PH8.5), 10% PEG8K, 20% ETHYLENE GLYCOL PROTEIN AT 10-12 MG/ML, 0.5mM INHIBITOR	Resolution 2.75 Å R-free 0.274
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain H； UniProt 1–79	Not recorded	Cyclin-dependent kinase 1 × 1 （P06493）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；CONDITIONS AROUND 0.1M TRIS/BICINE (PH8.5), 10% PEG8K, 20% ETHYLENE GLYCOL PROTEIN AT 10-12 MG/ML, 0.5mM INHIBITOR	Resolution 2.75 Å R-free 0.274

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6GU7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CKS HUMAN CKSHS2 ATOMIC STRUCTURE: A ROLE FOR ITS HEXAMERIC ASSEMBLY IN CELL CYCLE CONTROL Deposited 1993-09-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–79（79 aa） Chain B 1–79（79 aa） Chain C 1–79（79 aa）	Not recorded	SO4 SULFATE ION × 6	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å
4Y72 Human CDK1/CyclinB1/CKS2 With Inhibitor Deposited 2015-02-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: TRIMERIC	Chain C 1–79（79 aa） Fragment：residues 165-433	Not recorded	LZ9 {[(2,6-difluorophenyl)carbonyl]amino}-N-(4-fluorophenyl)-1H-pyrazole-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.7；277 K；Conditions around 0.1M MES/imidazole buffer (pH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K Protein at 10-12 mg/ml	Resolution 2.30 Å R-free 0.252
4YC3 CDK1/CyclinB1/CKS2 Apo Deposited 2015-02-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–79（79 aa）	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.7；277 K；0.1M MES/imidazole buffer (pH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K Protein at 10-12 mg/ml	Resolution 2.70 Å R-free 0.260
5HQ0 Ternary complex of human proteins CDK1, Cyclin B and CKS2, bound to an inhibitor Deposited 2016-01-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–79（79 aa）	Not recorded	LZ9 {[(2,6-difluorophenyl)carbonyl]amino}-N-(4-fluorophenyl)-1H-pyrazole-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.7；277 K；0.1 M MES pH6.7, 6.55 MPD, 5% PEG4K, 10% PEG 1K	Resolution 2.30 Å R-free 0.252
5LQF CDK1/CyclinB1/CKS2 in complex with NU6102 Deposited 2016-08-17	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–79（79 aa）	Not recorded	4SP O6-CYCLOHEXYLMETHOXY-2-(4'-SULPHAMOYLANILINO) PURINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.7；277 K；0.1M MES/IMIDAZOLE BUFFER (PH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K PROTEIN AT 10-12 MG/ML	Resolution 2.06 Å R-free 0.254
5LQF CDK1/CyclinB1/CKS2 in complex with NU6102 Deposited 2016-08-17	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 1–79（79 aa）	Not recorded	4SP O6-CYCLOHEXYLMETHOXY-2-(4'-SULPHAMOYLANILINO) PURINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.7；277 K；0.1M MES/IMIDAZOLE BUFFER (PH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K PROTEIN AT 10-12 MG/ML	Resolution 2.06 Å R-free 0.254
6GU2 CDK1/CyclinB/Cks2 in complex with Flavopiridol Deposited 2018-06-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–79（79 aa）	Not recorded	F9Z 2-(2-chlorophenyl)-8-[(3~{R},4~{R})-1-methyl-3-oxidanyl-piperidin-4-yl]-5,7-bis(oxidanyl)chromen-4-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1M MES/IMIDAZOLE BUFFER (PH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K PROTEIN AT 10-12 MG/ML + 0.5mM Inhibitor	Resolution 2.00 Å R-free 0.239
6GU3 CDK1/CyclinB/Cks2 in complex with AZD5438 Deposited 2018-06-19	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–79（79 aa）	Not recorded	FB8 4-(2-methyl-3-propan-2-yl-imidazol-4-yl)-~{N}-(4-methylsulfonylphenyl)pyrimidin-2-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1M MES/IMIDAZOLE BUFFER (PH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K PROTEIN AT 10-12 MG/ML + 0.5mM Inhibitor	Resolution 2.65 Å R-free 0.258
6GU4 CDK1/CyclinB/Cks2 in complex with CGP74514A Deposited 2018-06-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–79（79 aa）	Not recorded	FC8 ~{N}2-[(1~{R},2~{S})-2-azanylcyclohexyl]-~{N}6-(3-chlorophenyl)-9-ethyl-purine-2,6-diamine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1M MES/IMIDAZOLE BUFFER (PH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K PROTEIN AT 10-12 MG/ML + 0.5mM Inhibitor	Resolution 2.73 Å R-free 0.253
6GU6 CDK1/Cks2 in complex with Dinaciclib Deposited 2018-06-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–79（79 aa）	Not recorded	1QK 3-[({3-ethyl-5-[(2S)-2-(2-hydroxyethyl)piperidin-1-yl]pyrazolo[1,5-a]pyrimidin-7-yl}amino)methyl]-1-hydroxypyridinium × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；CONDITIONS AROUND 0.1M BIS-TRIS(PH6.5), 0.2M SODIUM NITRATE 20% PEG3350, PROTEIN AT 10-12 MG/ML, 0.5Mm INHIBITOR	Resolution 2.33 Å R-free 0.246

9 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CKS2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 6–84； UniProt 1–79 Author chain D； PDBConstruct 6–84； UniProt 1–79 Author chain F； PDBConstruct 6–84； UniProt 1–79 Author chain H； PDBConstruct 6–84； UniProt 1–79

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6gu7
Deposition date deposition_date	2018-06-19
Structure title title	CDK1/Cks2 in complex with AZD5438
Keywords keywords	CDK1, CKS2, INHIBITOR, CELL CYCLE; CELL CYCLE
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	36.31 Å
Radius of gyration Rg (electron density) rg_electron	35.20 Å
Forward intensity I(0) i0	394924000.00
Molecular weight molecular_weight	166610.0 kDa
Excluded volume excluded_volume	211210 Å³
Envelope volume envelope_volume	286520 Å³
Hydration-shell volume shell_volume	65360 Å³
Envelope diameter envelope_diameter	109.5 Å
Shell Rg shell_rg	43.96 Å
Envelope Rg envelope_rg	34.02 Å
Shape Rg shape_rg	35.18 Å
Total Rg total_rg	35.90 Å
Total atoms total_atoms	11768
Residues n_residues	1427
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	107.0 Å
Rg (real space) rg_real	36.00 Å
Rg uncertainty (real space) rg_real_error	0.55 Å
I(0) (real space) i0_real	3.9490e+08
I(0) uncertainty (real space) i0_real_error	6.1110e+06
Rg (reciprocal space) rg_reciprocal	36.20 Å
I(0) (reciprocal space) i0_reciprocal	395000000.0000
Solution quality estimate total_estimate	0.9021
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	48.6 Å
Skewness Skewness skewness	0.006
Kurtosis Kurtosis kurtosis	-0.564
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	63780000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.945; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.926

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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-dependent kinase 1
Molecular weight formula_weight	34553.9 kDa
EC 编号 ec_number	2.7.11.22,2.7.11.23
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	11781

GPLGSMEDYTKIEKIGEGTYGVVYKGRHKTTGQVVAMKKIRLESEEEGVPSTAIREISLLKELRHPNIVSLQDVLMQDSRLYLIFEFLSMDLKKYLDSIPPGQYMDSSLVKSYLYQILQGIVFCHSRRVLHRDLKPQNLLIDDKGTIKLADFGLARAFGIPIRVYTHEVVTLWYRSPEVLLGSARYSTPVDIWSIGTIFAELATKKPLFHGDSEIDQLFRIFRALGTPNNEVWPEVESLQDYKNTFPKWKPGSLASHVKNLDENGLDLLSKMLIYDPAKRISGKMALNHPYFNDLDNQIKKM

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	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Cyclin-dependent kinases regulatory subunit 2
Molecular weight formula_weight	10290.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H

GPLGSMAHKQIYYSDKYFDEHYEYRHVMLPRELSKQVPKTHLMSEEEWRRLGVQQSLGWVHYMIHEPEPHILLFRRPLPKDQQK

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	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	4-(2-methyl-3-propan-2-yl-imidazol-4-yl)-~{N}-(4-methylsulfonylphenyl)pyrimidin-2-amine
Molecular weight formula_weight	371.5 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	13

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7. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d6gu7a_
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

Domain ID domain_id	d6gu7b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.97 — Cell cycle regulatory proteins
Superfamily Superfamily superfamily	d.97.1 — Cell cycle regulatory proteins
Family Family family	d.97.1.1 — Cell cycle regulatory proteins

Domain ID domain_id	d6gu7c_
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

Domain ID domain_id	d6gu7d_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.97 — Cell cycle regulatory proteins
Superfamily Superfamily superfamily	d.97.1 — Cell cycle regulatory proteins
Family Family family	d.97.1.1 — Cell cycle regulatory proteins

Domain ID domain_id	d6gu7e_
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

Domain ID domain_id	d6gu7f_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.97 — Cell cycle regulatory proteins
Superfamily Superfamily superfamily	d.97.1 — Cell cycle regulatory proteins
Family Family family	d.97.1.1 — Cell cycle regulatory proteins

Domain ID domain_id	d6gu7g_
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

Domain ID domain_id	d6gu7h_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.97 — Cell cycle regulatory proteins
Superfamily Superfamily superfamily	d.97.1 — Cell cycle regulatory proteins
Family Family family	d.97.1.1 — Cell cycle regulatory proteins

CATH v4.4 (12 domains)

Domain ID domain_id	6gu7A01
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	6gu7A02
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

Domain ID domain_id	6gu7B00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	170 — Cyclin-Dependent Kinase Subunit Type 2
Homologous superfamily homologous superfamily	10 — Cyclin-dependent kinase, regulatory subunit

Domain ID domain_id	6gu7C01
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	6gu7C02
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

Domain ID domain_id	6gu7D00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	170 — Cyclin-Dependent Kinase Subunit Type 2
Homologous superfamily homologous superfamily	10 — Cyclin-dependent kinase, regulatory subunit

Domain ID domain_id	6gu7E01
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	6gu7E02
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

Domain ID domain_id	6gu7F00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	170 — Cyclin-Dependent Kinase Subunit Type 2
Homologous superfamily homologous superfamily	10 — Cyclin-dependent kinase, regulatory subunit

Domain ID domain_id	6gu7G01
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	6gu7G02
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

Domain ID domain_id	6gu7H00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	170 — Cyclin-Dependent Kinase Subunit Type 2
Homologous superfamily homologous superfamily	10 — Cyclin-dependent kinase, regulatory subunit

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8. Citations (1)

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Unit-cell length a length_a	67.995 Å
Unit-cell length b length_b	149.202 Å
Unit-cell length c length_c	87.260 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.23 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.750 Å
Low-resolution limit resolution_low	87.350 Å
R factor r_factor	0.2292
R_work r_work	0.2269
R_free r_free	0.2737

fit	/app/data/saxs_computation/gu/6gu7/6gu7.fit
pddf	/app/data/pr_computation/gu/6gu7/6gu7.pr.out
profile	/app/data/saxs_computation/gu/6gu7/6gu7.dat

CDK1/Cks2 in complex with AZD5438

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

Cyclin-dependent kinase 1

State in the Current Structure

Other States of the Same Protein in the Database

Cyclin-dependent kinases regulatory subunit 2

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) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)