Mechanism of CDK inhibition by active site phosphorylation: CDK2 Y15p T160p in complex with cyclin A structure
2CJM
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Cell Cycle
    Structure Weight: 128561.27
    Molecule: CELL DIVISION PROTEIN KINASE 2
    Polymer: 1 Type: protein Length: 298
    Chains: A, C
    EC#: 2.7.11.22   
    Details: PHOSPHORYLATED ON T160 AND Y15
    Organism: Homo sapiens
    Gene Names: Gene View for CDK2 CDKN2
    UniProtKB: Protein Feature View | Search PDB | P24941  
    Molecule: CYCLIN A2
    Polymer: 2 Type: protein Length: 258
    Chains: B, D
    Fragment: RESIDUES 175-432
    Organism: Homo sapiens
    Gene Names: Gene View for CCNA2 CCN1 CCNA
    UniProtKB: Protein Feature View | Search PDB | P20248  
     
  •   Structure Validation Hide

    View the full validation report  

     

  • MolProbity Ramachandran Plot
     

  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Homo sapiens   Taxonomy   Common Name: Human Expression System: Escherichia coli  
    Polymer: 2
    Scientific Name: Homo sapiens   Taxonomy   Common Name: Human Expression System: Escherichia coli  
     
  •   Related PDB Entries Hide
    Identifier Details
    1AQ1   HUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THE INHIBITOR STAUROSPORINE 
    1B38   HUMAN CYCLIN-DEPENDENT KINASE 2 
    1B39   HUMAN CYCLIN-DEPENDENT KINASE 2 PHOSPHORYLATED ON THR 160 
    1BUH   CRYSTAL STRUCTURE OF THE HUMAN CDK2 KINASE COMPLEX WITHCELL CYCLE-REGULATORY PROTEIN CKSHS1 
    1CKP   HUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THE INHIBITOR PURVALANOL B 
    1DI8   THE STRUCTURE OF CYCLIN-DEPENDENT KINASE 2 (CDK2) IN COMPLEX WITH 4-[3- HYDROXYANILINO]-6,7-DIMETHOXYQUINAZOLINE 
    1DM2   HUMAN CYCLIN-DEPENDENT KINASE 2 COMPLEXED WITH THE INHIBITOR HYMENIALDISINE 
    1E1V   HUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THE INHIBITOR NU2058 
    1E1X   HUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THE INHIBITOR NU6027 
    1E9H   THR 160 PHOSPHORYLATED CDK2 - HUMAN CYCLIN A3 COMPLEX WITH THE INHIBITOR INDIRUBIN-5- SULPHONATE BOUND 
    1F5Q   CRYSTAL STRUCTURE OF MURINE GAMMA HERPESVIRUS CYCLIN COMPLEXED TO HUMAN CYCLIN DEPENDANT KINASE 2 
    1FIN   CYCLIN A - CYCLIN-DEPENDENT KINASE 2 COMPLEX 
    1FQ1   CRYSTAL STRUCTURE OF KINASE ASSOCIATED PHOSPHATASE (KAP) INCOMPLEX WITH PHOSPHO-CDK2 
    1FVT   THE STRUCTURE OF CYCLIN-DEPENDENT KINASE 2 (CDK2) INCOMPLEX WITH AN OXINDOLE INHIBITOR 
    1FVV   THE STRUCTURE OF CDK2/CYCLIN A IN COMPLEX WITH AN OXINDOLEINHIBITOR 
    1G5S   CRYSTAL STRUCTURE OF HUMAN CYCLIN DEPENDENT KINASE 2 (CDK2)IN COMPLEX WITH THE INHIBITOR H717 
    1GIH   HUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THE CDK4INHIBITOR 
    1GII   HUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THE CDK4INHIBITOR 
    1GIJ   HUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THE CDK4INHIBITOR 
    1GY3   PCDK2/CYCLIN A IN COMPLEX WITH MGADP, NITRATE AND PEPTIDE SUBSTRATE 
    1GZ8   HUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THE INHIBITOR 2-AMINO-6-(3'-METHYL- 2'-OXO)BUTOXYPURINE 
    1H00   CDK2 IN COMPLEX WITH A DISUBSTITUTED 4, 6 -BIS ANILINO PYRIMIDINE CDK4 INHIBITOR 
    1H01   CDK2 IN COMPLEX WITH A DISUBSTITUTED 2, 4 -BIS ANILINO PYRIMIDINE CDK4 INHIBITOR 
    1H07   CDK2 IN COMPLEX WITH A DISUBSTITUTED 4, 6 -BIS ANILINO PYRIMIDINE CDK4 INHIBITOR 
    1H08   CDK2 IN COMPLEX WITH A DISUBSTITUTED 2, 4 -BIS ANILINO PYRIMIDINE CDK4 INHIBITOR 
    1H0V   HUMAN CYCLIN DEPENDENT PROTEIN KINASE 2 IN COMPLEX WITH THE INHIBITOR 2-AMINO-6-[(R )-PYRROLIDINO-5'-YL]METHOXYPURINE 
    1H0W   HUMAN CYCLIN DEPENDENT PROTEIN KINASE 2 IN COMPLEX WITH THE INHIBITOR 2-AMINO-6-[ CYCLOHEX-3-ENYL]METHOXYPURINE 
    1H1P   STRUCTURE OF HUMAN THR160-PHOSPHO CDK2/ CYCLIN A COMPLEXED WITH THE INHIBITOR NU2058 
    1H1Q   STRUCTURE OF HUMAN THR160-PHOSPHO CDK2/ CYCLIN A COMPLEXED WITH THE INHIBITOR NU6094 
    1H1R   STRUCTURE OF HUMAN THR160-PHOSPHO CDK2/ CYCLIN A COMPLEXED WITH THE INHIBITOR NU6086 
    1H1S   STRUCTURE OF HUMAN THR160-PHOSPHO CDK2/ CYCLIN A COMPLEXED WITH THE INHIBITOR NU6102 
    1H24   CDK2/CYCLINA IN COMPLEX WITH A 9 RESIDUE RECRUITMENT PEPTIDE FROM E2F 
    1H25   CDK2/CYCLINA IN COMPLEX WITH AN 11-RESIDUE RECRUITMENT PEPTIDE FROM E2F 
    1H26   CDK2/CYCLINA IN COMPLEX WITH AN 11-RESIDUE RECRUITMENT PEPTIDE FROM P53 
    1H27   CDK2/CYCLINA IN COMPLEX WITH AN 11-RESIDUE RECRUITMENT PEPTIDE FROM P27 
    1H28   CDK2/CYCLINA IN COMPLEX WITH AN 11-RESIDUE RECRUITMENT PEPTIDE FROM P107 
    1HCK   HUMAN CYCLIN-DEPENDENT KINASE 2 
    1HCL   HUMAN CYCLIN-DEPENDENT KINASE 2 
    1JST   PHOSPHORYLATED CYCLIN-DEPENDENT KINASE-2 BOUND TO CYCLIN A 
    1JSU   P27(KIP1)/CYCLIN A/CDK2 COMPLEX 
    1JSV   THE STRUCTURE OF CYCLIN-DEPENDENT KINASE 2 (CDK2) INCOMPLEX WITH 4-[(6-AMINO-4- PYRIMIDINYL)AMINO]BENZENESULFONAMIDE 
    1JVP   CRYSTAL STRUCTURE OF HUMAN CDK2 ( UNPHOSPHORYLATED) INCOMPLEX WITH PKF049-365 
    1KE5   CDK2 COMPLEXED WITH N-METHYL-4-{[(2-OXO- 1,2-DIHYDRO-3H-INDOL-3-YLIDENE)METHYL] AMINO}BENZENESULFONAMIDE 
    1KE6   CYCLIN-DEPENDENT KINASE 2 (CDK2) COMPLEXED WITH N-METHYL-{4-[2-(7-OXO-6,7-DIHYDRO -8H-[1,3]THIAZOLO[5,4-E]INDOL-8- YLIDENE)HYDRAZINO]PHENYL}METHANESULFONAMIDE 
    1KE7   CYCLIN-DEPENDENT KINASE 2 (CDK2) COMPLEXED WITH 3-{[(2,2-DIOXIDO-1,3-DIHYDRO-2- BENZOTHIEN-5-YL)AMINO]METHYLENE}-5-(1,3- OXAZOL-5-YL)-1,3-DIHYDRO-2H-INDOL-2- ONE 
    1KE8   CYCLIN-DEPENDENT KINASE 2 (CDK2) COMPLEXED WITH 4-{[(2-OXO-1,2-DIHYDRO-3H-INDOL-3 -YLIDENE)METHYL]AMINO}-N-(1,3-THIAZOL-2- YL)BENZENESULFONAMIDE 
    1KE9   CYCLIN-DEPENDENT KINASE 2 (CDK2) COMPLEXED WITH 3-{[4-({[AMINO(IMINO)METHYL] AMINOSULFONYL)ANILINO]METHYLENE}-2-OXO-2,3- DIHYDRO-1H-INDOLE 
    1OGU   STRUCTURE OF HUMAN THR160-PHOSPHO CDK2/ CYCLIN A COMPLEXED WITH A 2-ARYLAMINO-4- CYCLOHEXYLMETHYL-5-NITROSO-6-AMINOPYRIMIDINE INHIBITOR 
    1OI9   STRUCTURE OF HUMAN THR160-PHOSPHO CDK2/ CYCLIN A COMPLEXED WITH A 6- CYCLOHEXYLMETHYLOXY-2-ANILINO-PURINE INHIBITOR 
    1OIQ   IMIDAZOPYRIDINES: A POTENT AND SELECTIVE CLASS OF CYCLIN-DEPENDENT KINASE INHIBITORS IDENTIFIED THROUGH STRUCTURE-BASED HYBRIDISATION 
    1OIR   IMIDAZOPYRIDINES: A POTENT AND SELECTIVE CLASS OF CYCLIN-DEPENDENT KINASE INHIBITORS IDENTIFIED THROUGH STRUCTURE-BASED HYBRIDISATION 
    1OIT   IMIDAZOPYRIDINES: A POTENT AND SELECTIVE CLASS OF CYCLIN-DEPENDENT KINASE INHIBITORS IDENTIFIED THROUGH STRUCTURE-BASED HYBRIDISATION 
    1OIU   STRUCTURE OF HUMAN THR160-PHOSPHO CDK2/ CYCLIN A COMPLEXED WITH A 6- CYCLOHEXYLMETHYLOXY-2-ANILINO-PURINE INHIBITOR 
    1OIY   STRUCTURE OF HUMAN THR160-PHOSPHO CDK2/ CYCLIN A COMPLEXED WITH A 6- CYCLOHEXYLMETHYLOXY-2-ANILINO-PURINE INHIBITOR 
    1OKV   CYCLIN A BINDING GROOVE INHIBITOR H-ARG- ARG-LEU-ILE-PHE-NH2 
    1OKW   CYCLIN A BINDING GROOVE INHIBITOR AC-ARG- ARG-LEU-ASN-(M-CL-PHE)-NH2 
    1OL1   CYCLIN A BINDING GROOVE INHIBITOR H-CIT- CIT-LEU-ILE-(P-F-PHE)-NH2 
    1OL2   CYCLIN A BINDING GROOVE INHIBITOR H-ARG- ARG-LEU-ASN-(P-F-PHE)-NH2 
    1P2A   THE STRUCTURE OF CYCLIN DEPENDENT KINASE 2 (CKD2) WITH ATRISUBSTITUTED NAPHTHOSTYRIL INHIBITOR 
    1P5E   THE STRUCURE OF PHOSPHO-CDK2/CYCLIN A IN COMPLEX WITH THEINHIBITOR 4,5,6,7- TETRABROMOBENZOTRIAZOLE (TBS) 
    1PF8   CRYSTAL STRUCTURE OF HUMAN CYCLIN-DEPENDENT KINASE 2COMPLEXED WITH A NUCLEOSIDE INHIBITOR 
    1PKD   THE CRYSTAL STRUCTURE OF UCN-01 IN COMPLEX WITH PHOSPHO-CDK2/CYCLIN A 
    1PW2   APO STRUCTURE OF HUMAN CYCLIN-DEPENDENT KINASE 2 
    1PXI   HUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THEINHIBITOR 4-(2,5-DICHLORO-THIOPHEN- 3-YL)-PYRIMIDIN-2-YLAMINE 
    1PXJ   HUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THEINHIBITOR 4-(2,4-DIMETHYL-THIAZOL- 5-YL)-PYRIMIDIN-2-YLAMINE 
    1PXK   HUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THEINHIBITOR N-[4-(2,4-DIMETHYL- THIAZOL-5-YL)PYRIMIDIN-2-YL]-N'- HYDROXYIMINOFORMAMIDE 
    1PXL   HUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THEINHIBITOR [4-(2,4-DIMETHYL-THIAZOL- 5-YL)-PYRIMIDIN-2-YL]-(4-TRIFLUOROMETHYL- PHENYL)-AMINE 
    1PXM   HUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THEINHIBITOR 3-[4-(2,4-DIMETHYL- THIAZOL-5-YL)-PYRIMIDIN-2-YLAMINO]-PHENOL 
    1PXN   HUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THEINHIBITOR 4-[4-(4-METHYL-2- METHYLAMINO-THIAZOL-5-YL)-PYRIMIDIN-2- YLAMINO]-PHENOL 
    1PXO   HUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THEINHIBITOR [4-(2-AMINO-4-METHYL- THIAZOL-5-YL)-PYRIMIDIN-2-YL]-(3-NITRO- PHENYL)-AMINE 
    1PXP   HUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THEINHIBITOR N-[4-(2,4-DIMETHYL- THIAZOL-5-YL)-PYRIMIDIN-2-YL]-N',N'- DIMETHYL-BENZENE-1,4-DIAMINE 
    1PYE   CRYSTAL STRUCTURE OF CDK2 WITH INHIBITOR 
    1QMZ   PHOSPHORYLATED CDK2-CYCLYIN A-SUBSTRATE PEPTIDE COMPLEX 
    1R78   CDK2 COMPLEX WITH A 4-ALKYNYL OXINDOLE INHIBITOR 
    1URC   CYCLIN A BINDING GROOVE INHIBITOR H-ARG- ARG-LEU-ASN-(P-F-PHE)-NH2 
    1URW   CDK2 IN COMPLEX WITH AN IMIDAZO[1,2-B] PYRIDAZINE 
    1V1K   CDK2 IN COMPLEX WITH A DISUBSTITUTED 4, 6 -BIS ANILINO PYRIMIDINE CDK4 INHIBITOR 
    1VYW   STRUCTURE OF CDK2/CYCLIN A WITH PNU-292137 
    1VYZ   STRUCTURE OF CDK2 COMPLEXED WITH PNU-181227 
    1W0X   CRYSTALS STRUCTURE OF HUMAN CDK2 IN COMPLEX WITH THE INHIBITOR OLOMOUCINE. 
    1W8C   CO-CRYSTAL STRUCTURE OF 6-CYCLOHEXYLMETHOXY- 8-ISOPROPYL-9H-PURIN-2-YLAMINE AND MONOMERIC CDK2 
    1W98   THE STRUCTURAL BASIS OF CDK2 ACTIVATION BY CYCLIN E 
    1WCC   SCREENING FOR FRAGMENT BINDING BY X-RAY CRYSTALLOGRAPHY 
    1Y8Y   CRYSTAL STRUCTURE OF HUMAN CDK2 COMPLEXED WITH A PYRAZOLO[1,5-A]PYRIMIDINE INHIBITOR 
    1Y91   CRYSTAL STRUCTURE OF HUMAN CDK2 COMPLEXED WITH A PYRAZOLO[1,5-A]PYRIMIDINE INHIBITOR 
    1YKR   CRYSTAL STRUCTURE OF CDK2 WITH AN AMINOIMIDAZO PYRIDINEINHIBITOR 
    2A0C   HUMAN CDK2 IN COMPLEX WITH OLOMOUCINE II, A NOVEL 2,6,9-TRISUBSTITUTED PURINE CYCLIN -DEPENDENT KINASE INHIBITOR 
    2B52   HUMAN CYCLIN DEPENDENT KINASE 2 (CDK2) COMPLEXED WITH DPH-042562 
    2B53   HUMAN CYCLIN DEPENDENT KINASE 2 (CDK2) COMPLEXED WITH DIN-234325 
    2B54   HUMAN CYCLIN DEPENDENT KINASE 2 (CKD2) COMPLEXED WITH DIN-232305 
    2B55   HUMAN CYCLIN DEPENDENT KINASE 2 (CDK2) COMPLEXED WITHINDENOPYRAXOLE DIN-101312 
    2BHE   HUMAN CYCLIN DEPENDENT PROTEIN KINASE 2 IN COMPLEX WITH THE INHIBITOR 5-BROMO- INDIRUBINE 
    2BHH   HUMAN CYCLIN DEPENDENT PROTEIN KINASE 2 IN COMPLEX WITH THE INHIBITOR 4- HYDROXYPIPERINDINESULFONYL-INDIRUBINE 
    2BKZ   STRUCTURE OF CDK2-CYCLIN A WITH PHA-404611 
    2BPM   STRUCTURE OF CDK2-CYCLIN A WITH PHA-630529 
    2BTR   STRUCTURE OF CDK2 COMPLEXED WITH PNU-198873 
    2BTS   STRUCTURE OF CDK2 COMPLEXED WITH PNU-230032 
    2C4G   STRUCTURE OF CDK2-CYCLIN A WITH PHA-533514 
    2C5N   DIFFERENTIAL BINDING OF INHIBITORS TO ACTIVE AND INACTIVE CDK2 PROVIDES INSIGHTS FOR DRUG DESIGN 
    2C5O   DIFFERENTIAL BINDING OF INHIBITORS TO ACTIVE AND INACTIVE CDK2 PROVIDES INSIGHTS FOR DRUG DESIGN 
    2C5P   DIFFERENTIAL BINDING OF INHIBITORS TO ACTIVE AND INACTIVE CDK2 PROVIDES INSIGHTS FOR DRUG DESIGN 
    2C5T   DIFFERENTIAL BINDING OF INHIBITORS TO ACTIVE AND INACTIVE CDK2 PROVIDES INSIGHTS FOR DRUG DESIGN 
    2C5V   DIFFERENTIAL BINDING OF INHIBITORS TO ACTIVE AND INACTIVE CDK2 PROVIDES INSIGHTS FOR DRUG DESIGN 
    2C5X   DIFFERENTIAL BINDING OF INHIBITORS TO ACTIVE AND INACTIVE CDK2 PROVIDES INSIGHTS FOR DRUG DESIGN 
    2C5Y   DIFFERENTIAL BINDING OF INHIBITORS TO ACTIVE AND INACTIVE CDK2 PROVIDES INSIGHTS FOR DRUG DESIGN 
    2C68   CRYSTAL STRUCTURE OF THE HUMAN CDK2 COMPLEXED WITH THE TRIAZOLOPYRIMIDINE INHIBITOR 
    2C69   CRYSTAL STRUCTURE OF THE HUMAN CDK2 COMPLEXED WITH THE TRIAZOLOPYRIMIDINE INHIBITOR 
    2C6I   CRYSTAL STRUCTURE OF THE HUMAN CDK2 COMPLEXED WITH THE TRIAZOLOPYRIMIDINE INHIBITOR 
    2C6K   CRYSTAL STRUCTURE OF THE HUMAN CDK2 COMPLEXED WITH THE TRIAZOLOPYRIMIDINE INHIBITOR 
    2C6L   CRYSTAL STRUCTURE OF THE HUMAN CDK2 COMPLEXED WITH THE TRIAZOLOPYRIMIDINE INHIBITOR 
    2C6M   CRYSTAL STRUCTURE OF THE HUMAN CDK2 COMPLEXED WITH THE TRIAZOLOPYRIMIDINE INHIBITOR 
    2C6O   CRYSTAL STRUCTURE OF THE HUMAN CDK2 COMPLEXED WITH THE TRIAZOLOPYRIMIDINE INHIBITOR 
    2C6T   CRYSTAL STRUCTURE OF THE HUMAN CDK2 COMPLEXED WITH THE TRIAZOLOPYRIMIDINE INHIBITOR 
    2CCH   THE CRYSTAL STRUCTURE OF CDK2 CYCLIN A IN COMPLEX WITH A SUBSTRATE PEPTIDE DERIVED FROM CDC MODIFIED WITH A GAMMA-LINKED ATP ANALOGUE 
    2CCI   CRYSTAL STRUCTURE OF PHOSPHO-CDK2 CYCLIN A IN COMPLEX WITH A PEPTIDE CONTAINING BOTH THE SUBSTRATE AND RECRUITMENT SITES OF CDC6 
    2EXM   HUMAN CDK2 IN COMPLEX WITH ISOPENTENYLADENINE 
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    ATP
    Search 
    Download 
    ATP C10 H16 N5 O13 P3
    ADENOSINE-5'-TRIPHOSPHATE
    ATP:2CJM
    MG
    Search 
    Download 
    MG Mg
    MAGNESIUM ION
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    PTR
    Search 
    PTR C9 H12 N O6 P TYR lPeptideLinking
    TPO
    Search 
    TPO C4 H10 N O6 P THR lPeptideLinking
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
 
Data in orange boxes are gathered from external resources (when available).
  Biological Assembly 1       
Biological assembly 1 generated by PISA (software)
Downloadable viewers:
 
 
 
  •   MyPDB Personal Annotations Hide
     
  •   Deposition Summary Hide
    Authors:   Welburn, J.P.I.,  Tucker, J.,  Johnson, T.,  Lindert, L.,  Morgan, M.,  Willis, A.,  Noble, M.E.M.,  Endicott, J. A.

    Deposition:   2006-04-05
    Release:   2006-04-24
    Last Modified (REVDAT):   2013-07-10
     
  •   Revision History    Hide
    Mouse over text for details
    2013-07-10
    Function and keywords
    2013-07-10
    Version format compliance
    2013-07-10
    Geometry validation
    2013-07-10
    Non-polymer description
    2013-07-10
    Binding sites and description
    2013-07-10
    Source and taxonomy
    2013-07-10
    Entry authorship
    2013-07-10
    Polymer description
    2013-07-10
    Linkage
    2013-07-10
    Biological assembly
    2013-07-10
    Atom nomenclature
    2013-07-10
    Other
    2013-07-10
    Citation
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    EDS  
    Resolution[Å]:   2.30
    R-Value: 0.204 (obs.)
    R-Free: 0.265
    Space Group: P 21 21 21
    Unit Cell:
      Length [Å] Angles [°]
    a = 73.80 α = 90.00 
    b = 133.20 β = 90.00 
    c = 147.59 γ = 90.00