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Crystal structure of human CDK2 in complex with the inhibitor olomoucine.
1W0X
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Transferase
    Structure Weight: 34275.15
    Molecule: CYCLIN-DEPENDENT KINASE 2
    Polymer: 1 Type: protein Length: 298
    Chains: C
    EC#: 2.7.11.22   
    Details: INHIBITOR BOUND IN POCKET BETWEEN 2 DOMAINS
    Organism: Homo sapiens
    Gene Names: Gene View for CDK2 CDKN2
    UniProtKB: Protein Feature View | Search PDB | P24941  
     
  •   Structure Validation Hide

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  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Homo sapiens   Taxonomy   Common Name: Human Expression System: Spodoptera frugiperda  
     
  •   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 
    1OKU  CYCLIN A BINDING GROOVE INHIBITOR H-ALA- ALA-ABU-ARG-ER-LEU-ILE-(P-F-PHE)-NH2 
    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 
    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 
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    OLO
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    OLO C15 H18 N6 O
    OLOMOUCINE
    OLO:1W0X
     
  •   External Ligand Annotations Hide
    Identifier   Binding Affinity (Sequence Identity %)
    OLO
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    OLO
    IC50: 7 - 7000 nM (100) - data from BindingDB  
    N/Ain BindingMoad
    N/Ain PDBbind
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
 
Data in orange boxes are gathered from external resources (when available).
 
  Biological Assembly       
Biological assembly 1 assigned by authors and generated by PISA (software)
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  •   Deposition Summary Hide
    Authors:   Schulze-Gahmen, U.,  Meijer, L.,  Kim, S.-H.

    Deposition:   2004-06-14
    Release:   2005-01-14
    Last Modified (REVDAT):   2014-02-05
     
  •   Revision History    Hide
    Mouse over text for details
    2014-02-05
    Version format compliance
    2014-02-05
    Source and taxonomy
    2014-02-05
    Other
    2014-02-05
    Non-polymer description
    2014-02-05
    Geometry validation
    2014-02-05
    Citation
    2014-02-05
    Entry title
    2014-02-05
    Biological assembly
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    EDS  
    Resolution[Å]:   2.20
    R-Value: 0.190 (obs.)
    R-Free: 0.270
    Space Group: P 21 21 21
    Unit Cell:
      Length [Å] Angles [°]
    a = 73.77 α = 90.00 
    b = 72.55 β = 90.00 
    c = 54.06 γ = 90.00