Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CDK8-CYCC IN COMPLEX WITH 8-[2-AMINO-3-CHLORO-5-(1-METHYL-1H-INDAZOL-5-YL)-PYRIDIN-4-YL]-2,8-DIAZA-SPIRO[4.5]DECAN-1-ONE
 
Authors :  D. Musil, J. Blagg, A. Mallinger
Date :  31 Dec 15  (Deposition) - 03 Feb 16  (Release) - 24 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cdk8 Kinase / Cyclin C, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Mallinger, K. Schiemann, C. Rink, F. Stieber, M. Calderini, S. Crumpler, M. Stubbs, O. Adeniji-Popoola, O. Poeschke, M. Busch, P. Czodrowski, D. Musil, D. Schwarz, M. J. Ortiz-Ruiz, R. Schneider, C. Thai, M. Valenti, A. De Haven Brandon, R. Burke, P. Workman, T. Dale, D. Wienke, P. A. Clarke, C. Esdar, F. I. Raynaud, S. A. Eccles, F. Rohdich, J. Blagg
Discovery Of Potent, Selective, And Orally Bioavailable Small-Molecule Modulators Of The Mediator Complex-Associate Kinases Cdk8 And Cdk19.
J. Med. Chem. V. 59 1078 2016
PubMed-ID: 26796641  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B01685

(-) Compounds

Molecule 1 - CYCLIN-DEPENDENT KINASE 8
    Chains: A
    EC Number: 2.7.11.22, 2.7.11.23
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Fragment: KINASE DOMAIN, RESIDUES 3-362
    Gene: CDK8
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CELL DIVISION PROTEIN KINASE 8,MEDIATOR COMPLEX SUBUNIT CDK8,MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT CDK8,PROTEIN KINASE K35
 
Molecule 2 - CYCLIN-C
    Chains: B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Gene: CCNC
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SRB11 HOMOLOG,HSRB11

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
15Y81Ligand/Ion8-[2-AZANYL-3-CHLORANYL-5-(1-METHYLINDAZOL-5-YL)PYRIDIN-4-YL]-2,8-DIAZASPIRO[4.5]DECAN-1-ONE
2EDO1Ligand/Ion1,2-ETHANEDIOL
3FMT1Ligand/IonFORMIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:27 , TYR A:32 , VAL A:35 , ALA A:50 , LYS A:52 , ILE A:79 , ASP A:98 , ALA A:100 , ASP A:103 , LEU A:158 , ALA A:172 , ASP A:173 , ARG A:356binding site for residue 5Y8 A 401
2AC2SOFTWAREPRO A:124 , GLY A:126binding site for residue EDO A 402
3AC3SOFTWAREGLN B:41binding site for residue FMT B 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5HBJ)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:338 -Pro A:339

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5HBJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5HBJ)

(-) Exons   (0, 0)

(no "Exon" information available for 5HBJ)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:342
                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.hhhhhee....eeeee..eeeeeeee.......eeeeeee.....hhhhhhhhhhhhhh.......eeeeeee....eeeeeee...eehhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.........eee.................hhhhhh.....hhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhh......hhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhh.....hhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh........................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5hbj A  -1 DKMDYDFKVKLSSERERVEDLFEYEGCKVGRGTYGHVYKAKRKDGKDDKDYALKQIEGTGISMSACREIALLRELKHPNVISLQKVFLSHADRKVWLLFDYAEHDLWHIIKFHRASKAVQLPRGMVKSLLYQILDGIHYLHANWVLHRDLKPANILVMGEGPERGRVKIADMGFLFNSPLVTFWYRAPELLLGARHYTKAIDIWAIGCIFAELLTSEPIFHCRQSNPYHHDQLDRIFNVMGFPADKDWEDIKKMPEHSTLMKDFRRNTYTNCSLIKYMEKHKVKPDSKAFHLLQKLLTMDPIKRITSEQAMQDPYFLEDPLPTSDVFAGCQIPYPKREFLTE 361
                                     8        18        28        38        48        58        68        78        88        98       108       122       132       142       152       162       172   ||  184|      204       214       224       234   ||  249       259       269       279       289       299       309       319       329       339       349       359  
                                                                                                                                               116|                                                    176|  184|                                        238|                                                                                                                     
                                                                                                                                                121                                                     179   195                                         244                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:267
                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh.hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh........hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hbj B  -2 DKAMAGNFWQSSHYLQWILDKQDLLKERQKDLKFLSEEEYWKLQIFFTNVIQALGEHLKLRQQVIATATVYFKRFYARYSLKSIDPVLMAPTCVFLASKVEEFGVVSNTRLIAAATSVLKTRFSYAFPKEFPYRMNHILECEFYLLELMDCCLIVYHPYRPLLQYVQDMGQEDMLLPLAWRIVNDTYRTDLCLLYPPFMIALACLHVACVVQQKDARQWFAELSVDMEKILEIIRVILKLYEQWKNFDERKEMATILSKMPKPKPPP 264
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5HBJ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5HBJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5HBJ)

(-) Gene Ontology  (27, 37)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    5Y8  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FMT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asp A:338 - Pro A:339   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5hbj
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  CCNC_HUMAN | P24863
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  CDK8_HUMAN | P49336
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.11.22
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  2.7.11.23
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  CCNC_HUMAN | P24863
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  CDK8_HUMAN | P49336
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CCNC_HUMAN | P24863: 3rgf 4crl 4f6s 4f6u 4f6w 4f70 4f7j 4f7l 4f7n 4f7s 4g6l 5bnj 5cei 5fgk 5hbe 5hbh 5hnb 5hvy 5i5z 5icp 5idn 5idp
        CDK8_HUMAN | P49336: 3rgf 4crl 4f6s 4f6u 4f6w 4f70 4f7j 4f7l 4f7n 4f7s 4g6l 5bnj 5cei 5fgk 5hbe 5hbh 5hnb 5hvy 5i5z 5icp 5idn 5idp

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5HBJ)