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(-) Description

Title :  CDK8-CYCC IN COMPLEX WITH 5-{5-CHLORO-4-[1-(2-METHOXY-ETHYL)-1,8-DIAZA-SPIRO[4.5]DEC-8-YL]-PYRIDIN-3-YL}-1-METHYL-1,3-DIHYDRO-BENZO[C]ISOTHIAZOLE 2,2-DIOXIDE
 
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 :  2.50
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 1-362
    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, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
15Y71Ligand/Ion5-[5-CHLORANYL-4-[1-(2-METHOXYETHYL)-1,8-DIAZASPIRO[4.5]DECAN-8-YL]PYRIDIN-3-YL]-1-METHYL-3~{H}-2,1-BENZOTHIAZOLE 2,2-DIOXIDE
2EDO1Ligand/Ion1,2-ETHANEDIOL
3FMT3Ligand/IonFORMIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:27 , TYR A:32 , VAL A:35 , ALA A:50 , LYS A:52 , PHE A:97 , ASP A:98 , ALA A:100 , ASP A:103 , HIS A:106 , ALA A:155 , LEU A:158 , ASP A:173 , PHE A:176 , ARG A:356 , HOH A:507binding site for residue 5Y7 A 401
2AC2SOFTWAREARG A:150 , ASP A:151 , ARG A:200 , TYR A:211binding site for residue EDO A 402
3AC3SOFTWAREMET A:259 , GLN A:313 , LEU A:316 , LYS B:248binding site for residue FMT A 403
4AC4SOFTWAREHIS B:203 , LYS B:211 , ALA B:213binding site for residue FMT B 301
5AC5SOFTWAREALA B:0 , VAL B:152 , ARG B:157binding site for residue FMT B 302

(-) SS Bonds  (0, 0)

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

(-) 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 5HBH)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5HBH)

(-) 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:336
                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.hhhhhee....eeeee..eeeeeeee........eeeeee.....hhhhhhhhhhhhhh.......eeeeeee....eeeeeee...eehhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...........eee.........eee...............hhhhhh.....hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhh.....hhhhhhhhhhh..hhhhh.hhhhhhhhhhhh......................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5hbh A  -1 DKMDYDFKVKLSSERERVEDLFEYEGCKVGRGTYGHVYKAKRKDGKDDKDYALKQIEGTGISMSACREIALLRELKHPNVISLQKVFLSHADRKVWLLFDYAEHDLWHIIKFHRASQLPRGMVKSLLYQILDGIHYLHANWVLHRDLKPANILVMGEGPERGRVKIADMGFARLVVTFWYRAPELLLGARHYTKAIDIWAIGCIFAELLTSEPIFHCRQEPYHHDQLDRIFNVMGFPADKDWEDIKKMPEHSTLMKDFRRNTYTNCSLIKYMEKHKVKPDSKAFHLLQKLLTMDPIKRITSEQAMQDPYFLEDPLPTSDVFAGCQIPYPKREFLTE 361
                                     8        18        28        38        48        58        68        78        88        98       108     ||125       135       145       155       165       175   ||  199       209       219       229       239|      255       265       275       285       295       305       315       325       335       345       355      
                                                                                                                                             114|                                                      179|                                          239|                                                                                                                   
                                                                                                                                              122                                                       194                                           246                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:270
                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhhhhhhhh.hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh........hhhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5hbh B  -5 DDDDKAMAGNFWQSSHYLQWILDKQDLLKERQKDLKFLSEEEYWKLQIFFTNVIQALGEHLKLRQQVIATATVYFKRFYARYSLKSIDPVLMAPTCVFLASKVEEFGVVSNTRLIAAATSVLKTRFSYAFPKEFPYRMNHILECEFYLLELMDCCLIVYHPYRPLLQYVQDMGQEDMLLPLAWRIVNDTYRTDLCLLYPPFMIALACLHVACVVQQKDARQWFAELSVDMEKILEIIRVILKLYEQWKNFDERKEMATILSKMPKPKPPP 264
                                     4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264
   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 5HBH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (27, 37)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asp A:338 - Pro A:339   [ RasMol ]  
 

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  5hbh
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  CDK8_HUMAN | P49336
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  2.7.11.22
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  2.7.11.23
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 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 5hbj 5hnb 5hvy 5i5z 5icp 5idn 5idp
        CDK8_HUMAN | P49336: 3rgf 4crl 4f6s 4f6u 4f6w 4f70 4f7j 4f7l 4f7n 4f7s 4g6l 5bnj 5cei 5fgk 5hbe 5hbj 5hnb 5hvy 5i5z 5icp 5idn 5idp

(-) Related Entries Specified in the PDB File

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