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(-) Description

Title :  CRYSTAL STRUCTURE OF CDK8:CYCLIN C COMPLEX WITH COMPOUND 22
 
Authors :  J. R. Kiefer, E. V. Schneider, K. Maskos, M. F. T. Koehler
Date :  06 Jul 15  (Deposition) - 10 Feb 16  (Release) - 11 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.24
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Kinase, Inhibitor, Cdk8, Cyclin Dependent Kinase, Cyclin, Transcription-Transferase-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. F. Koehler, P. Bergeron, E. M. Blackwood, K. Bowman, K. R. Clark, R. Firestein, J. R. Kiefer, K. Maskos, M. L. Mccleland, L. Orren, L. Salphati, S. Schmidt, E. V. Schneider, J. Wu, M. H. Beresini
Development Of A Potent, Specific Cdk8 Kinase Inhibitor Which Phenocopies Cdk8/19 Knockout Cells.
Acs Med. Chem. Lett. V. 7 223 2016
PubMed-ID: 26985305  |  Reference-DOI: 10.1021/ACSMEDCHEMLETT.5B00278

(-) 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 Taxid: 7108
    Fragment: UNP RESIDUES 1-403
    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 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, 16)

Asymmetric/Biological Unit (3, 16)
No.NameCountTypeFull Name
150R1Ligand/Ion4-(4-IODOPHENOXY)-N-METHYLTHIENO[2,3-C]PYRIDINE-2-CARBOXAMIDE
2EDO8Ligand/Ion1,2-ETHANEDIOL
3FMT7Ligand/IonFORMIC ACID

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:71 , GLU A:72 , SER B:9 , GLN B:13binding site for residue EDO A 501
02AC2SOFTWARETYR A:141binding site for residue EDO A 502
03AC3SOFTWAREGLU A:17 , PHE A:20 , GLU A:21 , TYR A:22 , GLU A:23 , LYS A:41binding site for residue EDO A 503
04AC4SOFTWARELYS A:301 , VAL A:302 , LYS A:303binding site for residue EDO A 504
05AC5SOFTWARELYS A:52 , GLU A:66 , ALA A:172 , ASP A:173 , 50R A:508binding site for residue FMT A 505
06AC6SOFTWAREGLU A:165 , ARG A:166 , ARG A:168binding site for residue FMT A 506
07AC7SOFTWAREARG A:168 , SER A:343binding site for residue FMT A 507
08AC8SOFTWAREVAL A:27 , TYR A:32 , VAL A:35 , ALA A:50 , LYS A:52 , ILE A:79 , TYR A:99 , ALA A:100 , ASP A:103 , ALA A:155 , LEU A:158 , ASP A:173 , ARG A:356 , FMT A:505 , HOH A:668binding site for residue 50R A 508
09AC9SOFTWAREASP A:305 , HIS A:310 , LYS B:242 , ASN B:243binding site for residue EDO A 509
10AD1SOFTWAREHOH B:414binding site for residue EDO B 301
11AD2SOFTWAREGLU B:35 , GLU B:239 , GLN B:240 , ASN B:243binding site for residue EDO B 302
12AD3SOFTWAREALA B:0 , ALA B:2 , VAL B:152 , ARG B:157binding site for residue FMT B 303
13AD4SOFTWAREPHE B:31 , SER B:255 , LYS B:256 , MET B:257binding site for residue FMT B 304
14AD5SOFTWAREARG B:58 , GLN B:59binding site for residue FMT B 305
15AD6SOFTWARELEU B:57 , GLN B:59binding site for residue FMT B 306
16AD7SOFTWAREILE B:42 , ASN B:46 , TRP B:241 , PHE B:244 , GLU B:246 , HOH B:401binding site for residue EDO B 307

(-) SS Bonds  (0, 0)

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

(-) 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 5CEI)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5CEI)

(-) 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:345
                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.hhhhhee....eeee...eeeeeeee.......eeeeeee.....hhhhhhhhhhhh.........eeeeeee....eeeeeee...eehhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.......hhh.eee.........eee......hhhhh.........hhhhhh.....hhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhh......hhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhh.....hhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh......................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cei A   0 KMDYDFKVKLSSERERVEDLFEYEGCKVGRGTYGHVYKAKRKDGKDDKDYALKQIEGTGISMSACREIALLRELKHPNVISLQKVFLSHADRKVWLLFDYAEHDLWHIIKFHRASKAQLPRGMVKSLLYQILDGIHYLHANWVLHRDLKPANILVMGEGPERGRVKIADMGFARLFNSPLKPTFWYRAPELLLGARHYTKAIDIWAIGCIFAELLTSEPIFHCRQESNPYHHDQLDRIFNVMGFPADKDWEDIKKMPEHSTLMKDFRRNTYTNCSLIKYMEKHKVKPDSKAFHLLQKLLTMDPIKRITSEQAMQDPYFLEDPLPTSDVFAGCQIPYPKREFLTEE 362
                                     9        19        29        39        49        59        69        79        89        99       109      |124       134       144       154       164       174       184 ||    203       213       223       233     ||247       257       267       277       287       297       307       317       327       337       347       357     
                                                                                                                                              116|                                                             186|                                        239|                                                                                                                      
                                                                                                                                               122                                                              196                                         244                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:268
                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cei B  -3 DDKAMAGNFWQSSHYLQWILDKQDLLKERQKDLKFLSEEEYWKLQIFFTNVIQALGEHLKLRQQVIATATVYFKRFYARYSLKSIDPVLMAPTCVFLASKVEEFGVVSNTRLIAAATSVLKTRFSYAFPKEFPYRMNHILECEFYLLELMDCCLIVYHPYRPLLQYVQDMGQEDMLLPLAWRIVNDTYRTDLCLLYPPFMIALACLHVACVVQQKDARQWFAELSVDMEKILEIIRVILKLYEQWKNFDERKEMATILSKMPKPKPPP 264
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256
   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 5CEI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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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  CDK8_HUMAN | P49336
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 Related Entries

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

(-) Related Entries Specified in the PDB File

4g6l