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(-) Description

Title :  CRYSTAL STRUCTURE OF A CDK6/VCYCLIN COMPLEX WITH INHIBITOR BOUND
 
Authors :  D. E. Piper, N. Walker, Z. Wang
Date :  20 Jun 14  (Deposition) - 06 Aug 14  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Kinase, Transferase-Cell Cycle-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Li, X. Wang, J. Eksterowicz, M. W. Gribble, G. Q. Alba, M. Ayres, T. J. Carlson, A. Chen, X. Chen, R. Cho, R. V. Connors, M. Degraffenreid J. T. Deignan, J. Duquette, P. Fan, B. Fisher, J. Fu, J. N. Huard, J. Kaizerman, K. S. Keegan, C. Li, K. Li, Y. Li, L. Liang, W. Liu, S. E. Lively, M. C. Lo, J. Ma, D. L. Mcminn, J. T. Mihalic, K. Modi, R. Ngo, K. Pattabiraman, D. E. Piper, C. Queva, M. L. Ragains, J. Suchomel, S. Thibault, N. Walker, X. Wang, Z. Wang, M. Wanska, P. M. Wehn, M. F. Weidner, A. J. Zhang, X. Zhao, A. Kamb, D. Wickramasinghe, K. Dai, L. R. Mcgee, J. C. Medina
Discovery Of Amg 925, A Flt3 And Cdk4 Dual Kinase Inhibitor With Preferential Affinity For The Activated State Of Flt3.
J. Med. Chem. V. 57 3430 2014
PubMed-ID: 24641103  |  Reference-DOI: 10.1021/JM500118J

(-) Compounds

Molecule 1 - CYCLIN HOMOLOG
    Chains: A
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    Gene: 72, ECLF2
    Organism Common: SAHV-2
    Organism Scientific: SAIMIRIINE HERPESVIRUS 2
    Organism Taxid: 10383
    Strain: 11
    Synonym: V-CYCLIN
 
Molecule 2 - CYCLIN-DEPENDENT KINASE 6
    Chains: B
    EC Number: 2.7.11.22
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    Gene: CDK6, CDKN6
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CELL DIVISION PROTEIN KINASE 6,SERINE/THREONINE-PROTEIN KINASE PLSTIRE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
124V1Ligand/Ion9-CYCLOPENTYL-N-(5-PIPERAZIN-1-YLPYRIDIN-2-YL)PYRIDO[4,5]PYRROLO[1,2-D]PYRIMIDIN-2-AMINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE B:19 , VAL B:27 , ALA B:41 , PHE B:98 , GLU B:99 , VAL B:101 , ASP B:102 , ASP B:104 , THR B:107 , GLN B:149 , LEU B:152binding site for residue 24V B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4TTH)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu B:114 -Pro B:115

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4TTH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4TTH)

(-) Exons   (0, 0)

(no "Exon" information available for 4TTH)

(-) 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:244
                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh....hhhhhhhh..hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tth A   8 LNRAKIDSTTMKDPRVLNNLKLRELLLPKFTSLWEIQTEVTVDNRTILLTWMHLLCESFELDKSVFPLSVSILDRYLCKKQGTKKTLQKIGAACVLIGSKIRTVKPMTVSKLTYLSFTNLELINQEKDILEALKWDTEAVLATDFLIPLCNALKIPEDLWPQLYEAASTTICKALIQPNIALLSPGLICAGGLLTTIETDNTNCRPWTCYLEDLSSILNFSTNTVRTVKDQVSEAFSLYDLEIL 254
                                    17        27        37        47        57        67        77        87        97       107       117     ||130       140       150       160       170       180       190       200       210       220       230       240       250    
                                                                                                                                             123|                                                                                                                               
                                                                                                                                              127                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:256
                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................eeee.......hhhhhhhhhhhhhhhhhh......eeeee....eeeee...eehhhhhh.......hhhhhhhhhhhhhhhhhhhhhh.ee........eee.....eee......ee.................hhhhhh.....hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh.................hhhhhhhhh.........hhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tth B  15 CVAEIGEKVFKARDLKNGRFVALKRVRVEGMPLSTIREVAVLRHLETFEHPNVVRLFDVCTTKLTLVFEHVDQDLTTYLDKVPEPGVPTETIKDMMFQLLRGLDFLHSHRVVHRDLKPQNILVTSSGQIKLADFGLARIYSFQMALTSVVVTLWYRAPEVLLQSSYATPVDLWSVGCIFAEMFRRKPLFRGSSDVDQLGKILDVIGLPGEEDWPPIEKFDIDELGKDLLLKCLTFNPAKRISAYSALSHPYFQDLE 304
                                  ||28      ||39       |53        63        73        83||     100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   ||  268       278       288       298      
                                 21|       35|        47|                              84|                                                                                                                                                     244| 265|                                    
                                  26        37         52                               92                                                                                                                                                      261  268
   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 4TTH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4TTH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4TTH)

(-) Gene Ontology  (55, 57)

Asymmetric/Biological Unit(hide GO term definitions)

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  4tth
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  CGH2_SHV21 | Q01043
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 Related Entries

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

UniProtKB/Swiss-Prot
        CDK6_HUMAN | Q00534: 1bi7 1bi8 1blx 1g3n 1jow 1xo2 2euf 2f2c 3nup 3nux 4aua 4ez5 5l2i 5l2s 5l2t
        CGH2_SHV21 | Q01043: 1bu2 1jow 1xo2 2euf 2f2c

(-) Related Entries Specified in the PDB File

4p41 THIS IS USING THE SAME DATA SET AS WAS USED FOR 4P41, BUT PROCESSED WITH XDS. THE COMPOUND ELECTRON DENSITY IS SIGNIFICANTLY BETTER.