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(-) Description

Title :  CDK1/CYCLINB1/CKS2 IN COMPLEX WITH NU6102
 
Authors :  C. R. Coxon, E. Anscombe, S. J. Harnor, M. P. Martin, B. J. Carbain, I. R. Hardcastle, L. K. Harlow, S. Korolchuk, C. J. Matheson, M. E. Nobl D. R. Newell, D. M. Turner, M. Sivaprakasam, L. Z. Wang, C. Wong, B. T. Go R. J. Griffin, J. A. Endicott, C. Cano
Date :  17 Aug 16  (Deposition) - 11 Jan 17  (Release) - 22 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.06
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Cdk1 Cyclin B Cks2 Cell Cycle Nu6102, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. R. Coxon, E. Anscombe, S. J. Harnor, M. P. Martin, B. Carbain, B. T. Golding, I. R. Hardcastle, L. K. Harlow, S. Korolchuk, C. J. Matheson, D. R. Newell, M. E. Noble, M. Sivaprakasam, S. J. Tudhope, D. M. Turner, L. Z. Wang, S. R. Wedge, C. Wong, R. J. Griffin, J. A. Endicott, C. Cano
Cyclin-Dependent Kinase (Cdk) Inhibitors: Structure-Activit Relationships And Insights Into The Cdk-2 Selectivity Of 6-Substituted 2-Arylaminopurines.
J. Med. Chem. V. 60 1746 2017
PubMed-ID: 28005359  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B01254

(-) Compounds

Molecule 1 - CYCLIN-DEPENDENT KINASE 1
    Chains: A, D
    EC Number: 2.7.11.22, 2.7.11.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CDK1, CDC2, CDC28A, CDKN1, P34CDC2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CDK1,CELL DIVISION CONTROL PROTEIN 2 HOMOLOG,CELL DIVISION PROTEIN KINASE 1,P34 PROTEIN KINASE
 
Molecule 2 - G2/MITOTIC-SPECIFIC CYCLIN-B1
    Chains: B, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CCNB1, CCNB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - CYCLIN-DEPENDENT KINASES REGULATORY SUBUNIT 2
    Chains: C, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CKS2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CKS-2

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
14SP2Ligand/IonO6-CYCLOHEXYLMETHOXY-2-(4'-SULPHAMOYLANILINO) PURINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
14SP1Ligand/IonO6-CYCLOHEXYLMETHOXY-2-(4'-SULPHAMOYLANILINO) PURINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
14SP1Ligand/IonO6-CYCLOHEXYLMETHOXY-2-(4'-SULPHAMOYLANILINO) PURINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:10 , GLY A:13 , VAL A:18 , ALA A:31 , VAL A:64 , PHE A:80 , GLU A:81 , LEU A:83 , SER A:84 , MET A:85 , ASP A:86 , LYS A:89 , LEU A:135 , ASP A:146binding site for residue 4SP A 301
2AC2SOFTWAREILE D:10 , GLY D:13 , VAL D:18 , ALA D:31 , VAL D:64 , PHE D:80 , GLU D:81 , LEU D:83 , SER D:84 , MET D:85 , ASP D:86 , LYS D:89 , GLN D:132 , LEU D:135 , ASP D:146binding site for residue 4SP D 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Pro A:246 -Gly A:247
2Gly A:247 -Ser A:248
3Pro D:246 -Gly D:247

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5LQF)

(-) Sequences/Alignments

Asymmetric 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:287
                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhh.eeeeeeeee....eeeeeee.....eeeeee....hhhhh.hhhhhhhhhhhhhh.......eeeeeee..eeeeeee...eehhhhhhh.......hhhhhhhhhhhhhhhhhhhhh..ee....hhh.eee.....eee......ee..ee.........hhhhhh......hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh........hhhhh.............hhhhh....hhhhhhhhhhhh........hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lqf A  -2 LGSMEDYTKIEKIGEGTYGVVYKGRHKTTGQVVAMKKIRLESEEEGVPSTAIREISLLKELRHPNIVSLQDVLMQDSRLYLIFEFLSMDLKKYLDSIPPGQYMDSSLVKSYLYQILQGIVFCHSRRVLHRDLKPQNLLIDDKGTIKLADFGLARAFGIPIRVVTLWYRSPEVLLGSARYSTPVDIWSIGTIFAELATKKPLFHGDSEIDQLFRIFRALGTPNNEVWPEVESLQDYKNTFPKWKPGSLASHVKNLDENGLDLLSKMLIYDPAKRISGKMALNHPYFND 289
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157 ||    172       182       192       202       212       222       232       242       252       262       272       282       
                                                                                                                                                                                           159|                                                                                                                            
                                                                                                                                                                                            165                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:264
                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh....hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5lqf B 167 SSEYVKDIYAYLRQLEEEQAVRPKYLLGREVTGNMRAILIDWLVQVQMKFRLLQETMYMTVSIIDRFMQNNSVPKKMLQLVGVTAMFIASKYEEMYPPEIGDFAFVTDNTYTKHQIRQMEMKILRALNFGLGRPLPLHFLRRASKIGEVDVEQHTLAKYLMELTMLDYDMVHFPPSQIAAGAFSLALKILDNGEWTPTLQHYLSYTEESLLPVMQHLAKNVVMVNQGLTKHMTVKNKYATSKHAKISTLPQLNSALVQDLAKAV 430
                                   176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426    


Chain C from PDB  Type:PROTEIN  Length:74
                                                                                                          
               SCOP domains -------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee...ee...eeeeeee.hhhhhh........hhhhhhhh........eeeee......eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 5lqf C   1 MAHKQIYYSDKYFDEHYEYRHVMLPRELSKQVPKTHLMSEEEWRRLGVQQSLGWVHYMIHEPEPHILLFRRPLP  74
                                    10        20        30        40        50        60        70    


Chain D from PDB  Type:PROTEIN  Length:285
                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhh.eeeeeeeee....eeeeeee.....eeeeee..........hhhhhhhhhhhhhh.......eeeeeee..eeeeeee...eehhhhhhhh......hhhhhhhhhhhhhhhhhhhhh..ee....hhh.eee.....eee......ee..ee.......hhhhhh......hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh........hhhhh.............hhhhh....hhhhhhhhhhhh........hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lqf D  -2 LGSMEDYTKIEKIGEGTYGVVYKGRHKTTGQVVAMKKIRLESEEEGVPSTAIREISLLKELRHPNIVSLQDVLMQDSRLYLIFEFLSMDLKKYLDSIPPGQYMDSSLVKSYLYQILQGIVFCHSRRVLHRDLKPQNLLIDDKGTIKLADFGLARAFGIPIRTLWYRSPEVLLGSARYSTPVDIWSIGTIFAELATKKPLFHGDSEIDQLFRIFRALGTPNNEVWPEVESLQDYKNTFPKWKPGSLASHVKNLDENGLDLLSKMLIYDPAKRISGKMALNHPYFND 289
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157||     174       184       194       204       214       224       234       244       254       264       274       284     
                                                                                                                                                                                          158|                                                                                                                           
                                                                                                                                                                                           166                                                                                                                           


Chain E from PDB  Type:PROTEIN  Length:264
                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh....hhhhhhhh.....hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5lqf E 167 SSEYVKDIYAYLRQLEEEQAVRPKYLLGREVTGNMRAILIDWLVQVQMKFRLLQETMYMTVSIIDRFMQNNSVPKKMLQLVGVTAMFIASKYEEMYPPEIGDFAFVTDNTYTKHQIRQMEMKILRALNFGLGRPLPLHFLRRASKIGEVDVEQHTLAKYLMELTMLDYDMVHFPPSQIAAGAFSLALKILDNGEWTPTLQHYLSYTEESLLPVMQHLAKNVVMVNQGLTKHMTVKNKYATSKHAKISTLPQLNSALVQDLAKAV 430
                                   176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426    


Chain F from PDB  Type:PROTEIN  Length:74
                                                                                                          
               SCOP domains -------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee...ee...eeeeeee.hhhhhh........hhhhhhhh........eeee.......eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 5lqf F   1 MAHKQIYYSDKYFDEHYEYRHVMLPRELSKQVPKTHLMSEEEWRRLGVQQSLGWVHYMIHEPEPHILLFRRPLP  74
                                    10        20        30        40        50        60        70
   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 5LQF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (116, 148)

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 Related Entries

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

UniProtKB/Swiss-Prot
        CCNB1_HUMAN | P14635: 2b9r 2jgz 4y72 4yc3 5hq0
        CDK1_HUMAN | P06493: 1lc9 4y72 4yc3 4yc6 5hq0
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(-) Related Entries Specified in the PDB File

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