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(-) Description

Title :  IDENTIFICATION OF A NEW CLASS OF POTENT CDC7 INHIBITORS DESIGNED BY PUTATIVE PHARMACOPHORE MODEL: SYNTHESIS AND BIOLOGICAL EVALUATION OF 2,3-DIHYDROTHIENO[3,2-D]PYRIMIDIN-4(1H)-ONES
 
Authors :  I. D. Hoffman
Date :  12 Dec 16  (Deposition) - 29 Mar 17  (Release) - 05 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.15
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  A (1x),B (1x)
Biol. Unit 6:  C (1x),D (1x)
Keywords :  Serine/Threonine Kinase, Apo-Protein, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Kurasawa, Y. Oguro, T. Miyazaki, M. Homma, K. Mori, K. Iwai, H. Hara, R. Skene, I. Hoffman, A. Ohashi, S. Yoshida, T. Ishikawa, N. Cho
Identification Of A New Class Of Potent Cdc7 Inhibitors Designed By Putative Pharmacophore Model: Synthesis And Biological Evaluation Of 2, 3-Dihydrothieno[3, 2-D]Pyrimidin-4(1H)-Ones.
Bioorg. Med. Chem. V. 25 2133 2017
PubMed-ID: 28284870  |  Reference-DOI: 10.1016/J.BMC.2017.02.021

(-) Compounds

Molecule 1 - RHO-ASSOCIATED PROTEIN KINASE 2
    Chains: A, B, C, D
    EC Number: 2.7.11.1
    Engineered: YES
    Expression System: BACULOVIRUS EXPRESSION VECTOR PFASTBAC1-HM
    Expression System Strain: SF9
    Expression System Taxid: 274590
    Expression System Vector Type: PFASTBACHTB
    Fragment: UNP RESIDUES 23-417
    Gene: ROCK2, KIAA0619
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: RHO KINASE 2,RHO-ASSOCIATED,COILED-COIL-CONTAINING PROTEIN KINASE 2,COILED-COIL-CONTAINING PROTEIN KINASE II,ROCK-II,P164 ROCK- 2

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D
Biological Unit 5 (1x): A (1x)B (1x)  
Biological Unit 6 (1x):   C (1x)D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5U7Q)

(-) Sites  (0, 0)

(no "Site" information available for 5U7Q)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5U7Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5U7Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5U7Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5U7Q)

(-) Exons   (0, 0)

(no "Exon" information available for 5U7Q)

(-) 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:388
                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh.....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeeee....eeeeeee.....eeeeeeeehhhhhhh....hhhhhhhhhhhh.......eeeeee...eeeeee......hhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee......eee.....hhhhhhhhhhhhhhh.eee.hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh........hhhhhhhhhhhh.hhhhh.....hhhhhhhhhhh.......hhhhh..................................hhhhh...ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u7q A  25 SRQRKLEALIRDPRSPINVESLLDGLNSLVLDLDFPALRKNKNIDNFLNRYEKIVKKIRGLQMKAEDYDVVKVIGRGAFGEVQLVRHKASQKVYAMKLLSKFEMIKRSDSAFFWEERDIMAFANSPWVVQLFYAFQDDRYLYMVMEYMPGGDLVNLMSNYDVPEKWAKFYTAEVVLALDAIHSMGLIHRDVKPDNMLLDKHGHLKLADFGTCMKMDETGMVHCDTAVGTPDYISPEVLKSQGGDGFYGRECDWWSVGVFLYEMLVGDTPFYADSLVGTYSKIMDHKNSLCFPEDAEISKHAKNLICAFLTDREVRLGRNGVEEIRQHPFFKNDQWHWDNIRETAAPVVPELSSDIDSSNFDDIEVETFPIPKAFVGNQLPFIGFTYYR 417
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384   ||  399       409        
                                                                                                                                                                                                                                                                                                                                                                                                     388|                       
                                                                                                                                                                                                                                                                                                                                                                                                      394                       


Chain B from PDB  Type:PROTEIN  Length:385
                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh.....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeeee....eeeeeee.....eeeeeeeehhhhhhh....hhhhhhhhhhhh.......eeeeee...eeeeee......hhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee.....eee...........hhhhhhhh....eeehhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh........hhhhhhhhhhhh.hhhhh.....hhhhhhhhhhh.......hhhhh..................................hhhhh...ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u7q B  28 RKLEALIRDPRSPINVESLLDGLNSLVLDLDFPALRKNKNIDNFLNRYEKIVKKIRGLQMKAEDYDVVKVIGRGAFGEVQLVRHKASQKVYAMKLLSKFEMIKRSDSAFFWEERDIMAFANSPWVVQLFYAFQDDRYLYMVMEYMPGGDLVNLMSNYDVPEKWAKFYTAEVVLALDAIHSMGLIHRDVKPDNMLLDKHGHLKLADFGTCMKMDETGMVHCDTAVGTPDYISPEVLKSQGGDGFYGRECDWWSVGVFLYEMLVGDTPFYADSLVGTYSKIMDHKNSLCFPEDAEISKHAKNLICAFLTDREVRLGRNGVEEIRQHPFFKNDQWHWDNIRETAAPVVPELSSDIDSSNFDDIEVETFPIPKAFVGNQLPFIGFTYYR 417
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387||     402       412     
                                                                                                                                                                                                                                                                                                                                                                                                  388|                       
                                                                                                                                                                                                                                                                                                                                                                                                   394                       


Chain C from PDB  Type:PROTEIN  Length:390
                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeeee....eeeeeee.....eeeeeeeehhhhhhh....hhhhhhhhhhhh.......eeeeee...eeeeee......hhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee.....eeee.....hhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh........hhhhhhhhhhhh.hhhhh.....hhhhhhhhhhh.......hhhhh..................................hhhhh...ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5u7q C  23 GASRQRKLEALIRDPRSPINVESLLDGLNSLVLDLDFPALRKNKNIDNFLNRYEKIVKKIRGLQMKAEDYDVVKVIGRGAFGEVQLVRHKASQKVYAMKLLSKFEMIKRSDSAFFWEERDIMAFANSPWVVQLFYAFQDDRYLYMVMEYMPGGDLVNLMSNYDVPEKWAKFYTAEVVLALDAIHSMGLIHRDVKPDNMLLDKHGHLKLADFGTCMKMDETGMVHCDTAVGTPDYISPEVLKSQGGDGFYGRECDWWSVGVFLYEMLVGDTPFYADSLVGTYSKIMDHKNSLCFPEDAEISKHAKNLICAFLTDREVRLGRNGVEEIRQHPFFKNDQWHWDNIRETAAPVVPELSSDIDSSNFDDIEVETFPIPKAFVGNQLPFIGFTYYR 417
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382     ||397       407       417
                                                                                                                                                                                                                                                                                                                                                                                                       388|                       
                                                                                                                                                                                                                                                                                                                                                                                                        394                       


Chain D from PDB  Type:PROTEIN  Length:383
                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh.....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeeee....eeeeeee.....eeeeeeeehhhhhhh....hhhhhhhhhhhh.......eeeeee...eeeeee......hhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee.....ee.........hhhhhhhh.....eehhhhhhhhhhhhhhhhhh.......hhhhhhhhh.hhhhhh........hhhhhhhhhhhh.hhhhh.....hhhhhhhhhhh.......hhhhh..................................hhhhh...ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u7q D  27 QRKLEALIRDPRSPINVESLLDGLNSLVLDLDFPALRKNKNIDNFLNRYEKIVKKIRGLQMKAEDYDVVKVIGRGAFGEVQLVRHKASQKVYAMKLLSKFEMIKRSDSAFFWEERDIMAFANSPWVVQLFYAFQDDRYLYMVMEYMPGGDLVNLMSNYDVPEKWAKFYTAEVVLALDAIHSMGLIHRDVKPDNMLLDKHGHLKLADFGTCMKMDETGMVTAVGTPDYISPEVLKSQGGDGFYGRECDWWSVGVFLYEMLVGDTPFYADSLVGTYSKIMDHKNSLCFPEDAEISKHAKNLICAFLTDREVRLGRNGVEEIRQHPFFKNDQWHWDNIRETAAPVVPELSSDIDSSNFDDIEVETFPIPKAFVGNQLPFIGFTYYR 417
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       249       259       269       279       289       299       309       319       329       339       349       359       369       379       394       404       414   
                                                                                                                                                                                                                                                    245|                                                                                                                                        388|                       
                                                                                                                                                                                                                                                     249                                                                                                                                         394
   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 5U7Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5U7Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5U7Q)

(-) Gene Ontology  (51, 51)

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  5u7q
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 Related Entries

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

UniProtKB/Swiss-Prot
        ROCK2_HUMAN | O75116: 4l6q 4wot 5u7r

(-) Related Entries Specified in the PDB File

5u7r