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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, R. J. Skene
Date :  12 Dec 16  (Deposition) - 29 Mar 17  (Release) - 05 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.33
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (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: UNIDENTIFIED BACULOVIRUS
    Expression System Taxid: 10469
    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  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
181G4Ligand/Ion(1S,4S)-4-(4-FLUOROPHENYL)-4-HYDROXY-6'-(5-METHYL-1H-PYRAZOL-4-YL)-1'H-SPIRO[CYCLOHEXANE-1,2'-THIENO[3,2-D]PYRIMIDIN]-4'(3'H)-ONE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
181G2Ligand/Ion(1S,4S)-4-(4-FLUOROPHENYL)-4-HYDROXY-6'-(5-METHYL-1H-PYRAZOL-4-YL)-1'H-SPIRO[CYCLOHEXANE-1,2'-THIENO[3,2-D]PYRIMIDIN]-4'(3'H)-ONE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
181G2Ligand/Ion(1S,4S)-4-(4-FLUOROPHENYL)-4-HYDROXY-6'-(5-METHYL-1H-PYRAZOL-4-YL)-1'H-SPIRO[CYCLOHEXANE-1,2'-THIENO[3,2-D]PYRIMIDIN]-4'(3'H)-ONE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:98 , ALA A:119 , LYS A:121 , GLU A:170 , MET A:172 , ASP A:218 , LEU A:221 , ASP A:232 , PHE A:384binding site for residue 81G A 500
2AC2SOFTWAREILE B:98 , GLY B:101 , ALA B:119 , LYS B:121 , GLU B:170 , MET B:172 , ASP B:218 , LEU B:221 , ASP B:232 , PHE B:384binding site for residue 81G B 500
3AC3SOFTWAREALA C:119 , LYS C:121 , GLU C:140 , MET C:169 , GLU C:170 , TYR C:171 , MET C:172 , ASP C:218 , LEU C:221 , ALA C:231 , ASP C:232 , PHE C:384binding site for residue 81G C 500
4AC4SOFTWAREILE D:98 , ALA D:119 , LYS D:121 , GLU D:140 , MET D:169 , GLU D:170 , TYR D:171 , MET D:172 , ASP D:218 , LEU D:221 , PHE D:384binding site for residue 81G D 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5U7R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5U7R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5U7R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5U7R)

(-) Exons   (0, 0)

(no "Exon" information available for 5U7R)

(-) 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:387
                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh.....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeeee..eeeeeeee.....eeeeeeeehhhhhhh....hhhhhhhhhhhh.......eeeeee...eeeeee......hhhhhh.....hhhhhhhhhhhhhhhhhhhhh..ee....hhh.eee.....eee......ee...................hhhhhhh........hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh........hhhhhhhhhhhh...........hhhhhhhhhhh.......hhhhh.................................hhhhh...ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u7r A  25 SRQRKLEALIRDPRSPINVESLLDGLNSLVLDLDFPALRKNKNIDNFLNRYEKIVKKIRGLQMKAEDYDVVKVIGRGAFGEVQLVRHKASQKVYAMKLLSKFEMIKRSDSAFFWEERDIMAFANSPWVVQLFYAFQDDRYLYMVMEYMPGGDLVNLMSNYDVPEKWAKFYTAEVVLALDAIHSMGLIHRDVKPDNMLLDKHGHLKLADFGTCMKMDETGMVHCDTAVGTPDYISPEVLKSQGGDGYYGRECDWWSVGVFLYEMLVGDTPFYADSLVGTYSKIMDHKNSLCFPEDAEISKHAKNLICAFLTDREVRLGRNGVEEIRQHPFFKNDQWHWDNIRETAAPVVPELSSDIDSSNFDDIEETFPIPKAFVGNQLPFIGFTYYR 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   ||  400       410       
                                                                                                                                                                                                                                                                                                                                                                                                     388|                      
                                                                                                                                                                                                                                                                                                                                                                                                      395                      


Chain B from PDB  Type:PROTEIN  Length:387
                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh.....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeeeee..eeeeeeee.....eeeeeeeehhhhhhh....hhhhhhhhhhhh.......eeeeee...eeeeeee.....hhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee......eee.....hhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh........hhhhhhhhhhhh...........hhhhhhhhhhh.......hhhhh.................................hhhhh...ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u7r B  25 SRQRKLEALIRDPRSPINVESLLDGLNSLVLDLDFPALRKNKNIDNFLNRYEKIVKKIRGLQMKAEDYDVVKVIGRGAFGEVQLVRHKASQKVYAMKLLSKFEMIKRSDSAFFWEERDIMAFANSPWVVQLFYAFQDDRYLYMVMEYMPGGDLVNLMSNYDVPEKWAKFYTAEVVLALDAIHSMGLIHRDVKPDNMLLDKHGHLKLADFGTCMKMDETGMVHCDTAVGTPDYISPEVLKSQGGDGYYGRECDWWSVGVFLYEMLVGDTPFYADSLVGTYSKIMDHKNSLCFPEDAEISKHAKNLICAFLTDREVRLGRNGVEEIRQHPFFKNDQWHWDNIRETAAPVVPELSSDIDSSNFDDIEETFPIPKAFVGNQLPFIGFTYYR 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   ||  400       410       
                                                                                                                                                                                                                                                                                                                                                                                                     388|                      
                                                                                                                                                                                                                                                                                                                                                                                                      395                      


Chain C from PDB  Type:PROTEIN  Length:387
                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhh.eeeeeeeeee..eeeeeeee.....eeeeeeeehhhhhhh....hhhhhhhhhhhh.......eeeeee...eeeeee.....eehhhhhh....hhhhhhhhhhhhhhhhhhhhh..ee........eee.....eee.hhhhhee...................hhhhhhhh.......hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhh........hhhhhhhhhhhh.hhhhh.....hhhhhhhhhhh.......hhhhh.................................hhhhh...ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u7r C  25 SRQRKLEALIRDPRSPINVESLLDGLNSLVLDLDFPALRKNKNIDNFLNRYEKIVKKIRGLQMKAEDYDVVKVIGRGAFGEVQLVRHKASQKVYAMKLLSKFEMIKRSDSAFFWEERDIMAFANSPWVVQLFYAFQDDRYLYMVMEYMPGGDLVNLMSNYDVPEKWAKFYTAEVVLALDAIHSMGLIHRDVKPDNMLLDKHGHLKLADFGTCMKMDETGMVHCDTAVGTPDYISPEVLKSQGGDGYYGRECDWWSVGVFLYEMLVGDTPFYADSLVGTYSKIMDHKNSLCFPEDAEISKHAKNLICAFLTDREVRLGRNGVEEIRQHPFFKNDQWHWDNIRETAAPVVPELSSDIDSSNFDDIEETFPIPKAFVGNQLPFIGFTYYR 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   ||  400       410       
                                                                                                                                                                                                                                                                                                                                                                                                     388|                      
                                                                                                                                                                                                                                                                                                                                                                                                      395                      


Chain D from PDB  Type:PROTEIN  Length:382
                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhh.eeeeeeeee....eeeeeee.....eeeeeeeehhhhhh.....hhhhhhhhhhhh.......eeeeee...eeeeee......hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..ee........eee.....eee.hhhhhee.................hhhhhhh........hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.....hhhhhhhhhhhh..........hhhhhhhhhhhh.......hhhhh.................................hhhhh...ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u7r D  25 SRQRKLEALIRDPRSPINVESLLDGLNSLVLDLDFPALRKNKNIDNFLNRYEKIVKKIRGLQMKAEDYDVVKVIGRGAFGEVQLVRHKASQKVYAMKLLSKFEMIKRSDSAFFWEERDIMAFANSPWVVQLFYAFQDDRYLYMVMEYMPGGDLVNLMSNYDVPEKWAKFYTAEVVLALDAIHSMGLIHRDVKPDNMLLDKHGHLKLADFGTCMKMDETGMVHCDTGTPDYISPEVLKSQGGDGYYGRECDWWSVGVFLYEMLVGDTPFYADSLVGTYSKIMDHKNSLCFAEISKHAKNLICAFLTDREVRLGRNGVEEIRQHPFFKNDQWHWDNIRETAAPVVPELSSDIDSSNFDDIEETFPIPKAFVGNQLPFIGFTYYR 417
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244    || 256       266       276       286       296       306       319       329       339       349       359       369       379       395       405       415  
                                                                                                                                                                                                                                                          249|                                                            315|                                                                  388|                      
                                                                                                                                                                                                                                                           252                                                             319                                                                   395
   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 5U7R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5U7R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5U7R)

(-) Gene Ontology  (51, 51)

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  5u7r
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 Related Entries

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

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        ROCK2_HUMAN | O75116: 4l6q 4wot 5u7q

(-) Related Entries Specified in the PDB File

5u7q