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(-) Description

Title :  HUMAN DCK C4S-S74E MUTANT IN COMPLEX WITH UDP AND THE INHIBITOR 4 [1-[5-(4-{[(2,6-DIAMINOPYRIMIDIN-4-YL)SULFANYL]METHYL}-5-PROPYL-1,3-THIAZOL-2-YL)-2-METHOXYPHENOXY]-2-METHYLPROPAN-2-OL]
 
Authors :  J. Nomme, A. Lavie
Date :  03 Apr 14  (Deposition) - 05 Nov 14  (Release) - 17 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Phosphoryl Transfer, Phosphorylation, Deoxycytidine, Transferase, Inhibitor Complex, Kinase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Nomme, Z. Li, R. M. Gipson, J. Wang, A. L. Armijo, T. Le, S. Poddar, T. Smith, B. D. Santarsiero, H. A. Nguyen, J. Czernin, A. N. Alexandrova, M. E. Jung, C. G. Radu, A. Lavie
Structure-Guided Development Of Deoxycytidine Kinase Inhibitors With Nanomolar Affinity And Improved Metabolic Stability.
J. Med. Chem. V. 57 9480 2014
PubMed-ID: 25341194  |  Reference-DOI: 10.1021/JM501124J

(-) Compounds

Molecule 1 - DEOXYCYTIDINE KINASE
    Chains: A, B
    EC Number: 2.7.1.74
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET14B
    Expression System Strain: BL21 DE3 C41
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DCK
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DCK

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
12XJ4Ligand/Ion1-(5-(4-(((2,6-DIAMINOPYRIMIDIN-4-YL)THIO)METHYL)-5-PROPYLTHIAZOL-2-YL)-2-METHOXYPHENOXY)-2-METHYLPROPAN-2-OL
2UDP2Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:53 , VAL A:55 , LEU A:82 , TYR A:86 , PRO A:89 , PHE A:96 , GLN A:97 , ARG A:128 , ASP A:133 , PHE A:137 , SER A:144 , SER A:146 , TYR A:204 , 2XJ A:302 , HOH A:415 , HOH A:424BINDING SITE FOR RESIDUE 2XJ A 301
2AC2SOFTWAREILE A:30 , SER A:59 , TYR A:86 , GLU A:196 , GLU A:197 , GLY A:199 , ILE A:200 , TYR A:204 , 2XJ A:301BINDING SITE FOR RESIDUE 2XJ A 302
3AC3SOFTWAREALA A:31 , ALA A:32 , GLY A:33 , LYS A:34 , SER A:35 , THR A:36 , ARG A:188 , ARG A:192 , ASP A:241 , PHE A:242 , LYS A:243 , HOH A:429BINDING SITE FOR RESIDUE UDP A 303
4AC4SOFTWAREALA B:31 , ALA B:32 , GLY B:33 , LYS B:34 , SER B:35 , THR B:36 , ARG B:188 , ARG B:192 , ASP B:241 , PHE B:242 , LYS B:243 , HOH B:531BINDING SITE FOR RESIDUE UDP B 401
5AC5SOFTWAREGLU B:53 , VAL B:55 , LEU B:82 , MET B:85 , TYR B:86 , PRO B:89 , PHE B:96 , GLN B:97 , ARG B:128 , ASP B:133 , PHE B:137 , ASN B:140 , LEU B:141 , SER B:144 , TYR B:204 , LYS B:207 , 2XJ B:403BINDING SITE FOR RESIDUE 2XJ B 402
6AC6SOFTWAREILE B:30 , SER B:59 , TYR B:86 , ARG B:194 , GLU B:196 , GLU B:197 , GLY B:199 , ILE B:200 , PRO B:201 , TYR B:204 , 2XJ B:402BINDING SITE FOR RESIDUE 2XJ B 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Q18)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4Q18)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Q18)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Q18)

(-) Exons   (0, 0)

(no "Exon" information available for 4Q18)

(-) 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:230
                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhh..eeee.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.......hhhhhh..eeeee........hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q18 A  21 IKKISIEGNIAAGKSTFVNILKQLSEDWEVVPEPVARWSNLTMEQKNGGNVLQMMYEKPERWSFTFQTYACLSRIRAQLASLNGKLKDAEKPVLFFERSVYSDRYIFASNLYESESMNETEWTIYQDWHDWMNNQFGQSLELDGIIYLQATPETCLHRIYLRGRNEEQGIPLEYLEKLHYKHESWLLHRTLKTNFDYLQEVPILTLDVNEDFKDKYESLVEKVKEFLSTL 260
                                    30        40        50        60|       80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260
                                                                  60|                                                                                                                                                                                             
                                                                   71                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:231
                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.....hhhhhhhhhhhhh..eeee.hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.........eeeeee.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.......hhhhhhh.eeeee........hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q18 B  19 TRIKKISIEGNIAAGKSTFVNILKQLSEDWEVVPEPVARWSLTMEQKNGGNVLQMMYEKPERWSFTFQTYACLSRIRAQLASLNGKLKDAEKPVLFFERSVYSDRYIFASNLYESESMNETEWTIYQDWHDWMNNQFGQSLELDGIIYLQATPETCLHRIYLRGRNEEQGIPLEYLEKLHYKHESWLLHRTLKTNFDYLQEVPILTLDVNEDFKDKYESLVEKVKEFLSTL 260
                                    28        38        48        58||      79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259 
                                                                   59|                                                                                                                                                                                             
                                                                    71
   Legend:   → Mismatch (orange background)
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    → 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 4Q18)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Q18)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Q18)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  4q18
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  DCK_HUMAN | P27707
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  2.7.1.74
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 Related Entries

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

UniProtKB/Swiss-Prot
        DCK_HUMAN | P27707: 1p5z 1p60 1p61 1p62 2a2z 2a30 2a7q 2no0 2no1 2no6 2no7 2no9 2noa 2qrn 2qro 2zi3 2zi4 2zi5 2zi6 2zi7 2zi9 2zia 3hp1 3ipx 3ipy 3kfx 3mjr 3qej 3qen 3qeo 4jlj 4jlk 4jlm 4jln 4kcg 4l5b 4q19 4q1a 4q1b 4q1c 4q1d 4q1e 4q1f

(-) Related Entries Specified in the PDB File

4q19 4q1a 4q1b 4q1c 4q1d 4q1e 4q1f