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(-) Description

Title :  HUMAN DCK C4S-S74E MUTANT IN COMPLEX WITH UDP AND THE F2.2.1 INHIBITOR (2-[({2-[3-(2-FLUOROETHOXY)-4-METHOXYPHENYL]-5-METHYL-1,3-THIAZOL-4-YL}METHYL)SULFANYL]PYRIMIDINE-4,6-DIAMINE)
 
Authors :  J. Nomme, A. Lavie
Date :  12 Mar 13  (Deposition) - 18 Sep 13  (Release) - 27 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.89
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Phosphoryl Transfer, Phosphorylation, Kinase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Murphy, A. L. Armijo, J. Nomme, C. H. Lee, Q. A. Smith, Z. Li, D. O. Campbell, H. I. Liao, D. A. Nathanson, W. R. Austin, J. T. Lee, R. Darvish, L. Wei, J. Wang, Y. Su, R. Damoiseaux, S. Sadeghi, M. E. Phelps, H. R. Herschman, J. Czernin, A. N. Alexandrova, M. E. Jung A. Lavie, C. G. Radu
Development Of New Deoxycytidine Kinase Inhibitors And Noninvasive In Vivo Evaluation Using Positron Emission Tomography.
J. Med. Chem. V. 56 6696 2013
PubMed-ID: 23947754  |  Reference-DOI: 10.1021/JM400457Y

(-) 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: 562
    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
11NO4Ligand/Ion2-[({2-[3-(2-FLUOROETHOXY)-4-METHOXYPHENYL]-5-METHYL-1,3-THIAZOL-4-YL}METHYL)SULFANYL]PYRIMIDINE-4,6-DIAMINE
2UDP2Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:31 , ALA A:32 , GLY A:33 , LYS A:34 , SER A:35 , THR A:36 , ARG A:188 , LEU A:191 , ARG A:192 , ASP A:241 , PHE A:242 , LYS A:243 , HOH A:514 , HOH A:570BINDING SITE FOR RESIDUE UDP A 401
2AC2SOFTWAREGLU A:53 , VAL A:55 , PRO A:89 , GLN A:97 , ARG A:128 , ASP A:133 , PHE A:137 , ASN A:140 , LEU A:141 , SER A:144 , TYR A:204 , 1NO A:403BINDING SITE FOR RESIDUE 1NO A 402
3AC3SOFTWARELEU A:82 , TYR A:86 , ARG A:194 , GLU A:196 , GLU A:197 , GLY A:199 , ILE A:200 , PRO A:201 , TYR A:204 , 1NO A:402BINDING SITE FOR RESIDUE 1NO A 403
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:528 , HOH B:571BINDING SITE FOR RESIDUE UDP B 401
5AC5SOFTWAREGLU B:53 , VAL B:55 , LEU B:82 , TYR B:86 , PHE B:96 , GLN B:97 , ARG B:128 , ASP B:133 , PHE B:137 , SER B:144 , SER B:146 , TYR B:204 , 1NO B:403BINDING SITE FOR RESIDUE 1NO B 402
6AC6SOFTWARESER B:59 , TYR B:86 , GLU B:196 , GLU B:197 , ILE B:200 , PRO B:201 , 1NO B:402BINDING SITE FOR RESIDUE 1NO B 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JLK)

(-) 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:229
                                                                                                                                                                                                                                                                     
               SCOP domains d4jlka_ A: Deoxycytidine kinase                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhh....eeee.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhh..eeeeee.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.......hhhhhh..eeeee........hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jlk A  20 RIKKISIEGNIAAGKSTFVNILKQLSEDWEVVPEPVARWSNLTMEQKNGGNVLQMMYEKPERWSFTFQTYACLSRIRAQLASLNGKLKDAEKPVLFFERSVYSDRYIFASNLYESESMNETEWTIYQDWHDWMNNGQSLELDGIIYLQATPETCLHRIYLRGRNEEQGIPLEYLEKLHYKHESWLLHRTLKTNFDYLQEVPILTLDVNEDFKDKYESLVEKVKEFLSTL 260
                                    29        39        49        59||      79        89        99       109       119       129       139       149       159    || 171       181       191       201       211       221       231       241       251         
                                                                   60|                                                                                          164|                                                                                             
                                                                    71                                                                                           167                                                                                             


Chain B from PDB  Type:PROTEIN  Length:233
                                                                                                                                                                                                                                                                         
               SCOP domains d4jlkb_ B: Deoxycytidine kinase                                                                                                                                                                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.....hhhhhhhhhhh....eeee.hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.......eeeeee.hhhhhhhhhhhh.hhhhh..hhhhhhhhhhhhhhhhh.......hhhhhhh.eeeee........hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jlk B  19 TRIKKISIEGNIAAGKSTFVNILKQLSEDWEVVPEPVARWSNVLTMEQKNGGNVLQMMYEKPERWSFTFQTYACLSRIRAQLASLNGKLKDAEKPVLFFERSVYSDRYIFASNLYESESMNETEWTIYQDWHDWMNNQFGQSLELDGIIYLQATPETCLHRIYLRGRNEEQGIPLEYLEKLHYKHESWLLHRTLKTNFDYLQEVPILTLDVNEDFKDKYESLVEKVKEFLSTL 260
                                    28        38        48        58  ||    77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257   
                                                                     61|                                                                                                                                                                                             
                                                                      71
   Legend:   → Mismatch (orange background)
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  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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  DCK_HUMAN | P27707
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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 4jlm 4jln 4kcg 4l5b 4q18 4q19 4q1a 4q1b 4q1c 4q1d 4q1e 4q1f

(-) Related Entries Specified in the PDB File

4jlj THE SAME PROTEIN COMPLEXED WITH THE F2.1.1 INHIBITOR
4jlm
4jln