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(-) Description

Title :  HUMAN DCK C4S-S74E MUTANT IN COMPLEX WITH UDP AND THE F2.4.1 INHIBITOR (2-[({2-[3-(2-FLUOROETHOXY)-4-METHOXYPHENYL]-5-PROPYL-1,3-THIAZOL-4-YL}METHYL)SULFANYL]PYRIMIDINE-4,6-DIAMINE)
 
Authors :  J. Nomme, A. Lavie
Date :  12 Mar 13  (Deposition) - 22 Jan 14  (Release) - 19 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Phosphoryl Transfer, Phosphorylation, Kinase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Nomme, J. M. Murphy, Y. Su, N. D. Sansone, A. L. Armijo, S. T. Olson, C. Radu, A. Lavie
Structural Characterization Of New Deoxycytidine Kinase Inhibitors Rationalizes The Affinity-Determining Moieties O The Molecules.
Acta Crystallogr. , Sect. D V. 70 68 2014
PubMed-ID: 24419380  |  Reference-DOI: 10.1107/S1399004713025030

(-) 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, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
118V2Ligand/Ion2-[({2-[3-(2-FLUOROETHOXY)-4-METHOXYPHENYL]-5-PROPYL-1,3-THIAZOL-4-YL}METHYL)SULFANYL]PYRIMIDINE-4,6-DIAMINE
2UDP2Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:53 , VAL A:55 , LEU A:82 , TYR A:86 , GLN A:97 , ARG A:128 , ASP A:133 , PHE A:137 , LEU A:141 , SER A:146 , TYR A:204BINDING SITE FOR RESIDUE 18V A 301
2AC2SOFTWAREALA A:31 , ALA A:32 , GLY A:33 , LYS A:34 , SER A:35 , THR A:36 , GLU A:127 , ARG A:188 , ARG A:192 , ASP A:241 , PHE A:242 , LYS A:243 , HOH A:409 , HOH A:436BINDING SITE FOR RESIDUE UDP A 302
3AC3SOFTWAREILE B:30 , GLU B:53 , TYR B:86 , PHE B:96 , GLN B:97 , ARG B:128 , ASP B:133 , PHE B:137 , LEU B:141 , SER B:144 , SER B:146 , TYR B:204BINDING SITE FOR RESIDUE 18V B 301
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:442BINDING SITE FOR RESIDUE UDP B 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:117 -Asp A:118
2Thr B:19 -Arg B:20

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JLN)

(-) 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:232
                                                                                                                                                                                                                                                                        
               SCOP domains d4jlna_ A: Deoxycytidine kinase                                                                                                                                                                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhh....eeee.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh........hhhhhh.eeeee........hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jln A  20 RIKKISIEGNIAAGKSTFVNILKQLSEDWEVVPEPVARWSNELTMEQKNGGNVLQMMYEKPERWSFTFQTYACLSRIRAQLASLNGKLKDAEKPVLFFERSVYSDRYIFASNLYESESMNETEWTIYQDWHDWMNNQFGQSLELDGIIYLQATPETCLHRIYLRGRNEEQGIPLEYLEKLHYKHESWLLHRTLKTNFDYLQEVPILTLDVNEDFKDKYESLVEKVKEFLSTL 260
                                    29        39        49        59||      78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258  
                                                                   60|                                                                                                                                                                                              
                                                                    70                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:234
                                                                                                                                                                                                                                                                          
               SCOP domains d4jlnb_ B: Deoxycytidine kinase                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee.....hhhhhhhhhhh....eeee.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.........eeeeee.hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.......hhhhhh..eeeee........hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4jln B  18 GTRIKKISIEGNIAAGKSTFVNILKQLSEDWEVVPEPVARWSNELTMEQKNGGNVLQMMYEKPERWSFTFQTYACLSRIRAQLASLNGKLKDAEKPVLFFERSVYSDRYIFASNLYESESMNETEWTIYQDWHDWMNNQFGQSLELDGIIYLQATPETCLHRIYLRGRNEEQGIPLEYLEKLHYKHESWLLHRTLKTNFDYLQEVPILTLDVNEDFKDKYESLVEKVKEFLSTL 260
                                    27        37        47        57  ||    76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256    
                                                                     60|                                                                                                                                                                                              
                                                                      70
   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  (1, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Lys A:117 - Asp A:118   [ RasMol ]  
    Thr B:19 - Arg B:20   [ RasMol ]  
 

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  4jln
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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 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
4jlk THE SAME PROTEIN COMPLEXED WITH THE F2.2.1 INHIBITOR
4jlm THE SAME PROTEIN COMPLEXED WITH THE F2.3.1 INHIBITOR