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(-) Description

Title :  CRYSTAL STRUCTURE OF CHOLINE KINASE ALPHA-1 BOUND BY 5-[(4-METHYL-1,4-DIAZEPAN-1-YL)METHYL]-2-[4-[(4-METHYL-1,4-DIAZEPAN-1-YL) METHYL]PHENYL]BENZENECARBONITRILE (COMPOUND 65)
 
Authors :  T. Zhou, X. Zhu, D. C. Dalgarno
Date :  13 Nov 15  (Deposition) - 06 Jan 16  (Release) - 10 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Kinase, Inhibitor, Drug Target, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. G. Zech, A. Kohlmann, T. Zhou, F. Li, R. M. Squillace, L. E. Parillon, M. T. Greenfield, D. P. Miller, J. Qi, R. M. Thomas, Y. Wang, Y. Xu, J. J. Miret, W. C. Shakespeare, X. Zhu, D. C. Dalgarno
Novel Small Molecule Inhibitors Of Choline Kinase Identifie By Fragment-Based Drug Discovery.
J. Med. Chem. V. 59 671 2016
PubMed-ID: 26700752  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B01552

(-) Compounds

Molecule 1 - CHOLINE KINASE ALPHA
    Chains: A, B
    EC Number: 2.7.1.32, 2.7.1.82
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 75-457
    Gene: CHKA, CHK, CKI
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CK,CHETK-ALPHA,ETHANOLAMINE KINASE,EK

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
15RA2Ligand/Ion5-[(4-METHYL-1,4-DIAZEPAN-1-YL)METHYL]-2-[4-[(4-METHYL-1,4-DIAZEPAN-1-YL)METHYL]PHENYL]BENZENECARBONITRILE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:306 , GLN A:308 , TYR A:333 , GLU A:349 , TYR A:354 , PHE A:361 , TRP A:420 , TRP A:423 , GLU A:434 , PHE A:435binding site for residue 5RA A 501
2AC2SOFTWAREASP B:306 , GLN B:308 , TYR B:333 , GLU B:349 , TYR B:354 , TRP B:420 , ILE B:433 , GLU B:434 , PHE B:435binding site for residue 5RA B 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:359 -Pro A:360
2Tyr B:359 -Pro B:360

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5EQY)

(-) 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:352
                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhh..hhhhheeeeee.....eeeeee.............eeeeee....hhhhhhhhhhhhhhh.....eeeee..eeeee...eee..hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.hhhhhhhhhhhhhhh....eeee....hhh.eeee..........eee......eeeehhhhhhhhhhhh.ee.........ee.hhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5eqy A  82 QPEPRTRRRAYLWCKEFLPGAWRGLREDEFHISVIRGGLSNMLFQCSLPDTTATLGDEPRKVLLRLYGAEAMVLESVMFAILAERSLGPKLYGIFPQGRLEQFIPSRRLDTEELSLPDISAEIAEKMATFHGMKMPFNKEPKWLFGTMEKYLKEVLRIKFTEESRIKKLHKLLSYNLPLELENLRSLLESTPSPVVFCHNDCQEGNILLLEGRENSEKQKLMLIDFEYSSYNYRGFDIGNHFCEWMYDYSYEKYPFFRANIRKYPTKKQQLHFISSYLPAFQNDFENLSTEEKSIIKEEMLLEVNRFALASHFLWGLWSIVQAKISSIEFGYMDYAQARFDAYFHQKRKLGV 457
                                    91       101       111       121       131       141       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455  
                                                                                              150|                                                                                                                                                                                                                                                                                          
                                                                                               175                                                                                                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:351
                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhh......eeeeee...eeeeeeee.............eeeeeeee..hhhhhhhhhhhhhh.....eeeee..eeeee...eee.hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhhhhh....eeee....hhh.eeee..........eee......eeeehhhhhhhhhhh..ee.........ee.hhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5eqy B  82 QPEPRTRRRAYLWCKEFLPGAWRGLREDEFHISVIRGGLSNMLFQCSLPDTTATLGDEPRKVLLRLYGAAMVLESVMFAILAERSLGPKLYGIFPQGRLEQFIPSRRLDTEELSLPDISAEIAEKMATFHGMKMPFNKEPKWLFGTMEKYLKEVLRIKFTEESRIKKLHKLLSYNLPLELENLRSLLESTPSPVVFCHNDCQEGNILLLEGRENSEKQKLMLIDFEYSSYNYRGFDIGNHFCEWMYDYSYEKYPFFRANIRKYPTKKQQLHFISSYLPAFQNDFENLSTEEKSIIKEEMLLEVNRFALASHFLWGLWSIVQAKISSIEFGYMDYAQARFDAYFHQKRKLGV 457
                                    91       101       111       121       131       141       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456 
                                                                                              150|                                                                                                                                                                                                                                                                                         
                                                                                               176
   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  (0, 0)

(no "SCOP Domain" information available for 5EQY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (25, 25)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        CHKA_HUMAN | P35790: 2cko 2ckp 2ckq 2i7q 3f2r 3g15 3zm9 4br3 4cg8 4cg9 4cga 4da5 5afv 5eqe 5eqp 5ftg 5fut

(-) Related Entries Specified in the PDB File

5eqe 5eqp