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(-) Description

Title :  HUMAN CHOLINE KINASE A1 IN COMPLEX WITH COMPOUND 14
 
Authors :  B. Rubio-Ruiz, A. Figuerola-Conchas, A. Entrena-Guadix, R. Hurtado- A. Conejo-Garcia
Date :  21 Nov 13  (Deposition) - 15 Jan 14  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transferase, Drug Target, Cancer (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. Rubio-Ruiz, A. Figuerola-Conchas, J. Ramos-Torrecillas, F. Capitan-Canadas, P. Rios-Marco, M. P. Carrasco, M. A. Gallo, A. Espinosa, C. Marco, C. Concepcion, A. Entrena-Guadix, R. Hurtado-Guerrero, A. Conejo-Garcia
Discovery Of A New Binding Site On Human Choline Kinase A1: Design, Synthesis, Crystallographic Studies And Biological Evaluation Of Asymmetrical Bispyridinium Derivatives
J. Med. Chem. V. 57 507 2014
PubMed-ID: 24387243  |  Reference-DOI: 10.1021/JM401665X

(-) Compounds

Molecule 1 - CHOLINE KINASE ALPHA
    ChainsA
    EC Number2.7.1.32, 2.7.1.82
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMALC2X
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantSTAR
    Expression System Vector TypePLASMID
    FragmentRESIDUES 75-457
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCHOLINE KINASE A1, CK, CHETK-ALPHA, ETHANOLAMINE KINASE, EK

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1G8S1Ligand/Ion4-[(4-CHLOROPHENYL)(METHYL)AMINO]-1-{4-[4-(4-{[4-(DIMETHYLAMINO)PYRIDINIUM-1-YL]METHYL}PHENYL)BUTYL]BENZYL}PYRIDINIUM
2G8V1Ligand/Ion1-BENZYL-4-(DIMETHYLAMINO)PYRIDINIUM
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1G8S2Ligand/Ion4-[(4-CHLOROPHENYL)(METHYL)AMINO]-1-{4-[4-(4-{[4-(DIMETHYLAMINO)PYRIDINIUM-1-YL]METHYL}PHENYL)BUTYL]BENZYL}PYRIDINIUM
2G8V2Ligand/Ion1-BENZYL-4-(DIMETHYLAMINO)PYRIDINIUM

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:252 , TYR A:256 , ASN A:305 , ASP A:306 , GLN A:308 , TYR A:333 , TYR A:354 , LEU A:419 , TRP A:420 , TRP A:423 , ILE A:433 , TYR A:440BINDING SITE FOR RESIDUE G8S A1458
2AC2SOFTWAREARG A:270 , ARG A:318 , GLN A:324 , ALA A:428 , SER A:431 , PHE A:435BINDING SITE FOR RESIDUE G8V A1459

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4CG8)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Tyr A:359 -Pro A:360

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_054863S220GCHKA_HUMANPolymorphism17853641AS220G
2UniProtVAR_054864L422QCHKA_HUMANPolymorphism17853642AL422Q

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_054863S220GCHKA_HUMANPolymorphism17853641AS220G
2UniProtVAR_054864L422QCHKA_HUMANPolymorphism17853642AL422Q

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4CG8)

(-) Exons   (11, 11)

Asymmetric Unit (11, 11)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002656891bENSE00002184538chr11:67888671-67888295377CHKA_HUMAN1-1171171A:80-11738
1.2ENST000002656892ENSE00001201105chr11:67864597-67864486112CHKA_HUMAN117-154381A:117-14933
1.5cENST000002656895cENSE00001166770chr11:67848924-6784887154CHKA_HUMAN155-172180--
1.6ENST000002656896ENSE00001267789chr11:67842297-67842184114CHKA_HUMAN173-210381A:175-21036
1.7bENST000002656897bENSE00000736988chr11:67838324-67838191134CHKA_HUMAN211-255451A:211-25545
1.8bENST000002656898bENSE00000736987chr11:67837760-67837656105CHKA_HUMAN255-290361A:255-29036
1.9ENST000002656899ENSE00000736986chr11:67836404-6783634659CHKA_HUMAN290-310211A:290-31021
1.10cENST0000026568910cENSE00000736983chr11:67833983-6783389688CHKA_HUMAN310-339301A:310-33930
1.11ENST0000026568911ENSE00000736982chr11:67833361-67833253109CHKA_HUMAN339-375371A:339-37537
1.12ENST0000026568912ENSE00000736981chr11:67832098-67831992107CHKA_HUMAN376-411361A:376-41136
1.13ENST0000026568913ENSE00001117236chr11:67829501-6782942082CHKA_HUMAN411-438281A:411-43828
1.15dENST0000026568915dENSE00001166765chr11:67821514-678203261189CHKA_HUMAN439-457191A:439-45719

(-) 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:353
 aligned with CHKA_HUMAN | P35790 from UniProtKB/Swiss-Prot  Length:457

    Alignment length:378
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449        
           CHKA_HUMAN    80 DEQPEPRTRRRAYLWCKEFLPGAWRGLREDEFHISVIRGGLSNMLFQCSLPDTTATLGDEPRKVLLRLYGAILQMRSCNKEGSEQAQKENEFQGAEAMVLESVMFAILAERSLGPKLYGIFPQGRLEQFIPSRRLDTEELSLPDISAEIAEKMATFHGMKMPFNKEPKWLFGTMEKYLKEVLRIKFTEESRIKKLHKLLSYNLPLELENLRSLLESTPSPVVFCHNDCQEGNILLLEGRENSEKQKLMLIDFEYSSYNYRGFDIGNHFCEWMYDYSYEKYPFFRANIRKYPTKKQQLHFISSYLPAFQNDFENLSTEEKSIIKEEMLLEVNRFALASHFLWGLWSIVQAKISSIEFGYMDYAQARFDAYFHQKRKLGV 457
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhh..hhhhheeeeee.....eeeeee.............eeeeee..-------------------------hhhhhhhhhhhhhhhh.....eeeee..eeeee...eee.hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhhhhh....eeee....hhh.eeee..........eee......eeeehhhhhhhhhhhh.ee.........ee.hhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------G---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Q----------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1b  PDB: A:80-117 [INCOMPLETE] -------------------------------------Exon 1.5c  PDB: - Exon 1.6  PDB: A:175-210 [INCOMPLETE] Exon 1.7b  PDB: A:211-255 UniProt: 211-255   ------------------------------------------------------Exon 1.10c  PDB: A:310-339    ------------------------------------Exon 1.12  PDB: A:376-411           ---------------------------Exon 1.15d          Transcript 1 (1)
           Transcript 1 (2) -------------------------------------Exon 1.2  PDB: A:117-149 [INCOMPLETE] ----------------------------------------------------------------------------------------------------Exon 1.8b  PDB: A:255-290           ------------------------------------------------Exon 1.11  PDB: A:339-375            -----------------------------------Exon 1.13  PDB: A:411-438   ------------------- Transcript 1 (2)
           Transcript 1 (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9             --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (3)
                 4cg8 A  80 DEQPEPRTRRRAYLWCKEFLPGAWRGLREDEFHISVIRGGLSNMLFQCSLPDTTATLGDEPRKVLLRLYG-------------------------EAMVLESVMFAILAERSLGPKLYGIFPQGRLEQFIPSRRLDTEELSLPDISAEIAEKMATFHGMKMPFNKEPKWLFGTMEKYLKEVLRIKFTEESRIKKLHKLLSYNLPLELENLRSLLESTPSPVVFCHNDCQEGNILLLEGRENSEKQKLMLIDFEYSSYNYRGFDIGNHFCEWMYDYSYEKYPFFRANIRKYPTKKQQLHFISSYLPAFQNDFENLSTEEKSIIKEEMLLEVNRFALASHFLWGLWSIVQAKISSIEFGYMDYAQARFDAYFHQKRKLGV 457
                                    89        99       109       119       129       139       149         -         -     | 179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449        
                                                                                               149                       175                                                                                                                                                                                                                                                                                          

   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 4CG8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4CG8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CG8)

(-) Gene Ontology  (25, 25)

Asymmetric Unit(hide GO term definitions)
Chain A   (CHKA_HUMAN | P35790)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0033265    choline binding    Interacting selectively and non-covalently with choline, the amine 2-hydroxy-N,N,N-trimethylethanaminium.
    GO:0004103    choline kinase activity    Catalysis of the reaction: ATP + choline = ADP + choline phosphate + 2 H(+).
    GO:0004104    cholinesterase activity    Catalysis of the reaction: an acylcholine + H2O = choline + a carboxylic acid anion.
    GO:0008144    drug binding    Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
    GO:0004305    ethanolamine kinase activity    Catalysis of the reaction: ATP + ethanolamine = ADP + 2 H(+) + phosphoethanolamine.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006657    CDP-choline pathway    The phosphatidylcholine biosynthetic process that begins with the phosphorylation of choline and ends with the combination of CDP-choline with diacylglycerol to form phosphatidylcholine.
    GO:0019695    choline metabolic process    The chemical reactions and pathways involving choline (2-hydroxyethyltrimethylammonium), an amino alcohol that occurs widely in living organisms as a constituent of certain types of phospholipids and in the neurotransmitter acetylcholine.
    GO:0006580    ethanolamine metabolic process    The chemical reactions and pathways involving ethanolamine (2-aminoethanol), an important water-soluble base of phospholipid (phosphatidylethanolamine).
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0006869    lipid transport    The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0006656    phosphatidylcholine biosynthetic process    The chemical reactions and pathways resulting in the formation of phosphatidylcholines, any of a class of glycerophospholipids in which the phosphatidyl group is esterified to the hydroxyl group of choline.
    GO:0006646    phosphatidylethanolamine biosynthetic process    The chemical reactions and pathways resulting in the formation of phosphatidylethanolamine, any of a class of glycerophospholipids in which a phosphatidyl group is esterified to the hydroxyl group of ethanolamine.
    GO:0008654    phospholipid biosynthetic process    The chemical reactions and pathways resulting in the formation of phospholipids, any lipid containing phosphoric acid as a mono- or diester.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:1904681    response to 3-methylcholanthrene    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a 3-methylcholanthrene stimulus.
    GO:0009636    response to toxic substance    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CHKA_HUMAN | P357902cko 2ckp 2ckq 2i7q 3f2r 3g15 3zm9 4br3 4cg9 4cga 4da5 5afv 5eqe 5eqp 5eqy 5ftg 5fut

(-) Related Entries Specified in the PDB File

4cg9 HUMAN CHOLINE KINASE A1 IN COMPLEX WITH COMPOUND 12
4cga HUMAN CHOLINE KINASE A1 IN COMPLEX WITH COMPOUND 5