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(-) Description

Title :  HUMAN ADENOSINE KINASE IN COMPLEX WITH AN ACETYLINIC INHIBITOR
 
Authors :  S. W. Muchmore
Date :  28 Aug 06  (Deposition) - 02 Jan 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Protein-Ligand Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. W. Muchmore, R. A. Smith, A. O. Stewart, M. D. Cowart, A. Gomtsyan, M. A. Matulenko, H. Yu, J. M. Severin, S. S. Bhagwat, C. H. Lee, E. A. Kowaluk, M. F. Jarvis, C. L. Jakob
Crystal Structures Of Human Adenosine Kinase Inhibitor Complexes Reveal Two Distinct Binding Modes.
J. Med. Chem. V. 49 6726 2006
PubMed-ID: 17154503  |  Reference-DOI: 10.1021/JM060189A
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ADENOSINE KINASE
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneADK
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymADENYLATE KINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
189I2Ligand/Ion5-[4-(DIMETHYLAMINO)PHENYL]-6-[(6-MORPHOLIN-4-YLPYRIDIN-3-YL)ETHYNYL]PYRIMIDIN-4-AMINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
189I1Ligand/Ion5-[4-(DIMETHYLAMINO)PHENYL]-6-[(6-MORPHOLIN-4-YLPYRIDIN-3-YL)ETHYNYL]PYRIMIDIN-4-AMINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
189I1Ligand/Ion5-[4-(DIMETHYLAMINO)PHENYL]-6-[(6-MORPHOLIN-4-YLPYRIDIN-3-YL)ETHYNYL]PYRIMIDIN-4-AMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:14 , GLN A:38 , ILE A:39 , GLY A:64 , SER A:65 , ALA A:136 , LEU A:138 , PHE A:170 , THR A:173 , PHE A:201 , TYR A:206 , PHE B:205 , 89I B:500BINDING SITE FOR RESIDUE 89I A 500
2AC2SOFTWAREPHE A:205 , 89I A:500 , GLN B:38 , ILE B:39 , LEU B:40 , SER B:65 , LEU B:138 , PHE B:170 , TYR B:206 , HOH B:585BINDING SITE FOR RESIDUE 89I B 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2I6B)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gln A:79 -Pro A:80
2Ala A:327 -Ser A:328
3Gln B:79 -Pro B:80

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 6)

Asymmetric Unit (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_066640G30EADK_HUMANDisease (HMAKD)397514454A/BG13E
2UniProtVAR_066641D235AADK_HUMANDisease (HMAKD)397514453A/BD218A
3UniProtVAR_066642A318EADK_HUMANDisease (HMAKD)397514452A/BA301E

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_066640G30EADK_HUMANDisease (HMAKD)397514454AG13E
2UniProtVAR_066641D235AADK_HUMANDisease (HMAKD)397514453AD218A
3UniProtVAR_066642A318EADK_HUMANDisease (HMAKD)397514452AA301E

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_066640G30EADK_HUMANDisease (HMAKD)397514454BG13E
2UniProtVAR_066641D235AADK_HUMANDisease (HMAKD)397514453BD218A
3UniProtVAR_066642A318EADK_HUMANDisease (HMAKD)397514452BA301E

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PFKB_KINASES_2PS00584 pfkB family of carbohydrate kinases signature 2.ADK_HUMAN311-324
 
  2A:294-307
B:294-307
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PFKB_KINASES_2PS00584 pfkB family of carbohydrate kinases signature 2.ADK_HUMAN311-324
 
  1A:294-307
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PFKB_KINASES_2PS00584 pfkB family of carbohydrate kinases signature 2.ADK_HUMAN311-324
 
  1-
B:294-307

(-) Exons   (11, 22)

Asymmetric Unit (11, 22)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002866211aENSE00001248887chr10:75910987-75911101115ADK_HUMAN1-22222A:2-5
B:3-5
4
3
1.4ENST000002866214ENSE00001248864chr10:75960522-7596059675ADK_HUMAN22-47262A:5-30
B:5-30
26
26
1.5ENST000002866215ENSE00001248860chr10:75984296-7598434954ADK_HUMAN47-65192A:30-48
B:30-48
19
19
1.6ENST000002866216ENSE00001178540chr10:76074425-7607450379ADK_HUMAN65-91272A:48-74
B:48-74
27
27
1.7ENST000002866217ENSE00001024568chr10:76153899-76154071173ADK_HUMAN92-149582A:75-132
B:75-132
58
58
1.8ENST000002866218ENSE00001024570chr10:76158229-76158337109ADK_HUMAN149-185372A:132-168
B:132-168
37
37
1.9aENST000002866219aENSE00001310865chr10:76285014-76285184171ADK_HUMAN186-242572A:169-225
B:169-225
57
57
1.11ENST0000028662111ENSE00001248835chr10:76349040-7634907536ADK_HUMAN243-254122A:226-237
B:226-237
12
12
1.12ENST0000028662112ENSE00001248829chr10:76360137-76360251115ADK_HUMAN255-293392A:238-276
B:238-276
39
39
1.13ENST0000028662113ENSE00001248825chr10:76429941-7643002787ADK_HUMAN293-322302A:276-305
B:276-305
30
30
1.14aENST0000028662114aENSE00001879300chr10:76468079-76468233155ADK_HUMAN322-362412A:305-330
B:305-328
26
24

(-) 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:329
 aligned with ADK_HUMAN | P55263 from UniProtKB/Swiss-Prot  Length:362

    Alignment length:329
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338         
            ADK_HUMAN    19 QALRENILFGMGNPLLDISAVVDKDFLDKYSLKPNDQILAEDKHKELFDELVKKFKVEYHAGGSTQNSIKVAQWMIQQPHKAATFFGCIGIDKFGEILKRKAAEAHVDAHYYEQNEQPTGTCAACITGDNRSLIANLAAANCYKKEKHLDLEKNWMLVEKARVCYIAGFFLTVSPESVLKVAHHASENNRIFTLNLSAPFISQFYKESLMKVMPYVDILFGNETEAATFAREQGFETKDIKEIAKKTQALPKMNSKRQRIVIFTQGRDDTIMATESEVTAFAVLDQDQKEIIDTNGAGDAFVGGFLSQLVSDKPLTECIRAGHYAASII 347
               SCOP domains d2i6ba_ A: Adenosine kinase                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee...eeeeeee...............eee....hhhhhhhhh.....eeeeehhhhhhhhhhhhh.......eeeeeeee.hhhhhhhhhhhhh...eeeeeee....eeeeeeee.....eeeeeee.hhhh.......hhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhh....hhhhhhhhhhh..........eeeee.....eeee.....ee................hhhhhhhhhhhhhh...hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -----------E------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A----------------------------------------------------------------------------------E----------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFKB_KINASES_2----------------------- PROSITE
           Transcript 1 (1) 1.1a------------------------Exon 1.5           --------------------------Exon 1.7  PDB: A:75-132 UniProt: 92-149                   ------------------------------------Exon 1.9a  PDB: A:169-225 UniProt: 186-242               Exon 1.11   Exon 1.12  PDB: A:238-276              ----------------------------Exon 1.14a  PDB: A:305-330 Transcript 1 (1)
           Transcript 1 (2) ---Exon 1.4  PDB: A:5-30     -----------------Exon 1.6  PDB: A:48-74     ---------------------------------------------------------Exon 1.8  PDB: A:132-168             -----------------------------------------------------------------------------------------------------------Exon 1.13  PDB: A:276-305     ------------------------- Transcript 1 (2)
                 2i6b A   2 TSVRENILFGMGNPLLDISAVVDKDFLDKYSLKPNDQILAEDKHKELFDELVKKFKVEYHAGGSTQNSIKVAQWMIQQPHKAATFFGCIGIDKFGEILKRKAAEAHVDAHYYEQNEQPTGTCAACITGDNRSLIANLAAANCYKKEKHLDLEKNWMLVEKARVCYIAGFFLTVSPESVLKVAHHASENNRIFTLNLSAPFISQFYKESLMKVMPYVDILFGNETEAATFAREQGFETKDIKEIAKKTQALPKMNSKRQRIVIFTQGRDDTIMATESEVTAFAVLDQDQKEIIDTNGAGDAFVGGFLSQLVSDKPLTECIRAGHYAASII 330
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321         

Chain B from PDB  Type:PROTEIN  Length:326
 aligned with ADK_HUMAN | P55263 from UniProtKB/Swiss-Prot  Length:362

    Alignment length:326
                                    29        39        49        59        69        79        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      
            ADK_HUMAN    20 ALRENILFGMGNPLLDISAVVDKDFLDKYSLKPNDQILAEDKHKELFDELVKKFKVEYHAGGSTQNSIKVAQWMIQQPHKAATFFGCIGIDKFGEILKRKAAEAHVDAHYYEQNEQPTGTCAACITGDNRSLIANLAAANCYKKEKHLDLEKNWMLVEKARVCYIAGFFLTVSPESVLKVAHHASENNRIFTLNLSAPFISQFYKESLMKVMPYVDILFGNETEAATFAREQGFETKDIKEIAKKTQALPKMNSKRQRIVIFTQGRDDTIMATESEVTAFAVLDQDQKEIIDTNGAGDAFVGGFLSQLVSDKPLTECIRAGHYAAS 345
               SCOP domains d2i6bb_ B: Adenosine kinase                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee....eeeee...hhhhhhhhh....eeee.hhhhh............eeeeehhhhhhhhhhhhhh.......ee..eee.hhhhhhhhhhhhh...ee..eee......eeeeee....eeeee.hhhhhh........hhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhh....hhhhhhhhhhh..........eeee.......eee....eee................hhhhhhhhhhhhhh...hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------E------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A----------------------------------------------------------------------------------E--------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFKB_KINASES_2--------------------- PROSITE
           Transcript 1 (1) 1.1------------------------Exon 1.5           --------------------------Exon 1.7  PDB: B:75-132 UniProt: 92-149                   ------------------------------------Exon 1.9a  PDB: B:169-225 UniProt: 186-242               Exon 1.11   Exon 1.12  PDB: B:238-276              ----------------------------Exon 1.14a [INCOMPLETE]  Transcript 1 (1)
           Transcript 1 (2) --Exon 1.4  PDB: B:5-30     -----------------Exon 1.6  PDB: B:48-74     ---------------------------------------------------------Exon 1.8  PDB: B:132-168             -----------------------------------------------------------------------------------------------------------Exon 1.13  PDB: B:276-305     ----------------------- Transcript 1 (2)
                 2i6b B   3 SVRENILFGMGNPLLDISAVVDKDFLDKYSLKPNDQILAEDKHKELFDELVKKFKVEYHAGGSTQNSIKVAQWMIQQPHKAATFFGCIGIDKFGEILKRKAAEAHVDAHYYEQNEQPTGTCAACITGDNRSLIANLAAANCYKKEKHLDLEKNWMLVEKARVCYIAGFFLTVSPESVLKVAHHASENNRIFTLNLSAPFISQFYKESLMKVMPYVDILFGNETEAATFAREQGFETKDIKEIAKKTQALPKMNSKRQRIVIFTQGRDDTIMATESEVTAFAVLDQDQKEIIDTNGAGDAFVGGFLSQLVSDKPLTECIRAGHYAAS 328
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322      

   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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2I6B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2I6B)

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ADK_HUMAN | P55263)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004001    adenosine kinase activity    Catalysis of the reaction: ATP + adenosine = ADP + AMP.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0016773    phosphotransferase activity, alcohol group as acceptor    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
    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:0006167    AMP biosynthetic process    The chemical reactions and pathways resulting in the formation of AMP, adenosine monophosphate.
    GO:0044209    AMP salvage    The chemical reactions and pathways resulting in the formation of adenosine monophosphate (AMP) from derivatives of it (either adenine, ADP or adenosine 3',5'-bisphosphate) without de novo synthesis.
    GO:0046085    adenosine metabolic process    The chemical reactions and pathways involving adenosine, adenine riboside, a ribonucleoside found widely distributed in cells of every type as the free nucleoside and in combination in nucleic acids and various nucleoside coenzymes.
    GO:0032922    circadian regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression such that an expression pattern recurs with a regularity of approximately 24 hours.
    GO:0006175    dATP biosynthetic process    The chemical reactions and pathways resulting in the formation of dATP, deoxyadenosine triphosphate (2'-deoxyadenosine 5'-triphosphate).
    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:0042102    positive regulation of T cell proliferation    Any process that activates or increases the rate or extent of T cell proliferation.
    GO:0010613    positive regulation of cardiac muscle hypertrophy    Any process that increases the rate, frequency or extent of the enlargement or overgrowth of all or part of the heart due to an increase in size (not length) of individual cardiac muscle fibers, without cell division.
    GO:0006166    purine ribonucleoside salvage    Any process which produces a purine nucleoside from derivatives of it, without de novo synthesis.
    GO:0043101    purine-containing compound salvage    Any process that generates a purine-containing compound, any nucleobase, nucleoside, nucleotide or nucleic acid that contains a purine base, from derivatives of them without de novo synthesis.
    GO:0009156    ribonucleoside monophosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of a ribonucleoside monophosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with phosphate on the sugar.
    GO:0044342    type B pancreatic cell proliferation    The multiplication or reproduction of pancreatic B cells, resulting in the expansion of an pancreatic B cell population. Pancreatic B cell are cells of the pancreas that secrete insulin.
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.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ADK_HUMAN | P552631bx4 2i6a 4o1l

(-) Related Entries Specified in the PDB File

2i6a 2I6A IS THE STRUCTURE OF HUMAN ADENOSINE KINASE IN COMPLEX WITH 5-IODO-TUBERCIDIN