Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  DISCOVERY OF VX-509 (DECERNOTINIB): A POTENT AND SELECTIVE JANUS KINASE (JAK) 3 INHIBITOR FOR THE TREATMENT OF AUTOIMMUNE DISEASE
 
Authors :  H. J. Zuccola, M. Ledeboer
Date :  17 Mar 15  (Deposition) - 12 Aug 15  (Release) - 07 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.16
Chains :  Asym./Biol. Unit :  A
Keywords :  Janus Kinase, Kinase, Inhibitor, Autoimmune, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. J. Farmer, M. W. Ledeboer, T. Hoock, M. J. Arnost, R. S. Bethiel, Y. L. Bennani, J. J. Black, C. L. Brummel, A. Chakilam, W. A. Dorsch, B. Fan, J. E. Cochran, S. Halas, E. M. Harrington, J. K. Hogan, D. Howe, H. Huang, D. H. Jacobs, L. M. Laitinen, S. Liao, S. Mahajan, V. Marone, G. Martinez-Botella, P. Mccarthy, D. Messersmith, M. Namchuk, L. Oh, M. S. Penney, A. C. Pierce, S. A. Raybuck, A. Rugg, F. G. Salituro, K. Saxena, D. Shannon, D. Shlyakter, L. Swenson, S. K. Tian, C. Town, J. Wang, T. Wang, M. W. Wannamaker, R. J. Winquist, H. J. Zuccola
Discovery Of Vx-509 (Decernotinib): A Potent And Selective Janus Kinase 3 Inhibitor For The Treatment Of Autoimmune Diseases.
J. Med. Chem. V. 58 7195 2015
PubMed-ID: 26230873  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B00301

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN KINASE JAK2
    ChainsA
    EC Number2.7.10.2
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Taxid7108
    FragmentUNP RESIDUES 842-1132
    GeneJAK2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymJANUS KINASE 2,JAK-2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
14HW1Ligand/IonN~3~-PHENYL-1-[6-(PHENYLAMINO)PYRIMIDIN-4-YL]-1H-1,2,4-TRIAZOLE-3,5-DIAMINE
2PTR2Mod. Amino AcidO-PHOSPHOTYROSINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:855 , VAL A:863 , ALA A:880 , VAL A:911 , MET A:929 , GLU A:930 , TYR A:931 , LEU A:932 , GLY A:935 , ARG A:980 , LEU A:983 , ASP A:994 , HOH A:4137binding site for residue 4HW A 4000

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YTC)

(-) 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:286
                                                                                                                                                                                                                                                                                                                               
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhh.eeeeeeee...eeeeeee........eeeeeee....hhhhhhhhhhhhhhhhh........eeeee.......eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeeee..eeee......ee.......ee.......hhhhhhhhhhhhheehhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ytc A  842 TQFEERHLKFLQQLGKGGSVEMCRYDPLQDNTGEVVAVKKLQHSTEEHLRDFEREIEILKSLQHDNIVKYKGVCYSARRNLKLIMEYLPYGSLRDYLQKHKERIDHIKLLQYTSQICKGMEYLGTKRYIHRDLATRNILVENENRVKIGDFGLTKVLPQDKEyyKVKEPGESPIFWYAPESLTESKFSVASDVWSFGVVLYELFTYIEKSKSPPAEFMRMIGNDKQGQMIVFHLIELLKNNGRLPRPDGCPDEIYMIMTECWNNNVNQRPSFRDLALRVDQIRDNM 1130
                                   851      |863       873       883       893       903       913      |924       934       944       954       964       974       984       994      1004  ||  1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      
                                          858|                                                        920|                                                                                 1007-PTR                                                                                                                       
                                           861                                                         922                                                                                  1008-PTR                                                                                                                      

   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 4YTC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (114, 114)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    4HW  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PTR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4ytc)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4ytc
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  JAK2_HUMAN | O60674
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.10.2
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  JAK2_HUMAN | O60674
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        JAK2_HUMAN | O606742b7a 2w1i 2xa4 3e62 3e63 3e64 3fup 3io7 3iok 3jy9 3kck 3krr 3lpb 3q32 3rvg 3tjc 3tjd 3ugc 3zmm 4aqc 4bbe 4bbf 4c61 4c62 4d0w 4d0x 4d1s 4e4m 4e6d 4e6q 4f08 4f09 4fvp 4fvq 4fvr 4gfm 4gmy 4hge 4iva 4ji9 4jia 4p7e 4ytf 4yth 4yti 4z32 4zim 5aep 5cf4 5cf5 5cf6 5cf8 5hez 5i4n 5l3a 5tq3 5tq4 5tq5 5tq6 5tq7 5tq8 5usy 5usz 5ut0 5ut1 5ut2 5ut3 5ut4 5ut5 5ut6

(-) Related Entries Specified in the PDB File

4ytf 4yth 4yti