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 :  DLK IN COMPLEX WITH INHIBITOR N-(1-ISOPROPYL-5-(PIPERIDIN-4-YL)-1H-PYRAZOL-3-YL)-4-(TRIFLUOROMETHYL)PYRIDIN-2-AMINE
 
Authors :  S. F. Harris, J. Yin
Date :  07 Jul 15  (Deposition) - 14 Oct 15  (Release) - 04 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym./Biol. Unit :  A
Keywords :  Kinase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Patel, S. F. Harris, P. Gibbons, G. Deshmukh, A. Gustafson, T. Kellar, H. Lin, X. Liu, Y. Liu, Y. Liu, C. Ma, K. Scearce-Levie, A. S. Ghosh, Y. G. Shin, H. Solanoy, J. Wang, B. Wang, J. Yin, M. Siu, J. W. Lewcock
Scaffold-Hopping And Structure-Based Discovery Of Potent, Selective, And Brain Penetrant N-(1H-Pyrazol-3-Yl)Pyridin-2-Amine Inhibitors Of Dual Leucine Zipper Kinase (Dlk, Map3K12).
J. Med. Chem. V. 58 8182 2015
PubMed-ID: 26431428  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B01072

(-) Compounds

Molecule 1 - MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 12
    Chains: A
    EC Number: 2.7.11.25
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell Line: HI5
    Expression System Common: CABBAGE LOOPER
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Fragment: KINASE DOMAIN (UNP RESIDUES 115-402)
    Gene: MAP3K12, ZPK
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DUAL LEUCINE ZIPPER BEARING KINASE,DLK,LEUCINE-ZIPPER PROTEIN KINASE,ZPK,MAPK-UPSTREAM KINASE,MUK,MIXED LINEAGE KINASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
150E1Ligand/IonN-(5-PIPERIDIN-4-YL-1-PROPAN-2-YL-PYRAZOL-3-YL)-4-(TRIFLUOROMETHYL)PYRIDIN-2-AMINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:132 , GLN A:136 , VAL A:139 , ALA A:150 , LYS A:152 , MET A:190 , GLU A:191 , PHE A:192 , CYS A:193 , GLY A:196 , GLN A:197 , LEU A:243binding site for residue 50E A 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:133 -Gly A:134
2Ala A:183 -Pro A:184

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5CEP)

(-) 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:269
                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhheeeeeeeee..eeeeeeee..eeeeeee..hhhhhhhhhhh.........eeeee......eeeee....eehhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee.......hhhhhhhhhhh......hhhhhhhhhhhhhhhhh.......hhhhhhhhhhh...........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cep A 117 LWEVPFEEILDLQWVGSGAQGAVFLGRFHGEEVAVKKVRDLKETDIKHLRKLKHPNIITFKGVCTQAPCYCILMEFCAQGQLYEVLRAGRPVTPSLLVDWSMGIAGGMNYLHLHKIIHRDLKSPNMLITYDDVVKISDFGFAGTVAWMAPEVIRNEPVSEKVDIWSFGVVLWELLTGEIPYKDVDSSAIIWGVGSNSLHLPVPSSCPDGFKILLRQCWNSKPRNRPSFRQILLHLDIASADVLSTPQETYFKSQAEWREEVKLHFEKIK 398
                                   126       136       146       156       166       176       186       196       206       216       226       236       246       256|      279       289       299       309       319       329       339       349       359       369       379       389         
                                                                                                                                                                     256|                                                                                                                                
                                                                                                                                                                      270
   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 5CEP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (27, 27)

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
    50E  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:183 - Pro A:184   [ RasMol ]  
    Ser A:133 - Gly A:134   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5cep
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  M3K12_HUMAN | Q12852
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.11.25
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  M3K12_HUMAN | Q12852
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        M3K12_HUMAN | Q12852: 5cen 5ceo 5ceq

(-) Related Entries Specified in the PDB File

5cen 5ceo 5ceq