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 NOVEL, DUAL MECHANISM ERK INHIBITORS BY AFFINITY SELECTION SCREENING OF AN INACTIVE KINASE STATE
 
Authors :  Y. Deng, G. W. Shipps, A. Cooper, J. M. English, D. A. Annis, D. Carr, Y. Na Y. H. Zhu, C. Chuang, P. Dayananth, A. W. Hruza, L. Xiao, W. Jin, P. Kirsc W. T. Windsor, A. A. Samatar
Date :  26 Jul 14  (Deposition) - 12 Nov 14  (Release) - 17 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Transferase, Serine/Threonine-Protein Kinase, Map Kinase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Deng, G. W. Shipps, A. Cooper, J. M. English, D. A. Annis, D. Carr, Y. Nan, T. Wang, H. Y. Zhu, C. C. Chuang, P. Dayananth, A. W. Hruza, L. Xiao, W. Jin, P. Kirschmeier, W. T. Windsor, A. A. Samatar
Discovery Of Novel, Dual Mechanism Erk Inhibitors By Affinity Selection Screening Of An Inactive Kinase.
J. Med. Chem. V. 57 8817 2014
PubMed-ID: 25313996  |  Reference-DOI: 10.1021/JM500847M

(-) Compounds

Molecule 1 - MITOGEN-ACTIVATED PROTEIN KINASE 1
    Chains: A
    EC Number: 2.7.11.24
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MAPK1, ERK2, MAPK, PRKM1
    Organism Common: BROWN RAT,RAT,RATS
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: MAP KINASE 1, MAPK 1, ERT1, EXTRACELLULAR SIGNAL-REGULATED KINASE 2, ERK-2, MAP KINASE ISOFORM P42, P42-MAPK, MITOGEN-ACTIVATED PROTEIN KINASE 2, MAP KINASE 2, MAPK 2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
13G71Ligand/Ion(3R)-1-{2-[4-(4-ACETYLPHENYL)PIPERAZIN-1-YL]-2-OXOETHYL}-N-(3-CHLORO-4-HYDROXYPHENYL)PYRROLIDINE-3-CARBOXAMIDE
2SO43Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:33 , TYR A:34 , ALA A:50 , LYS A:52 , ILE A:54 , TYR A:62 , GLU A:69 , GLN A:103 , ASP A:104 , LEU A:105 , MET A:106 , LEU A:154 , ASP A:165 , GLY A:167 , HOH A:766BINDING SITE FOR RESIDUE 3G7 A 401
2AC2SOFTWARETYR A:185 , ARG A:189 , ARG A:192 , TYR A:231 , HOH A:722 , HOH A:731BINDING SITE FOR RESIDUE SO4 A 402
3AC3SOFTWAREASN A:121 , GLY A:180 , LYS A:257 , HOH A:637 , HOH A:644 , HOH A:708BINDING SITE FOR RESIDUE SO4 A 403
4AC4SOFTWAREGLN A:64 , ARG A:65 , LEU A:168BINDING SITE FOR RESIDUE SO4 A 404

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:20 -Pro A:21

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QYY)

(-) 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:337
                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeeee..eeeeeeee.....eeeeeee....hhhhhhhhhhhhhhhhhh.........eee..........eeeeee...eehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee.hhhhh..........hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhhhh..hhhhhhhhhhh......hhhhhh...hhhhhhhhhhhh........hhhhhhhhhhhh...hhhhh............hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qyy A  13 RGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNLNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKLDDLPKEKLKELIFEETARFQ 353
                                    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     ||336       346       
                                                                                                                                                                                                                                                                                                                                                     328|                    
                                                                                                                                                                                                                                                                                                                                                      333
   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 4QYY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (89, 89)

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
    3G7  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:20 - Pro A:21   [ 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
  4qyy
    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
  MK01_RAT | P63086
    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)
  2.7.11.24
    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
  MK01_RAT | P63086
    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
        MK01_RAT | P63086: 1erk 1gol 2erk 2fys 2gph 2z7l 3c9w 3erk 3o71 3qyw 3qyz 3r63 3zu7 3zuv 4erk 4gsb 4gt3 4gva 4i5h 4n4s 4s2z 4s30 4s31 4s32 4s33 4s34 4xne 4xoy 4xoz 4xp0 4xp2 4xp3 4xrj 4xrl 5hd4 5hd7 5ke0 5u6i 5umo

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4QYY)