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 :  RAPID DISCOVERY OF PYRIDO[3,4-D]PYRIMIDINE INHIBITORS OF MONOPOLAR SPINDLE KINASE 1 (MPS1) USING A STRUCTURE-BASED HYDRIDIZATION APPROACH
 
Authors :  P. Innocenti, H. L. Woodward, S. Solanki, N. Naud, I. M. Westwood, N. Cro A. Hayes, J. Roberts, A. T. Henley, R. Baker, A. Faisal, G. Mak, G. Box, M A. De Haven Brandon, L. O'Fee, J. Saville, J. Schmitt, R. Burke, R. L. Montfort, F. I. Raymaud, S. A. Eccles, S. Linardopoulos, J. Blagg, S. H
Date :  29 Oct 15  (Deposition) - 20 Apr 16  (Release) - 11 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.67
Chains :  Asym./Biol. Unit :  A
Keywords :  Spindle Assembly Checkpoint (Sac), Oncology Target Pyrido[3, 4- D]Pyrimidine Based Inhibitors Selective Against Mps1, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Innocenti, H. L. Woodward, S. Solanki, S. Naud, I. M. Westwood, N. Cronin, A. Hayes, J. Roberts, A. T. Henley, R. Baker, A. Faisal, G. W. Mak, G. Box, M. Valenti, A. De Haven Brandon, L. O'Fee, H. Saville, J. Schmitt, B. Matijssen, R. Burke, R. L. Van Montfort, F. I. Raynaud, S. A. Eccles, S. Linardopoulos, J. Blagg, S. Hoelder
Rapid Discovery Of Pyrido[3, 4-D]Pyrimidine Inhibitors Of Monopolar Spindle Kinase 1 (Mps1) Using A Structure-Based Hybridization Approach.
J. Med. Chem. V. 59 3671 2016
PubMed-ID: 27055065  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B01811

(-) Compounds

Molecule 1 - DUAL SPECIFICITY PROTEIN KINASE TTK
    ChainsA
    EC Number2.7.12.1
    EngineeredYES
    GeneTTK, MPS1, MPS1L1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsN-(2,4-DIMETHOXYPHENYL)-8-(1-METHYL-1H-PYRAZOL-4-YL) PYRIDO[3,4-D]PYRIMIDIN-2-AMINE
    SynonymPHOSPHOTYROSINE PICKED THREONINE-PROTEIN KINASE,PYT

 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
15O71Ligand/Ion~{N}-(2,4-DIMETHOXYPHENYL)-8-(1-METHYLPYRAZOL-4-YL)PYRIDO[3,4-D]PYRIMIDIN-2-AMINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:529 , ILE A:531 , GLN A:541 , ALA A:551 , ILE A:586 , MET A:602 , GLU A:603 , CYS A:604 , GLY A:605 , ASN A:606 , ASP A:608 , SER A:611 , LEU A:654 , HOH A:1001binding site for residue 5O7 A 901

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5EI2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5EI2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5EI2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5EI2)

(-) Exons   (0, 0)

(no "Exon" information available for 5EI2)

(-) 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:256
                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeeeeeeeeee...eeeeeee.....eeeeeeee....hhhhhhhhhhhhhhhhhhhhhh.....eeeeee...eeeeee....eehhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.......hhh.eeee..eeee................hhhhhhhh..hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh...........hhhhhhhhhhhh........hhhhhh.hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ei2 A 516 QSMSVKGRIYSILKQIGSGGSSKVFQVLNEKKQIYAIKYVNLEEADNQTLDSYRNEIAYLNKLQQHSDKIIRLYDYEITDQYIYMVMECGNIDLNSWLKKKKSIDPWERKSYWKNMLEAVHTIHQHGIVHSDLKPANFLIVDGMLKLIDFGIANQMQGTVNYMPPEAIKDMKISPKSDVWSLGCILYYMTYGKTPFQQIINQISKLHAIIDPNHEIEFPDIPEKDLQDVLKCCLKRDPKQRISIPELLAHPYVQIQ 794
                                   525       535       545       555       565       575       585       595       605       615       625       635       645       655       665      |687       697||     718       728       738       748       758       768       778       788      
                                                                                                                                                                                      672|          698|                                                                                    
                                                                                                                                                                                       685           710                                                                                    

   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 5EI2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5EI2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5EI2)

(-) Gene Ontology  (21, 21)

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
    5O7  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5ei2)
 

(-) 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
  5ei2
    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
  TTK_HUMAN | P33981
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.12.1
    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
  TTK_HUMAN | P33981
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        TTK_HUMAN | P339812x9e 2zmc 2zmd 3cek 3dbq 3gfw 3h9f 3hmn 3hmo 3hmp 3vqu 3w1f 3wyx 3wyy 3wzj 3wzk 4b94 4bhz 4bi0 4bi1 4bi2 4c4e 4c4f 4c4g 4c4h 4c4i 4c4j 4cv8 4cv9 4cva 4d2s 4h7x 4h7y 4js8 4jt3 4o6l 4zeg 5ap0 5ap1 5ap2 5ap3 5ap4 5ap5 5ap6 5ap7 5eh0 5ehl 5eho 5ehy 5ei6 5ei8 5ljj 5n7v 5n84 5n87 5n93 5n9s 5na0 5nad

(-) Related Entries Specified in the PDB File

5eh0 5EH0 CONTAINS THE SAME PROTEIN COMPLEXED WITH N2-(2-METHOXY-4-(1- METHYL-1H-PYRAZOL-4-YL)PHENYL)-N8-NEOPENTYLPYRIDO[3,4-D]PYRIMIDINE- 2,8-DIAMINE