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 :  CRYSTAL STRUCTURE OF C-MET IN COMPLEX WITH AMG 337
 
Authors :  D. A. Whittington, A. M. Long
Date :  24 Nov 15  (Deposition) - 10 Feb 16  (Release) - 06 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A
Keywords :  Phosphotransferase, Inhibitor, Cancer, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Boezio, K. W. Copeland, K. Rex, B. K Albrecht, D. Bauer, S. F. Bellon, C. Boezio, M. A. Broome, D. Choquette, A. Coxon, I. Dussault, S. Hirai, R. Lewis, M. H. Lin, J. Lohman, J. Liu, E. A. Peterson, M. Potashman, R. Shimanovich, Y. Teffera, D. A. Whittington, K. R. Vaida, J. C. Harmange
Discovery Of (R)-6-(1-(8-Fluoro-6-(1-Methyl-1H-Pyrazol-4-Yl)-[1, 2, 4]Triazolo[4, 3-A]Pyridin-3-Yl)Ethyl)-3-(2-Methoxyethoxy)-1, 6-Naphthyridin-5(6H)-One (Amg 337), A Potent And Selective Inhibitor Of Met With High Unbound Target Coverage And Robust In Vivo Antitumor Activity.
J. Med. Chem. V. 59 2328 2016
PubMed-ID: 26812066  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B01716

(-) Compounds

Molecule 1 - HEPATOCYTE GROWTH FACTOR RECEPTOR
    Chains: A
    EC Number: 2.7.10.1
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Fragment: RESIDUES 1048-1351
    Gene: MET
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HGF RECEPTOR,HGF/SF RECEPTOR,PROTO-ONCOGENE C-MET,SCATTER FACTOR RECEPTOR,SF RECEPTOR,TYROSINE-PROTEIN KINASE MET

 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
15T11Ligand/Ion6-[(1~{R})-1-[8-FLUORANYL-6-(1-METHYLPYRAZOL-4-YL)-[1,2,4]TRIAZOLO[4,3-A]PYRIDIN-3-YL]ETHYL]-3-(2-METHOXYETHOXY)-1,6-NAPHTHYRIDIN-5-ONE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:1084 , VAL A:1092 , ALA A:1108 , LEU A:1157 , PRO A:1158 , MET A:1160 , GLY A:1163 , ASP A:1164 , ASN A:1167 , ARG A:1208 , ASN A:1209 , MET A:1211 , ALA A:1221 , ASP A:1222 , TYR A:1230 , HOH A:1639 , HOH A:1644binding site for residue 5T1 A 1401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5EYD)

(-) 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:289
                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhheehhhhheeeeeeeeee....eeeeee...eeeee.........hhhhhhhhhhhhhhh.........eee.....eeeee.....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee..hhhhh...hhhhhee......eehhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5eyd A 1052 HIDLSALNPELVQAVQHVVIGPSSLIVHFNEVIGRGHFGCVYHGTLKIHCAVKSLNRITDIGEVSQFLTEGIIMKDFSHPNVLSLLGICLRSSPLVVLPYMKHGDLRNFIRNETHNPTVKDLIGFGLQVAKGMKYLASKKFVHRDLAARNCMLDEKFTVKVADFGLARDMYDKEYYSVHNKTGAKLPVKWMALESLQTQKFTTKSDVWSFGVLLWELMTRGAPPYPDVNTFDITVYLLQGRRLLQPEYCPDPLYEVMLKCWHPKAEMRPSFSELVSRISAIFSTFIGEH 1348
                                  1061      1071      1081      1091     |1107      1117      1127      1137      1147 ||   1159      1169      1179      1189      1199      1209      1219      1229      1239      1249      1259      1269      1279      1289      1299      1309      1319      1329      1339         
                                                                      1097|                                         1149|                                                                                                                                                                                                    
                                                                       1104                                          1152
   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 5EYD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (33, 33)

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
    5T1  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5eyd)
 

(-) 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
  5eyd
    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
  MET_HUMAN | P08581
    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)
  2.7.10.1
    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
  MET_HUMAN | P08581
    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
        MET_HUMAN | P08581: 1fyr 1r0p 1r1w 1shy 1ssl 1ux3 2cew 2g15 2rfn 2rfs 2uzx 2uzy 2wd1 2wgj 2wkm 3a4p 3bux 3c1x 3ccn 3cd8 3ce3 3cth 3ctj 3dkc 3dkf 3dkg 3efj 3efk 3f66 3f82 3i5n 3l8v 3lq8 3q6u 3q6w 3qti 3r7o 3rhk 3u6h 3u6i 3vw8 3zbx 3zc5 3zcl 3zxz 3zze 4aoi 4ap7 4deg 4deh 4dei 4eev 4gg5 4gg7 4iwd 4k3j 4knb 4mxc 4o3t 4o3u 4r1v 4r1y 4xmo 4xyf 5dg5 5eob 5eyc 5hlw 5hni 5ho6 5hoa 5hor 5hti 5t3q 5uab 5uad 5uaf

(-) Related Entries Specified in the PDB File

5eyc