|Entry||Database: PDB / ID: 5ya5|
|Title||CRYSTAL STRUCTURE OF c-MET IN COMPLEX WITH NOVEL INHIBITOR|
|Components||Hepatocyte growth factor receptorC-Met|
|Keywords||TRANSFERASE/INHIBITOR / c-MET inhibitor / TRANSFERASE-INHIBITOR complex|
|Function / homology|
Function and homology information
hepatocyte growth factor receptor activity / Drug-mediated inhibition of MET activation / MET activates STAT3 / endothelial cell morphogenesis / negative regulation of hydrogen peroxide-mediated programmed cell death / negative regulation of guanyl-nucleotide exchange factor activity / MET interacts with TNS proteins / MET Receptor Activation / positive regulation of endothelial cell chemotaxis / semaphorin receptor activity ...hepatocyte growth factor receptor activity / Drug-mediated inhibition of MET activation / MET activates STAT3 / endothelial cell morphogenesis / negative regulation of hydrogen peroxide-mediated programmed cell death / negative regulation of guanyl-nucleotide exchange factor activity / MET interacts with TNS proteins / MET Receptor Activation / positive regulation of endothelial cell chemotaxis / semaphorin receptor activity / MET receptor recycling / Sema4D mediated inhibition of cell attachment and migration / MET activates PTPN11 / pancreas development / MET activates RAP1 and RAC1 / MET activates PI3K/AKT signaling / negative regulation of Rho protein signal transduction / negative regulation of stress fiber assembly / semaphorin-plexin signaling pathway / MET activates PTK2 signaling / negative regulation of thrombin-activated receptor signaling pathway / branching morphogenesis of an epithelial tube / positive chemotaxis / establishment of skin barrier / MET activates RAS signaling / MECP2 regulates neuronal receptors and channels / phagocytosis / positive regulation of microtubule polymerization / negative regulation of autophagy / basal plasma membrane / InlB-mediated entry of Listeria monocytogenes into host cell / liver development / molecular function activator activity / neuron differentiation / Negative regulation of MET activity / receptor protein-tyrosine kinase / transmembrane receptor protein tyrosine kinase activity / positive regulation of kinase activity / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / nervous system development / transmembrane receptor protein tyrosine kinase signaling pathway / cell migration / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protein phosphatase binding / protein tyrosine kinase activity / positive regulation of protein kinase B signaling / cell surface receptor signaling pathway / receptor complex / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular region / ATP binding / membrane / identical protein binding / plasma membrane
Similarity search - Function
Tyrosine-protein kinase, HGF/MSP receptor / Plexin family / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / IPT/TIG domain ...Tyrosine-protein kinase, HGF/MSP receptor / Plexin family / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / IPT/TIG domain / ig-like, plexins, transcription factors / PSI domain / domain found in Plexins, Semaphorins and Integrins / IPT domain / Immunoglobulin E-set / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / WD40/YVTN repeat-like-containing domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-6TD / Hepatocyte growth factor receptor
Similarity search - Component
|Biological species||Homo sapiens (human)|
|Method||X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 Å|
|Authors||Liu, Q. / Xu, Y.|
|Citation||Journal: Eur J Med Chem / Year: 2018|
Title: Discovery, optimization and biological evaluation for novel c-Met kinase inhibitors
Authors: Yuan, H. / Liu, Q. / Zhang, L. / Hu, S. / Chen, T. / Li, H. / Chen, Y. / Xu, Y. / Lu, T.
|Structure viewer||Molecule: |
Downloads & links
A: Hepatocyte growth factor receptor
|#1: Protein|| |
Mass: 36033.594 Da / Num. of mol.: 1 / Fragment: UNP residues 1038-1346
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MET / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta
References: UniProt: P08581, receptor protein-tyrosine kinase
|#2: Chemical|| ChemComp-6TD / |
|#3: Water|| ChemComp-HOH / |
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 1|
|Crystal||Density Matthews: 2.21 Å3/Da / Density % sol: 44.29 %|
|Crystal grow||Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 |
Details: 0.1M Tris pH7.5, 15% glycerol, 12% MPD, 5% isopropanol, 15% PEG5Kmme
|Diffraction||Mean temperature: 100 K|
|Diffraction source||Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å|
|Detector||Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 15, 2013|
|Radiation||Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray|
|Radiation wavelength||Wavelength: 0.9791 Å / Relative weight: 1|
|Reflection||Resolution: 1.89→40.927 Å / Num. obs: 49233 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.802 % / Biso Wilson estimate: 28.59 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.046 / Rrim(I) all: 0.053 / Χ2: 0.974 / Net I/σ(I): 17.33 / Num. measured all: 187189 / Scaling rejects: 16|
|Phasing||Method: molecular replacement|
|Refinement||Method to determine structure: MOLECULAR REPLACEMENT|
Starting model: 4GG5
Resolution: 1.89→40.927 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.26 / Phase error: 22.99
|Solvent computation||Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å|
|Displacement parameters||Biso max: 82.15 Å2 / Biso mean: 38.1 Å2 / Biso min: 15.49 Å2|
|Refinement step||Cycle: final / Resolution: 1.89→40.927 Å|
|Refine LS restraints|
|LS refinement shell|
Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
-Feb 9, 2022. New format data for meta-information of EMDB entries
New format data for meta-information of EMDB entries
- Version 3 of the EMDB header file is now the official format.
- The previous official version 1.9 will be removed from the archive.
Related info.:EMDB header
External links:wwPDB to switch to version 3 of the EMDB data model
-Aug 12, 2020. Covid-19 info
New page: Covid-19 featured information page in EM Navigator.
Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data
+Mar 5, 2020. Novel coronavirus structure data
Novel coronavirus structure data
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
- The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info
+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
+Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
- This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
- Now, EM Navigator and Yorodumi are based on the updated data.
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
- The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi