[English] 日本語
Yorodumi- PDB-5fdp: Structure of DDR1 receptor tyrosine kinase in complex with D2099 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fdp | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of DDR1 receptor tyrosine kinase in complex with D2099 inhibitor at 2.25 Angstroms resolution. | ||||||
Components | Epithelial discoidin domain-containing receptor 1 | ||||||
Keywords | TRANSFERASE / DDR1 Kinase / inhibitors / Structural Genomics / PSI-Biology / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information protein tyrosine kinase collagen receptor activity / smooth muscle cell-matrix adhesion / regulation of extracellular matrix disassembly / ear development / regulation of cell-matrix adhesion / collagen-activated tyrosine kinase receptor signaling pathway / branching involved in mammary gland duct morphogenesis / wound healing, spreading of cells / smooth muscle cell migration / neuron projection extension ...protein tyrosine kinase collagen receptor activity / smooth muscle cell-matrix adhesion / regulation of extracellular matrix disassembly / ear development / regulation of cell-matrix adhesion / collagen-activated tyrosine kinase receptor signaling pathway / branching involved in mammary gland duct morphogenesis / wound healing, spreading of cells / smooth muscle cell migration / neuron projection extension / axon development / Non-integrin membrane-ECM interactions / mammary gland alveolus development / peptidyl-tyrosine autophosphorylation / collagen binding / transmembrane receptor protein tyrosine kinase activity / lactation / embryo implantation / regulation of cell growth / receptor protein-tyrosine kinase / positive regulation of neuron projection development / protein autophosphorylation / cell population proliferation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / cell adhesion / negative regulation of cell population proliferation / extracellular space / extracellular exosome / ATP binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Bartual, S.G. / Pinkas, D.M. / Wang, Z. / Ding, K. / Mahajan, P. / Kupinska, K. / Mukhopadhyay, S. / Strain-Damerell, C. / Borkowska, O. / Talon, R. ...Bartual, S.G. / Pinkas, D.M. / Wang, Z. / Ding, K. / Mahajan, P. / Kupinska, K. / Mukhopadhyay, S. / Strain-Damerell, C. / Borkowska, O. / Talon, R. / Kopec, J. / Williams, E. / Tallant, C. / Chaikuad, A. / Sorell, F. / Newman, J. / Burgess-Brown, N. / Arrowsmith, C.H. / von Delft, F. / Edwards, A.M. / Bountra, C. / Bullock, A. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: J.Med.Chem. / Year: 2016 Title: Structure-Based Design of Tetrahydroisoquinoline-7-carboxamides as Selective Discoidin Domain Receptor 1 (DDR1) Inhibitors. Authors: Wang, Z. / Bian, H. / Bartual, S.G. / Du, W. / Luo, J. / Zhao, H. / Zhang, S. / Mo, C. / Zhou, Y. / Xu, Y. / Tu, Z. / Ren, X. / Lu, X. / Brekken, R.A. / Yao, L. / Bullock, A.N. / Su, J. / Ding, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5fdp.cif.gz | 83.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5fdp.ent.gz | 59.3 KB | Display | PDB format |
PDBx/mmJSON format | 5fdp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fdp_validation.pdf.gz | 731 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5fdp_full_validation.pdf.gz | 733.2 KB | Display | |
Data in XML | 5fdp_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 5fdp_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/5fdp ftp://data.pdbj.org/pub/pdb/validation_reports/fd/5fdp | HTTPS FTP |
-Related structure data
Related structure data | 4ckrS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 38282.805 Da / Num. of mol.: 1 / Fragment: UNP residues 601-903 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DDR1, CAK, EDDR1, NEP, NTRK4, PTK3A, RTK6, TRKE / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q08345, receptor protein-tyrosine kinase | ||
---|---|---|---|
#2: Chemical | ChemComp-5WR / ( | ||
#3: Chemical | ChemComp-PEG / | ||
#4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.63 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20% Polyethylene glycol 3350, 10% ethylene glycol, 0.1M Bis-tris propane pH 6.5, 0.2M Sodium Acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→41.75 Å / Num. obs: 15300 / % possible obs: 100 % / Redundancy: 9.5 % / Biso Wilson estimate: 22.52 Å2 / Rmerge(I) obs: 0.344 / Rpim(I) all: 0.168 / Net I/σ(I): 4.4 |
Reflection shell | Resolution: 2.25→2.32 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.876 / Mean I/σ(I) obs: 2.5 / Rpim(I) all: 0.445 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4CKR Resolution: 2.25→41.75 Å / Cor.coef. Fo:Fc: 0.9063 / Cor.coef. Fo:Fc free: 0.8393 / SU R Cruickshank DPI: 0.307 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.394 / SU Rfree Blow DPI: 0.262 / SU Rfree Cruickshank DPI: 0.249
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.33 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.266 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→41.75 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.25→2.4 Å / Total num. of bins used: 8
|