+
Open data
-
Basic information
| Entry | Database: PDB / ID: 2c0i | ||||||
|---|---|---|---|---|---|---|---|
| Title | Src family kinase Hck with bound inhibitor A-420983 | ||||||
 Components | TYROSINE-PROTEIN KINASE HCK | ||||||
 Keywords | TRANSFERASE / TYROSINE-PROTEIN KINASE / ATP-BINDING / KINASE / LIPOPROTEIN / MYRISTATE / NUCLEOTIDE-BINDING / PALMITATE / PHOSPHORYLATION / SH2 DOMAIN / SH3 DOMAIN | ||||||
| Function / homology |  Function and homology informationleukocyte degranulation / innate immune response-activating signaling pathway / leukocyte migration involved in immune response / respiratory burst after phagocytosis / regulation of podosome assembly / FLT3 signaling through SRC family kinases / regulation of phagocytosis / regulation of DNA-binding transcription factor activity / Nef and signal transduction / positive regulation of actin filament polymerization ...leukocyte degranulation / innate immune response-activating signaling pathway / leukocyte migration involved in immune response / respiratory burst after phagocytosis / regulation of podosome assembly / FLT3 signaling through SRC family kinases / regulation of phagocytosis / regulation of DNA-binding transcription factor activity / Nef and signal transduction / positive regulation of actin filament polymerization / Fc-gamma receptor signaling pathway involved in phagocytosis / mesoderm development / FCGR activation / type II interferon-mediated signaling pathway / transport vesicle / Signaling by CSF3 (G-CSF) / phosphotyrosine residue binding / FCGR3A-mediated IL10 synthesis / cell surface receptor protein tyrosine kinase signaling pathway / lipopolysaccharide-mediated signaling pathway / peptidyl-tyrosine phosphorylation / integrin-mediated signaling pathway / cell projection / regulation of actin cytoskeleton organization / non-membrane spanning protein tyrosine kinase activity / FCGR3A-mediated phagocytosis / Regulation of signaling by CBL / non-specific protein-tyrosine kinase / negative regulation of inflammatory response to antigenic stimulus / Inactivation of CSF3 (G-CSF) signaling / caveola / cytoplasmic side of plasma membrane / cytokine-mediated signaling pathway / Signaling by CSF1 (M-CSF) in myeloid cells / regulation of cell shape / protein autophosphorylation / regulation of inflammatory response / protein tyrosine kinase activity / cell differentiation / cytoskeleton / lysosome / protein phosphorylation / cell adhesion / defense response to Gram-positive bacterium / intracellular signal transduction / inflammatory response / signaling receptor binding / focal adhesion / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / lipid binding / negative regulation of apoptotic process / Golgi apparatus / ATP binding / nucleus / plasma membrane / cytosol Similarity search - Function  | ||||||
| Biological species |  HOMO SAPIENS (human) | ||||||
| Method |  X-RAY DIFFRACTION /  SYNCHROTRON /  MOLECULAR REPLACEMENT / Resolution: 2.3 Å  | ||||||
 Authors | Borhani, D.W. / Burchat, A. / Calderwood, D.J. / Hirst, G.C. / Li, B. / Loew, A. | ||||||
 Citation |  Journal: Bioorg.Med.Chem.Lett. / Year: 2006Title: Discovery of A-770041, a Src-Family Selective Orally Active Lck Inhibitor that Prevents Organ Allograft Rejection. Authors: Burchat, A. / Borhani, D.W. / Calderwood, D.J. / Hirst, G.C. / Li, B. / Stachlewitz, R.F. #1: Journal: Bioorg.Med.Chem.Lett. / Year: 2004 Title: A-420983: A Potent, Orally Active Inhibitor of Lck with Efficacy in a Model of Transplant Rejection Authors: Borhani, D.W. / Calderwood, D.J. / Friedman, M.M. / Hirst, G.C. / Li, B. / Leung, A.K.W. / Mcrae, B. / Ratnofsky, S. / Ritter, K. / Waegell, W.  | ||||||
| History | 
  | 
-
Structure visualization
| Structure viewer | Molecule:  Molmil Jmol/JSmol | 
|---|
-
Downloads & links
-
Download
| PDBx/mmCIF format |  2c0i.cif.gz | 196.3 KB | Display |  PDBx/mmCIF format | 
|---|---|---|---|---|
| PDB format |  pdb2c0i.ent.gz | 155.6 KB | Display |  PDB format | 
| PDBx/mmJSON format |  2c0i.json.gz | Tree view |  PDBx/mmJSON format | |
| Others |  Other downloads | 
-Validation report
| Summary document |  2c0i_validation.pdf.gz | 874.8 KB | Display |  wwPDB validaton report | 
|---|---|---|---|---|
| Full document |  2c0i_full_validation.pdf.gz | 892.8 KB | Display | |
| Data in XML |  2c0i_validation.xml.gz | 36.2 KB | Display | |
| Data in CIF |  2c0i_validation.cif.gz | 51.2 KB | Display | |
| Arichive directory |  https://data.pdbj.org/pub/pdb/validation_reports/c0/2c0i ftp://data.pdbj.org/pub/pdb/validation_reports/c0/2c0i | HTTPS FTP  | 
-Related structure data
| Related structure data | ![]() 2c0oC ![]() 2c0tC ![]() 1ad5S S: Starting model for refinement C: citing same article (  | 
|---|---|
| Similar structure data | 
-
Links
-
Assembly
| Deposited unit | ![]() 
  | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | ![]() 
  | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 2 | ![]() 
  | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Unit cell | 
  | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Noncrystallographic symmetry (NCS) | NCS domain: 
 NCS domain segments: Component-ID: 1 
 NCS ensembles : 
 NCS oper: (Code: given Matrix: (0.944154, 0.025026, -0.328552), Vector:  | 
-
Components
| #1: Protein | Mass: 52000.227 Da / Num. of mol.: 2 / Fragment: SH3-SH2-SH1, RESIDUES 80-525 / Mutation: YES Source method: isolated from a genetically manipulated source Details: SRC NUMBERING USED. ADD 20 TO THE RESIDUE NUMBERS IN THIS ENTRY TO OBTAIN ACTUAL HUMAN HCK RESIDUE NUMBERS. RESIDUE Y501 (HCK Y521) IS PHOSPHORYLATED Source: (gene. exp.)  HOMO SAPIENS (human) / Cell: LYMPHOCYTE / Plasmid: PBC HCK002 / Cell line (production host): SF9 / Production host: ![]() #2: Chemical | #3: Chemical | #4: Water |  ChemComp-HOH /  | Compound details | ENGINEERED RESIDUE IN CHAIN A, GLN 502 TO GLU ENGINEERED RESIDUE IN CHAIN A, GLN 503 TO GLU  ...ENGINEERED | Has protein modification | Y | Sequence details | THE PROTEIN CRYSTALLIZED INCLUDED EIGHT NON-NATIVE N-TERMINAL RESIDUES: GLY-ALA-MET-GLY-SER-GLY-ILE- ...THE PROTEIN CRYSTALLIZ |  | 
|---|
-Experimental details
-Experiment
| Experiment | Method:  X-RAY DIFFRACTION / Number of used crystals: 1  | 
|---|
-
Sample preparation
| Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 59.9 % | 
|---|---|
| Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8  Details: HCK (10 MG/ML IN 150 MM NACL, 20 MM TRIS.HCL PH 8.0) WAS MIXED WITH A-420983 [100 MM STOCK SOLUTION OF THE BIS-MALEIC ACID SALT IN DMSO) TO GIVE A FINAL A-420983 CONCENTRATION OF 1 MM. HCK/A- ...Details: HCK (10 MG/ML IN 150 MM NACL, 20 MM TRIS.HCL PH 8.0) WAS MIXED WITH A-420983 [100 MM STOCK SOLUTION OF THE BIS-MALEIC ACID SALT IN DMSO) TO GIVE A FINAL A-420983 CONCENTRATION OF 1 MM. HCK/A-420983 WAS THEN MIXED WITH RESERVOIR SOLUTION (12% PEG 6000, 3% 1, 5-DIAMINOPENTANE, 20% GLYCEROL, 200 MM CA(OAC)2, 100 MM TRIS.HCL PH 8.0) AND EQUILBRATED AGAINST THE RESERVOIR SOLUTION BY VAPOR DIFFUSION (SITTING DROPS) AT 277 K.  | 
-Data collection
| Diffraction | Mean temperature: 100 K | 
|---|---|
| Diffraction source | Source:  SYNCHROTRON / Site:  APS   / Beamline: 17-ID / Wavelength: 1.0332  | 
| Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 7, 2002 | 
| Radiation | Monochromator: SI(111) DOUBLE MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | 
| Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 | 
| Reflection | Resolution: 2.3→15 Å / Num. obs: 50423 / % possible obs: 88.9 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 54.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.8 | 
| Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.3 / % possible all: 75.5 | 
-
Processing
| Software | 
  | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Refinement | Method to determine structure:  MOLECULAR REPLACEMENTStarting model: PDB ENTRY 1AD5 Resolution: 2.3→19.96 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.91 / SU B: 15.259 / SU ML: 0.192 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.341 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ACTIVATION LOOP (RESIDUES A386-A398 AND B386-B398) IS DISORDERED IN BOTH HCK MOLECULES (CHAINS A AND B). HCK CHAIN A IS SLIGHTLY BETTER ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ACTIVATION LOOP (RESIDUES A386-A398 AND B386-B398) IS DISORDERED IN BOTH HCK MOLECULES (CHAINS A AND B). HCK CHAIN A IS SLIGHTLY BETTER ORDERED THAN CHAIN B. SIMILARLY, THE LIGAND A1506 IS BETTER ORDERED THAN B1506. SEVEN N-TERMINAL RESIDUES (FROM THE EXPRESSION VECTOR, GLY-ALA -MET-GLY-SER-GLY-ILE) ARE DISORDERED IN BOTH CHAINS. RESIDUE ARG-59 IS NON-NATIVE (EXPRESSION VECTOR). 
  | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso  mean: 50.47 Å2
  | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement step | Cycle: LAST / Resolution: 2.3→19.96 Å
  | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refine LS restraints | 
  | 
Movie
Controller
About Yorodumi




HOMO SAPIENS (human)
X-RAY DIFFRACTION
Citation




























PDBj

















