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- PDB-6ced: Crystal structure of fragment 3-(3-Methyl-4-oxo-3,4-dihydroquinaz... -
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Basic information
Entry | Database: PDB / ID: 6ced | ||||||
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Title | Crystal structure of fragment 3-(3-Methyl-4-oxo-3,4-dihydroquinazolin-2-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain | ||||||
![]() | Histone deacetylase 6 | ||||||
![]() | HYDROLASE / HISTONE DEACETYLASE / HDAC / HDAC6 / UBIQUITIN / STRUCTURAL GENOMICS CONSORTIUM / SGC | ||||||
Function / homology | ![]() negative regulation of hydrogen peroxide metabolic process / cellular response to topologically incorrect protein / polyubiquitinated misfolded protein transport / positive regulation of cellular response to oxidative stress / erythrocyte enucleation / negative regulation of aggrephagy / positive regulation of cholangiocyte proliferation / response to misfolded protein / negative regulation of oxidoreductase activity / regulation of microtubule-based movement ...negative regulation of hydrogen peroxide metabolic process / cellular response to topologically incorrect protein / polyubiquitinated misfolded protein transport / positive regulation of cellular response to oxidative stress / erythrocyte enucleation / negative regulation of aggrephagy / positive regulation of cholangiocyte proliferation / response to misfolded protein / negative regulation of oxidoreductase activity / regulation of microtubule-based movement / parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / negative regulation of protein-containing complex disassembly / protein-containing complex disassembly / negative regulation of axon extension involved in axon guidance / regulation of establishment of protein localization / positive regulation of tubulin deacetylation / tubulin deacetylation / regulation of autophagy of mitochondrion / Cilium Assembly / peptidyl-lysine deacetylation / tubulin deacetylase activity / collateral sprouting / Transcriptional regulation by RUNX2 / lysosome localization / misfolded protein binding / negative regulation of protein acetylation / negative regulation of microtubule depolymerization / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein deacetylation / cilium disassembly / response to growth factor / dendritic spine morphogenesis / histone deacetylase / aggresome assembly / regulation of androgen receptor signaling pathway / protein lysine deacetylase activity / positive regulation of signaling receptor activity / cellular response to misfolded protein / positive regulation of dendrite morphogenesis / cellular response to parathyroid hormone stimulus / aggresome / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / regulation of fat cell differentiation / microtubule associated complex / histone deacetylase activity / response to corticosterone / dynein complex binding / negative regulation of gene expression, epigenetic / protein quality control for misfolded or incompletely synthesized proteins / positive regulation of epithelial cell migration / axonal transport of mitochondrion / Notch-HLH transcription pathway / response to dexamethasone / beta-tubulin binding / cell leading edge / RUNX2 regulates osteoblast differentiation / histone deacetylase complex / response to immobilization stress / polyubiquitin modification-dependent protein binding / cilium assembly / alpha-tubulin binding / HSF1 activation / regulation of macroautophagy / negative regulation of protein-containing complex assembly / inclusion body / axon cytoplasm / response to amphetamine / multivesicular body / epigenetic regulation of gene expression / positive regulation of synaptic transmission, glutamatergic / transcription corepressor binding / ciliary basal body / ubiquitin binding / regulation of autophagy / caveola / actin filament organization / negative regulation of proteolysis / intracellular protein transport / Late endosomal microautophagy / protein destabilization / Hsp90 protein binding / regulation of protein stability / tau protein binding / NOTCH1 Intracellular Domain Regulates Transcription / histone deacetylase binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / beta-catenin binding / autophagy / Aggrephagy / Chaperone Mediated Autophagy / cellular response to hydrogen peroxide / protein polyubiquitination / positive regulation of peptidyl-serine phosphorylation / actin binding / cellular response to heat / microtubule binding / perikaryon / microtubule / RNA polymerase II cis-regulatory region sequence-specific DNA binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Harding, R.J. / Halabelian, L. / Ferreira de Freitas, R. / Franzoni, I. / Ravichandran, M. / Lautens, M. / Santhakumar, V. / Schapira, M. / Bountra, C. / Edwards, A.M. ...Harding, R.J. / Halabelian, L. / Ferreira de Freitas, R. / Franzoni, I. / Ravichandran, M. / Lautens, M. / Santhakumar, V. / Schapira, M. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.M. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Identification and Structure-Activity Relationship of HDAC6 Zinc-Finger Ubiquitin Binding Domain Inhibitors. Authors: Ferreira de Freitas, R. / Harding, R.J. / Franzoni, I. / Ravichandran, M. / Mann, M.K. / Ouyang, H. / Lautens, M. / Santhakumar, V. / Arrowsmith, C.H. / Schapira, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 38.3 KB | Display | ![]() |
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PDB format | ![]() | 24 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6ce6C ![]() 6ce8C ![]() 6ceaC ![]() 6cecC ![]() 6ceeC ![]() 6cefC ![]() 5kh3S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 11932.607 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-EYA / | #4: Chemical | ChemComp-UNX / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.07 % / Mosaicity: 0 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 2 M Na-formate, 0.2 M Na-acetate pH4.6, 5 % ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: May 18, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→34.74 Å / Num. obs: 11530 / % possible obs: 99.5 % / Redundancy: 6.7 % / CC1/2: 1 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.014 / Rrim(I) all: 0.037 / Net I/σ(I): 38.8 / Num. measured all: 76686 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Starting model: pdbid 5KH3 Resolution: 1.7→34.74 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.742 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: Users of this crystal structure: verify our intepretion of the electron density. Amplitudes and unmerged intensities are included with this deposition. Diffraction images will be deposited ...Details: Users of this crystal structure: verify our intepretion of the electron density. Amplitudes and unmerged intensities are included with this deposition. Diffraction images will be deposited at a later date in a public repository. Geometry restraints for the ligand were prepared with GRADE. Additional density at Cys1148 suggests radiation damage of this residue during data collection.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 56.87 Å2 / Biso mean: 18.646 Å2 / Biso min: 11.11 Å2
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Refinement step | Cycle: final / Resolution: 1.7→34.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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