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- PDB-5wbn: Crystal structure of fragment 3-(3-Benzyl-2-oxo-2H-[1,2,4]triazin... -

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Basic information

Entry
Database: PDB / ID: 5wbn
TitleCrystal structure of fragment 3-(3-Benzyl-2-oxo-2H-[1,2,4]triazino[2,3-c]quinazolin-6-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain
ComponentsHistone deacetylase 6
Keywordshydrolase/hydrolase inhibitor / HISTONE DEACETYLASE / HDAC / HDAC6 / FRAGMENT SCREENING / STRUCTURAL GENOMICS CONSORTIUM / SGC / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


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 / negative regulation of aggrephagy / positive regulation of cholangiocyte proliferation / response to misfolded protein / positive regulation of protein oligomerization / negative regulation of axon extension involved in axon guidance / positive regulation of RIG-I signaling pathway ...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 / negative regulation of aggrephagy / positive regulation of cholangiocyte proliferation / response to misfolded protein / positive regulation of protein oligomerization / negative regulation of axon extension involved in axon guidance / positive regulation of RIG-I signaling pathway / type 2 mitophagy / negative regulation of protein-containing complex disassembly / peroxidase inhibitor activity / erythrocyte enucleation / regulation of autophagy of mitochondrion / Cilium Assembly / regulation of microtubule-based movement / tubulin deacetylation / protein-containing complex disassembly / regulation of establishment of protein localization / collateral sprouting / Transcriptional regulation by RUNX2 / tubulin deacetylase activity / negative regulation of microtubule depolymerization / lysosome localization / positive regulation of dendrite morphogenesis / ATPase inhibitor activity / cilium disassembly / histone deacetylase activity, hydrolytic mechanism / misfolded protein binding / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / dendritic spine morphogenesis / positive regulation of type 2 mitophagy / protein deacetylation / aggresome assembly / regulation of androgen receptor signaling pathway / regulation of mitochondrion organization / Transferases; Acyltransferases; Aminoacyltransferases / cellular response to misfolded protein / regulation of fat cell differentiation / protein lysine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / aggresome / histone deacetylase activity / microtubule associated complex / cellular response to parathyroid hormone stimulus / response to corticosterone / positive regulation of intracellular estrogen receptor signaling pathway / response to dexamethasone / Notch-HLH transcription pathway / negative regulation of gene expression, epigenetic / axonal transport of mitochondrion / RUNX2 regulates osteoblast differentiation / histone deacetylase complex / cell leading edge / response to immobilization stress / dynein complex binding / protein quality control for misfolded or incompletely synthesized proteins / positive regulation of epithelial cell migration / polyubiquitin modification-dependent protein binding / cilium assembly / regulation of macroautophagy / HSF1 activation / positive regulation of synaptic transmission, glutamatergic / alpha-tubulin binding / negative regulation of protein-containing complex assembly / beta-tubulin binding / negative regulation of proteolysis / multivesicular body / inclusion body / axon cytoplasm / antiviral innate immune response / epigenetic regulation of gene expression / actin filament organization / response to amphetamine / ubiquitin binding / transcription corepressor binding / intracellular protein transport / Hsp90 protein binding / Late endosomal microautophagy / beta-catenin binding / protein destabilization / regulation of protein stability / caveola / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / tau protein binding / histone deacetylase binding / epidermal growth factor receptor signaling pathway / cellular response to hydrogen peroxide / protein polyubiquitination / Chaperone Mediated Autophagy / Aggrephagy / cellular response to heat / actin binding / perikaryon / microtubule binding / microtubule / regulation of autophagy
Similarity search - Function
Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Zinc/RING finger domain, C3HC4 (zinc finger) ...Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Ureohydrolase domain superfamily / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-9ZV / ACETATE ION / FORMIC ACID / Protein deacetylase HDAC6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.64 Å
AuthorsHarding, R.J. / Walker, J.R. / Ferreira de Freitas, R. / Ravichandran, M. / Santhakumar, V. / Schapira, M. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H.
CitationJournal: To be published
Title: Crystal structure of fragment 3-(3-Benzyl-2-oxo-2H-[1,2,4]triazino[2,3-c]quinazolin-6-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain
Authors: Harding, R.J. / Walker, J.R. / Ferreira de Freitas, R. / Ravichandran, M. / Santhakumar, V. / Schapira, M. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H.
History
DepositionJun 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,26519
Polymers11,9331
Non-polymers4,33218
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.850, 43.740, 55.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Histone deacetylase 6 / HD6


Mass: 11932.607 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC6, KIAA0901, JM21 / Plasmid: PET28-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q9UBN7, histone deacetylase

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Non-polymers , 7 types, 166 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-9ZV / 3-(3-benzyl-2-oxo-2H-[1,2,4]triazino[2,3-c]quinazolin-6-yl)propanoic acid


Mass: 360.366 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H16N4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Mass: 435.516 Da / Num. of mol.: 8 / Source method: obtained synthetically
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.07 % / Mosaicity: 0 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 2M Na-formate, 0.2M Na-acetate pH4.6, 5% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Dec 17, 2015 / Details: A200
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.64→32.62 Å / Num. obs: 11842 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.037 / Rrim(I) all: 0.097 / Net I/σ(I): 21.2 / Num. measured all: 80148 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
1.69-1.736.60.3610.9320.150.392100
7.56-32.625.50.02410.0110.02698.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimless0.5.31data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementResolution: 1.64→34.44 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.449 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1675 564 4.8 %RANDOM
Rwork0.1319 ---
obs0.1336 11278 93.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 51.62 Å2 / Biso mean: 9.104 Å2 / Biso min: 1.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2--0.51 Å2-0 Å2
3----0.41 Å2
Refinement stepCycle: final / Resolution: 1.64→34.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms801 0 56 149 1006
Biso mean--14.44 21.65 -
Num. residues----103
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.019917
X-RAY DIFFRACTIONr_bond_other_d0.0030.02754
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.9261256
X-RAY DIFFRACTIONr_angle_other_deg1.1593.0091751
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2745110
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.77924.7540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.28815119
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.354151
X-RAY DIFFRACTIONr_chiral_restr0.1180.2124
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211163
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02186
LS refinement shellResolution: 1.645→1.687 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.171 14 -
Rwork0.182 227 -
all-241 -
obs--26.22 %

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