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- PDB-9jwj: Structure of Human HDAC2 in complex with inhibitor N-(2-amino-5-(... -

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Basic information

Entry
Database: PDB / ID: 9jwj
TitleStructure of Human HDAC2 in complex with inhibitor N-(2-amino-5-(furan-2-yl)phenyl)-4-(1-((phenylsulfonyl)methyl)-1H-1,2,3-triazol-4-yl)benzamid
ComponentsHistone deacetylase 2
KeywordsTRANSCRIPTION / Histone deacetylase 2
Function / homology
Function and homology information


positive regulation of male mating behavior / protein de-2-hydroxyisobutyrylase activity / protein lysine delactylase activity / negative regulation of dendritic spine development / p75NTR negatively regulates cell cycle via SC1 / epidermal cell differentiation / histone decrotonylase activity / fungiform papilla formation / behavioral response to ethanol / NuRD complex ...positive regulation of male mating behavior / protein de-2-hydroxyisobutyrylase activity / protein lysine delactylase activity / negative regulation of dendritic spine development / p75NTR negatively regulates cell cycle via SC1 / epidermal cell differentiation / histone decrotonylase activity / fungiform papilla formation / behavioral response to ethanol / NuRD complex / positive regulation of interleukin-1 production / regulation of cell fate specification / negative regulation of transcription by competitive promoter binding / EGR2 and SOX10-mediated initiation of Schwann cell myelination / negative regulation of stem cell population maintenance / histone deacetylase activity, hydrolytic mechanism / ESC/E(Z) complex / histone deacetylase / regulation of stem cell differentiation / cardiac muscle hypertrophy / cellular response to dopamine / STAT3 nuclear events downstream of ALK signaling / response to caffeine / protein lysine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / embryonic digit morphogenesis / histone deacetylase activity / positive regulation of intracellular estrogen receptor signaling pathway / Notch-HLH transcription pathway / Sin3-type complex / eyelid development in camera-type eye / odontogenesis of dentin-containing tooth / positive regulation of stem cell population maintenance / dendrite development / response to amyloid-beta / histone deacetylase complex / RNA Polymerase I Transcription Initiation / positive regulation of oligodendrocyte differentiation / positive regulation of proteolysis / progesterone receptor signaling pathway / Regulation of MECP2 expression and activity / hair follicle placode formation / response to hyperoxia / NF-kappaB binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / cellular response to transforming growth factor beta stimulus / positive regulation of epithelial to mesenchymal transition / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / MECP2 regulates neuronal receptors and channels / Regulation of TP53 Activity through Acetylation / cellular response to retinoic acid / heat shock protein binding / SUMOylation of chromatin organization proteins / negative regulation of cell migration / response to amphetamine / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Regulation of PTEN gene transcription / transcription coregulator binding / Regulation of endogenous retroelements by KRAB-ZFP proteins / response to nicotine / response to cocaine / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / promoter-specific chromatin binding / circadian regulation of gene expression / negative regulation of transforming growth factor beta receptor signaling pathway / NoRC negatively regulates rRNA expression / NOTCH1 Intracellular Domain Regulates Transcription / protein modification process / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / histone deacetylase binding / cellular response to hydrogen peroxide / positive regulation of tumor necrosis factor production / heterochromatin formation / negative regulation of neuron projection development / cellular response to heat / Factors involved in megakaryocyte development and platelet production / histone binding / response to lipopolysaccharide / Potential therapeutics for SARS / RNA polymerase II-specific DNA-binding transcription factor binding / chromosome, telomeric region / chromatin remodeling / response to xenobiotic stimulus / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / chromatin binding / negative regulation of apoptotic process / chromatin / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Histone deacetylase / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Histone deacetylase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsTojo, T. / Itoh, Y. / Kurohara, T. / Li, Y. / Singh, R. / Narozny, R. / Wiel, A. / Miyake, Y. / Yamashita, Y. / Kusakabe, K. ...Tojo, T. / Itoh, Y. / Kurohara, T. / Li, Y. / Singh, R. / Narozny, R. / Wiel, A. / Miyake, Y. / Yamashita, Y. / Kusakabe, K. / Uchida, S. / Suzuki, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Discovery of an HDAC2-selective inhibitor based on enzyme-inhibitor binding thermodynamics and kinetics, and its potential as a therapeutic drug for neurological disorders
Authors: Tojo, T. / Itoh, Y. / Kurohara, T. / Li, Y. / Singh, R. / Narozny, R. / Wiel, A. / Miyake, Y. / Yamashita, Y. / Kusakabe, K. / Uchida, S. / Suzuki, T.
History
DepositionOct 10, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone deacetylase 2
B: Histone deacetylase 2
C: Histone deacetylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,64933
Polymers137,9943
Non-polymers3,65530
Water13,223734
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.279, 98.562, 139.597
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Histone deacetylase 2 / HD2 / Protein deacylase HDAC2


Mass: 45997.965 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC2 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q92769, histone deacetylase, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides

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Non-polymers , 9 types, 764 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-A1L4X / N-(2-amino-5-(furan-2-yl)phenyl)-4-(1-((phenylsulfonyl)methyl)-1H-1,2,3-triazol-4-yl)benzamid / ~{N}-[2-azanyl-5-(furan-2-yl)phenyl]-4-[2-(phenylsulfonylmethyl)-1,2$l^{4},3-triazacyclopenta-2,4-dien-4-yl]benzamide


Mass: 499.541 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C26H21N5O4S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 734 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.3 Å3/Da / Density % sol: 46.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 0.1 M CHES pH 9.5, 35-38% (v/v) PEG 600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 110377 / % possible obs: 91.2 % / Redundancy: 4.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.038 / Rrim(I) all: 0.088 / Net I/σ(I): 10.8
Reflection shellResolution: 1.78→1.88 Å / % possible obs: 91.8 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.611 / Num. measured all: 77155 / Num. unique obs: 16112 / CC1/2: 0.805 / Rpim(I) all: 0.287 / Rrim(I) all: 0.679 / Net I/σ(I) obs: 3.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
SCALAdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LY1

4ly1


Resolution: 1.78→50 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.252 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20248 5595 5.1 %RANDOM
Rwork0.15988 ---
obs0.16207 104661 90.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.272 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å2-0 Å20 Å2
2--1.63 Å2-0 Å2
3----0.74 Å2
Refinement stepCycle: 1 / Resolution: 1.78→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8884 0 200 734 9818
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0199724
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9511.96813135
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85151194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.62223.825468
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.091151663
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8961553
X-RAY DIFFRACTIONr_chiral_restr0.1610.21318
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0217567
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6172.574629
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.5133.8355857
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.4073.1635095
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.16836.84715158
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.78→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 411 -
Rwork0.247 7754 -
obs--91.66 %

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