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- PDB-7mox: Structure of HDAC2 in complex with an inhibitor (compound 14) -

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Basic information

Entry
Database: PDB / ID: 7mox
TitleStructure of HDAC2 in complex with an inhibitor (compound 14)
ComponentsHistone deacetylase 2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HISTONE DEACETYLASE / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


positive regulation of male mating behavior / protein de-2-hydroxyisobutyrylase activity / protein lysine delactylase activity / p75NTR negatively regulates cell cycle via SC1 / epidermal cell differentiation / negative regulation of dendritic spine development / histone decrotonylase activity / fungiform papilla formation / negative regulation of MHC class II biosynthetic process / behavioral response to ethanol ...positive regulation of male mating behavior / protein de-2-hydroxyisobutyrylase activity / protein lysine delactylase activity / p75NTR negatively regulates cell cycle via SC1 / epidermal cell differentiation / negative regulation of dendritic spine development / histone decrotonylase activity / fungiform papilla formation / negative regulation of MHC class II biosynthetic process / behavioral response to ethanol / positive regulation of interleukin-1 production / NuRD complex / 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 H4K16 deacetylase activity, hydrolytic mechanism / ESC/E(Z) complex / histone H4K5 deacetylase activity, hydrolytic mechanism / histone H4K8 deacetylase activity, hydrolytic mechanism / histone H3K4 deacetylase activity, hydrolytic mechanism / histone H3K14 deacetylase activity, hydrolytic mechanism / histone H4K12 deacetylase activity, hydrolytic mechanism / histone deacetylase / regulation of stem cell differentiation / cellular response to dopamine / cardiac muscle hypertrophy / STAT3 nuclear events downstream of ALK signaling / histone H3K9 deacetylase activity, hydrolytic mechanism / 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 / positive regulation of stem cell population maintenance / dendrite development / odontogenesis of dentin-containing tooth / response to amyloid-beta / positive regulation of proteolysis / RNA Polymerase I Transcription Initiation / histone deacetylase complex / positive regulation of oligodendrocyte differentiation / Regulation of MECP2 expression and activity / positive regulation of collagen biosynthetic process / hair follicle placode formation / response to hyperoxia / NF-kappaB binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / progesterone receptor signaling pathway / positive regulation of epithelial to mesenchymal transition / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / MECP2 regulates neuronal receptors and channels / cellular response to transforming growth factor beta stimulus / cellular response to retinoic acid / Regulation of TP53 Activity through Acetylation / heat shock protein binding / response to amphetamine / SUMOylation of chromatin organization proteins / negative regulation of cell migration / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Regulation of PTEN gene transcription / Regulation of endogenous retroelements by KRAB-ZFP proteins / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / negative regulation of DNA-binding transcription factor activity / response to nicotine / promoter-specific chromatin binding / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / response to cocaine / NoRC negatively regulates rRNA expression / protein modification process / NOTCH1 Intracellular Domain Regulates Transcription / cellular response to hydrogen peroxide / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / histone deacetylase binding / positive regulation of tumor necrosis factor production / heterochromatin formation / negative regulation of neuron projection development / Factors involved in megakaryocyte development and platelet production / cellular response to heat / RNA polymerase II-specific DNA-binding transcription factor binding / response to lipopolysaccharide / histone binding / Potential therapeutics for SARS / 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
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 / Chem-ZLS / Histone deacetylase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.69 Å
AuthorsKlein, D.J. / Yu, W.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2021
Title: Discovery of macrocyclic HDACs 1, 2, and 3 selective inhibitors for HIV latency reactivation.
Authors: Yu, W. / Fells, J. / Clausen, D. / Liu, J. / Klein, D.J. / Christine Chung, C. / Myers, R.W. / Wu, J. / Wu, G. / Howell, B.J. / Barnard, R.J.O. / Kozlowski, J.
History
DepositionMay 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1May 22, 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 2
B: Histone deacetylase 2
C: Histone deacetylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,93032
Polymers129,1863
Non-polymers3,74429
Water19,1861065
1
A: Histone deacetylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,44512
Polymers43,0621
Non-polymers1,38311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Histone deacetylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1479
Polymers43,0621
Non-polymers1,0858
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Histone deacetylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,33911
Polymers43,0621
Non-polymers1,27710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.560, 99.190, 139.780
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, 3 molecules ABC

#1: Protein Histone deacetylase 2 / HD2


Mass: 43061.988 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

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Non-polymers , 6 types, 1094 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-ZLS / (1S)-N-[(1S)-7,7-dihydroxy-1-{4-[(1R,4S)-1,2,3,4-tetrahydro-1,4-methanonaphthalen-6-yl]-1H-imidazol-2-yl}nonyl]-6-methyl-6-azaspiro[2.5]octane-1-carboxamide


Mass: 534.733 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C32H46N4O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1065 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.48 Å3/Da / Density % sol: 50.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.688→139.7 Å / Num. obs: 144815 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.999 / Net I/σ(I): 15.7
Reflection shellResolution: 1.688→1.693 Å / Num. unique obs: 1469 / CC1/2: 0.778

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (10-DEC-2020)refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.69→24.42 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.946 / SU R Cruickshank DPI: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.099 / SU Rfree Blow DPI: 0.094 / SU Rfree Cruickshank DPI: 0.091
RfactorNum. reflection% reflectionSelection details
Rfree0.2021 7204 5 %RANDOM
Rwork0.176 ---
obs0.1773 143989 100 %-
Displacement parametersBiso max: 125.44 Å2 / Biso mean: 27.55 Å2 / Biso min: 8.72 Å2
Baniso -1Baniso -2Baniso -3
1-4.3383 Å20 Å20 Å2
2---6.551 Å20 Å2
3---2.2128 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: final / Resolution: 1.69→24.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8869 0 225 1072 10166
Biso mean--47.96 41.07 -
Num. residues----1102
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3372SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1653HARMONIC8
X-RAY DIFFRACTIONt_it9503HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1144SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9306SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d9503HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg12876HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion2.81
X-RAY DIFFRACTIONt_other_torsion16.16
LS refinement shellResolution: 1.69→1.7 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2419 148 5.14 %
Rwork0.2542 2732 -
all0.2536 2880 -
obs--100 %

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