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- PDB-9ntb: Crystal structure of human HDAC2 in complex with TNG260 -

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Basic information

Entry
Database: PDB / ID: 9ntb
TitleCrystal structure of human HDAC2 in complex with TNG260
ComponentsHistone deacetylase 2
KeywordsHYDROLASE / inhibitor / zinc metalloenzyme / HDAC1 / CoREST
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 / positive regulation of stem cell population maintenance / eyelid development in camera-type eye / odontogenesis of dentin-containing tooth / dendrite development / 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 / progesterone receptor signaling pathway / 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 / Regulation of PTEN gene transcription / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / transcription coregulator binding / Regulation of endogenous retroelements by KRAB-ZFP proteins / response to nicotine / response to cocaine / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / promoter-specific chromatin binding / NOTCH1 Intracellular Domain Regulates Transcription / circadian regulation of gene expression / negative regulation of transforming growth factor beta receptor signaling pathway / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / NoRC negatively regulates rRNA expression / protein modification process / 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: 1.8 Å
AuthorsMcMillan, B.J. / Whittington, D.A.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Cancer Res. / Year: 2025
Title: TNG260 is a Small-Molecule CoREST Inhibitor that Sensitizes STK11-Mutant Tumors to Anti-PD-1 Immunotherapy.
Authors: Ahronian, L.G. / Sahu, S. / Zhang, M. / Patel, A.S. / Geng, K. / Bhattacharya, R. / Falchook, G.S. / Goldman, J.W. / Spira, A.I. / Punekar, S.R. / Spigel, D.R. / Wang, J.S. / Skoulidis, F. / ...Authors: Ahronian, L.G. / Sahu, S. / Zhang, M. / Patel, A.S. / Geng, K. / Bhattacharya, R. / Falchook, G.S. / Goldman, J.W. / Spira, A.I. / Punekar, S.R. / Spigel, D.R. / Wang, J.S. / Skoulidis, F. / Stephens, J. / Meynardie, M. / Powell, J.M. / Lopez, A. / Ranieri, M. / Ploszaj, M.A. / Tan, Y.J. / Lee, Y.T. / Yu, Y. / Deng, J. / Chen, T. / McCarren, P. / Tsai, A. / Hussain, S.S. / Doyon, B. / Amemiya, K. / Ermolieff, J. / Shahagadkar, P. / Das, N.M. / Flynn, L.R. / Shields, J.A. / Danielczyk, L. / McMillan, B.J. / Mignault, A. / Meier, S.R. / Wu, H.J. / Guerin, D.J. / Whittington, D.A. / Min, C. / Sienczylo, I. / Maxwell, J.P. / DiBenedetto, H.J. / Watanabe, H. / Haines, B.B. / Huang, A. / Crystal, A. / Andersen, J.N. / Wu, X. / Wong, K.K.
History
DepositionMar 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 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)143,00552
Polymers137,9943
Non-polymers5,01149
Water16,628923
1
A: Histone deacetylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,99222
Polymers45,9981
Non-polymers1,99421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone deacetylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,02619
Polymers45,9981
Non-polymers2,02818
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Histone deacetylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,98711
Polymers45,9981
Non-polymers99010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.230, 97.310, 139.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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
Details: Expressed as full-length protein with C-terminal His-6 tag, proteolyzed by trypsin overnight (1:200 ratio) to produce final protein for crystallography
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, 972 molecules

#2: Chemical ChemComp-A1B1V / (R)-N-(4-amino-4'-fluoro-[1,1'-biphenyl]-3-yl)-4-(S-methylsulfonimidoyl)benzamide


Mass: 383.439 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H18FN3O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#9: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 923 / 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: 2.26 Å3/Da / Density % sol: 45.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 9 / Details: 35% PEG 600, 100 mM CHES pH 9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→48.66 Å / Num. obs: 221686 / % possible obs: 99 % / Redundancy: 3.6 % / Biso Wilson estimate: 23.58 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.101 / Net I/σ(I): 9.1
Reflection shellResolution: 1.8→1.849 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.54 / Num. unique obs: 15079 / CC1/2: 0.561 / Rrim(I) all: 0.819 / % possible all: 90.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→48.66 Å / SU ML: 0.1836 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.2517
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1967 3815 1.72 %
Rwork0.1604 217862 -
obs0.1611 221677 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.61 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8879 0 313 923 10115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00629461
X-RAY DIFFRACTIONf_angle_d0.798612708
X-RAY DIFFRACTIONf_chiral_restr0.05421281
X-RAY DIFFRACTIONf_plane_restr0.00831631
X-RAY DIFFRACTIONf_dihedral_angle_d14.36243590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.3221290.28977187X-RAY DIFFRACTION87.93
1.82-1.850.26651240.26757637X-RAY DIFFRACTION93.61
1.85-1.870.28191510.25677909X-RAY DIFFRACTION96.98
1.87-1.90.27891430.24368077X-RAY DIFFRACTION98.96
1.9-1.930.25011460.22778107X-RAY DIFFRACTION99.69
1.93-1.960.2561200.22398171X-RAY DIFFRACTION99.88
1.96-1.990.26441630.21438184X-RAY DIFFRACTION99.96
1.99-2.020.27611470.19688087X-RAY DIFFRACTION99.99
2.02-2.060.20981310.18478146X-RAY DIFFRACTION99.96
2.06-2.10.17251370.17898213X-RAY DIFFRACTION99.95
2.1-2.140.29731470.17368144X-RAY DIFFRACTION99.98
2.14-2.190.26181370.17278095X-RAY DIFFRACTION99.93
2.19-2.240.22851380.16728191X-RAY DIFFRACTION99.9
2.24-2.30.18851530.16068110X-RAY DIFFRACTION99.93
2.3-2.360.2011310.16618197X-RAY DIFFRACTION99.95
2.36-2.430.23191570.16578116X-RAY DIFFRACTION99.96
2.43-2.510.19661250.16088178X-RAY DIFFRACTION99.94
2.51-2.60.18631490.15988085X-RAY DIFFRACTION99.88
2.6-2.70.22031310.15578186X-RAY DIFFRACTION99.89
2.7-2.820.18931430.15158148X-RAY DIFFRACTION99.89
2.82-2.970.171510.15398170X-RAY DIFFRACTION99.88
2.97-3.160.21661430.15948104X-RAY DIFFRACTION99.76
3.16-3.40.19091360.14288116X-RAY DIFFRACTION99.63
3.4-3.740.17441410.13648074X-RAY DIFFRACTION99.04
3.74-4.280.1441360.12348087X-RAY DIFFRACTION99.19
4.29-5.40.16241510.13018058X-RAY DIFFRACTION98.68
5.4-48.660.16911550.16348085X-RAY DIFFRACTION99.44

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