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- PDB-3znr: HDAC7 bound with inhibitor TMP269 -

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Basic information

Entry
Database: PDB / ID: 3znr
TitleHDAC7 bound with inhibitor TMP269
ComponentsHISTONE DEACETYLASE 7
KeywordsHYDROLASE / CLASS IIA HDACS / TFMO
Function / homology
Function and homology information


regulation of mRNA processing / histone H4K16 deacetylase activity, hydrolytic mechanism / 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 / protein deacetylation / histone deacetylase / histone H3K9 deacetylase activity, hydrolytic mechanism ...regulation of mRNA processing / histone H4K16 deacetylase activity, hydrolytic mechanism / 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 / protein deacetylation / histone deacetylase / histone H3K9 deacetylase activity, hydrolytic mechanism / cell-cell junction assembly / negative regulation of non-canonical NF-kappaB signal transduction / SUMO transferase activity / protein lysine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of interleukin-2 production / histone deacetylase activity / Notch-HLH transcription pathway / protein sumoylation / histone deacetylase complex / negative regulation of osteoblast differentiation / SUMOylation of DNA damage response and repair proteins / vasculogenesis / 14-3-3 protein binding / epigenetic regulation of gene expression / protein kinase C binding / Regulation of PTEN gene transcription / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / transcription corepressor activity / DNA-binding transcription factor binding / chromatin binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Histone deacetylase domain / Arginase; Chain A / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Chem-NU9 / Histone deacetylase 7
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLobera, m. / madauss, k. / pohlhaus, d. / trump, r. / nolan, m.
CitationJournal: Nat.Chem.Biol. / Year: 2013
Title: Selective Class Iia Histone Deacetylase Inhibition Via a Non-Chelating Zinc Binding Group
Authors: Lobera, M. / Madauss, K.P. / Pohlhaus, D.T. / Wright, Q.G. / Trocha, M. / Schmidt, D.R. / Baloglu, E. / Trump, R.P. / Head, M.S. / Hofmann, G.A. / Murray-Thompson, M. / Schwartz, B. / ...Authors: Lobera, M. / Madauss, K.P. / Pohlhaus, D.T. / Wright, Q.G. / Trocha, M. / Schmidt, D.R. / Baloglu, E. / Trump, R.P. / Head, M.S. / Hofmann, G.A. / Murray-Thompson, M. / Schwartz, B. / Chakravorty, S. / Wu, Z. / Mander, P.K. / Kruidenier, L. / Reid, R.A. / Burkhart, W. / Turunen, B.J. / Rong, J.X. / Wagner, C. / Moyer, M.B. / Wells, C. / Hong, X. / Moore, J.T. / Williams, J.D. / Soler, D. / Ghosh, S. / Nolan, M.A.
History
DepositionFeb 15, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 1.2May 1, 2013Group: Atomic model / Database references
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HISTONE DEACETYLASE 7
B: HISTONE DEACETYLASE 7
C: HISTONE DEACETYLASE 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,69716
Polymers136,5553
Non-polymers1,14213
Water79344
1
A: HISTONE DEACETYLASE 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2426
Polymers45,5181
Non-polymers7245
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HISTONE DEACETYLASE 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7275
Polymers45,5181
Non-polymers2094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: HISTONE DEACETYLASE 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7275
Polymers45,5181
Non-polymers2094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.393, 81.393, 149.265
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein HISTONE DEACETYLASE 7 / HDAC7 / HD7 / HISTONE DEACETYLASE 7A / HD7A


Mass: 45518.340 Da / Num. of mol.: 3 / Fragment: CATALYTIC DOMAIN, RESIDUES 482-903
Source method: isolated from a genetically manipulated source
Details: LIGAND IS A TFMO INHIBITOR / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8WUI4, histone deacetylase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-NU9 / N-{[4-(4-phenyl-1,3-thiazol-2-yl)tetrahydro-2H-pyran-4-yl]methyl}-3-[5-(trifluoromethyl)-1,2,4-oxadiazol-3-yl]benzamide


Mass: 514.519 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H21F3N4O3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 41.16 % / Description: NONE
Crystal growpH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97
DetectorType: MARRESEARCH MX-300 / Detector: CCD / Date: Jun 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 40790 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.8
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.1 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKLdata reduction
HKLdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→70.49 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.932 / SU B: 21.381 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R: 0.572 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.COMPLETE LIGAND DENISTY NOT SEEN IN ALL SUBUNITS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24102 2165 5 %RANDOM
Rwork0.21235 ---
obs0.21385 40790 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.375 Å2
Baniso -1Baniso -2Baniso -3
1-2.27 Å21.13 Å20 Å2
2--2.27 Å20 Å2
3----3.4 Å2
Refinement stepCycle: LAST / Resolution: 2.4→70.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8346 0 48 44 8438
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0218605
X-RAY DIFFRACTIONr_bond_other_d0.0010.025670
X-RAY DIFFRACTIONr_angle_refined_deg0.8121.93811691
X-RAY DIFFRACTIONr_angle_other_deg0.765313765
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.54551106
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5423.753389
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.279151295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3841553
X-RAY DIFFRACTIONr_chiral_restr0.0450.21258
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0219867
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021786
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_it0.131.55474
X-RAY DIFFRACTIONr_mcbond_other0.0141.52279
X-RAY DIFFRACTIONr_mcangle_it0.24528694
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.27733131
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.4674.52995
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 156 -
Rwork0.304 3017 -
obs--98.63 %

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