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- PDB-6h0x: Crystal Structure of KDM4D with tetrazolylhydrazide ligand AA040 -

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Basic information

Entry
Database: PDB / ID: 6h0x
TitleCrystal Structure of KDM4D with tetrazolylhydrazide ligand AA040
ComponentsLysine-specific demethylase 4D
KeywordsOXIDOREDUCTASE / KDM4D / ligand binding / Tetrazolylhydrazide / tetrazole / inhibitor design / cancer / epigenetics
Function / homology
Function and homology information


positive regulation of chromatin binding / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9me2/H3K9me3 demethylase activity / positive regulation of double-strand break repair via nonhomologous end joining / histone H3K9 demethylase activity / histone demethylase activity / regulation of protein phosphorylation / pericentric heterochromatin / cellular response to ionizing radiation / HDMs demethylate histones ...positive regulation of chromatin binding / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9me2/H3K9me3 demethylase activity / positive regulation of double-strand break repair via nonhomologous end joining / histone H3K9 demethylase activity / histone demethylase activity / regulation of protein phosphorylation / pericentric heterochromatin / cellular response to ionizing radiation / HDMs demethylate histones / chromatin DNA binding / double-strand break repair via homologous recombination / site of double-strand break / regulation of gene expression / blood microparticle / damaged DNA binding / chromatin remodeling / inflammatory response / chromatin / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Jelly Rolls ...JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-FJB / NICKEL (II) ION / Lysine-specific demethylase 4D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsMalecki, P.H. / Weiss, M.S. / Heinemann, U. / Link, A.
CitationJournal: Eur.J.Med.Chem. / Year: 2024
Title: Structure-based mapping of the histone-binding pocket of KDM4D using functionalized tetrazole and pyridine core compounds.
Authors: Malecki, P.H. / Fassauer, G.M. / Ruger, N. / Schulig, L. / Link, A. / Krylova, O. / Heinemann, U. / Weiss, M.S.
History
DepositionJul 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.value / _struct_conn.pdbx_dist_value / _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
Revision 1.2Jul 22, 2026Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysine-specific demethylase 4D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1568
Polymers39,4921
Non-polymers6647
Water7,909439
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-13 kcal/mol
Surface area14880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.882, 71.882, 150.946
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-724-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lysine-specific demethylase 4D / JmjC domain-containing histone demethylation protein 3D / Jumonji domain-containing protein 2D


Mass: 39491.793 Da / Num. of mol.: 1 / Fragment: JMJD2D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM4D, JHDM3D, JMJD2D / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q6B0I6, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor

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Non-polymers , 6 types, 446 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#6: Chemical ChemComp-FJB / [[(2~{R})-2-(5-phenylpentanoylamino)-2-(2~{H}-1,2,3,4-tetrazol-5-yl)ethanoyl]amino]azanium


Mass: 318.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N7O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.57 Å3/Da / Density % sol: 52.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 100mM HEPES, 180mM ammonium sulphate, 24% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 25, 2016
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.64→48.171 Å / Num. obs: 48623 / % possible obs: 98.6 % / Redundancy: 10.2 % / Biso Wilson estimate: 14.86 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.159 / Rrim(I) all: 0.167 / Χ2: 0.902 / Net I/σ(I): 14.23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.64-1.7410.8481.1411.9976730.7231.19798.5
1.74-1.8610.7660.7922.9873760.8490.831100
1.86-2.018.8890.6514.1865830.9990.69495.5
2.01-2.210.5980.3558.2763450.9680.37399.9
2.2-2.4610.020.21712.2456140.9810.22996.9
2.46-2.849.710.12617.6151340.9940.13399.8
2.84-3.4711.0440.06532.2143840.9990.068100
3.47-4.99.4640.04446.7134650.9990.04799.4
4.9-48.1719.8770.03154.8520490.9990.03399

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ETS

6ets


Resolution: 1.64→48.171 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.88
RfactorNum. reflection% reflection
Rfree0.2184 2099 4.32 %
Rwork0.1822 --
obs0.1838 48590 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 116.49 Å2 / Biso mean: 20.9608 Å2 / Biso min: 6.9 Å2
Refinement stepCycle: final / Resolution: 1.64→48.171 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2678 0 76 458 3212
Biso mean--30.71 28.49 -
Num. residues----329
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6402-1.67830.25851320.22062940307296
1.6783-1.72030.21141400.213930933233100
1.7203-1.76680.23281400.218430943234100
1.7668-1.81880.22611400.204431003240100
1.8188-1.87750.21521390.219330953234100
1.8775-1.94460.41391260.34062794292090
1.9446-2.02250.21951400.195430843224100
2.0225-2.11450.23081410.189831333274100
2.1145-2.2260.21491380.17723059319799
2.226-2.36550.28371360.2293000313696
2.3655-2.54810.18141420.152631483290100
2.5481-2.80450.19451420.157231513293100
2.8045-3.21030.17541440.148531863330100
3.2103-4.04430.18751450.15393209335499
4.0443-48.19130.20951540.16533405355999

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