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- PDB-6h11: Crystal Structure of KDM4D with tetrazolylhydrazide ligand AA028 -

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Basic information

Entry
Database: PDB / ID: 6h11
TitleCrystal Structure of KDM4D with tetrazolylhydrazide ligand AA028
ComponentsLysine-specific demethylase 4D
KeywordsOXIDOREDUCTASE / KDM4D / ligand binding / Tetrazolylhydrazide / tetrazole / inhibitor design / cancer / epigenetics / fragment screening
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-FHT / NICKEL (II) ION / Lysine-specific demethylase 4D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.516 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)40,30310
Polymers39,4921
Non-polymers8119
Water7,945441
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-8 kcal/mol
Surface area14870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.928, 71.928, 151.178
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-911-

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, 450 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.: 5 / 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-FHT / [[(2~{R})-2-[(4-bromophenyl)carbonylamino]-2-(2~{H}-1,2,3,4-tetrazol-5-yl)ethanoyl]amino]azanium


Mass: 341.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H11BrN7O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / 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: 2.58 Å3/Da / Density % sol: 52.24 %
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 20, 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: 1.51→48.206 Å / Num. obs: 114697 / % possible obs: 97.3 % / Redundancy: 6.71 % / Biso Wilson estimate: 12.22 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.108 / Χ2: 1.524 / Net I/σ(I): 16.55
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.51-1.616.7630.8952.12188430.7610.96998.8
1.61-1.726.3540.6182.93179100.8180.674100
1.72-1.857.1760.3775.12166490.9410.406100
1.85-2.036.620.210.25135910.9870.21888.6
2.03-2.276.2720.13315.48129560.9930.14693.4
2.27-2.626.5870.0821.59121400.9960.08799.4
2.62-3.217.3110.04736.79103190.9990.05199.6
3.21-4.536.2840.03154.4678690.9990.03498.6
4.53-48.2067.4230.0270.34442010.02199.9

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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: 1.516→42.198 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.87 / Phase error: 22.51
RfactorNum. reflection% reflection
Rfree0.2223 2067 1.83 %
Rwork0.1911 --
obs0.1917 113080 96.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.84 Å2 / Biso mean: 19.7206 Å2 / Biso min: 5.26 Å2
Refinement stepCycle: final / Resolution: 1.516→42.198 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2678 0 84 469 3231
Biso mean--31.96 32.7 -
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 (%)
1.5163-1.55160.40091150.40866389650483
1.5516-1.59040.22351450.237676977842100
1.5904-1.63340.28371440.214876947838100
1.6334-1.68140.2881430.21276827825100
1.6814-1.73570.22011390.193176927831100
1.7357-1.79770.20311430.170576987841100
1.7977-1.86970.21251430.172276517794100
1.8697-1.95480.47731180.36266066618479
1.9548-2.05790.20771350.1887435757097
2.0579-2.18680.25291330.19557469760297
2.1868-2.35560.30011300.23266920705090
2.3556-2.59270.16451450.146277097854100
2.5927-2.96780.18671420.14887640778299
2.9678-3.73870.15721440.14767651779599
3.7387-42.21410.17021480.16467620776899

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