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- PDB-6f5r: Crystal Structure of KDM4D with GF028 ligand -

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Basic information

Entry
Database: PDB / ID: 6f5r
TitleCrystal Structure of KDM4D with GF028 ligand
ComponentsLysine-specific demethylase 4D
KeywordsOXIDOREDUCTASE / KDM4D / KDM4 ligand binding / ligand optimization / drug development / 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-CQZ / NICKEL (II) ION / Lysine-specific demethylase 4D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.607 Å
AuthorsMalecki, P.H. / Link, A. / Weiss, M.S. / Heinemann, U.
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
DepositionDec 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2018Provider: 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_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)38,85716
Polymers37,7511
Non-polymers1,10615
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-22 kcal/mol
Surface area15480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.149, 72.149, 152.392
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-755-

HOH

21A-815-

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: 37750.777 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 , 7 types, 341 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.: 9 / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-CQZ / 2-(3-oxidanylpropylamino)pyridine-4-carboxylic acid


Mass: 196.203 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12N2O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.63 Å3/Da / Density % sol: 53.17 %
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: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 31, 2017
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.6→48.378 Å / Num. obs: 99966 / % possible obs: 99.2 % / Redundancy: 5.643 % / Biso Wilson estimate: 26.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.094 / Χ2: 1.17 / Net I/σ(I): 12.54
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.75.4312.3450.64155460.2152.59495.6
1.7-1.825.6151.2121.37153100.5391.338100
1.82-1.965.1480.563.1142570.8420.62399.9
1.96-2.155.7130.2517.21130950.9690.276100
2.15-2.46.040.14412.83118800.990.158100
2.4-2.775.9760.09218.99104760.9960.101100
2.77-3.395.5970.05527.888330.9980.061100
3.39-4.795.5510.03343.7467950.9990.03699.5
4.79-48.3786.3460.0350.4237740.9990.03399.7

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Processing

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

6ets


Resolution: 1.607→29.412 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.89 / Phase error: 21.34
RfactorNum. reflection% reflection
Rfree0.1923 2094 2.1 %
Rwork0.1674 --
obs0.168 99820 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.35 Å2 / Biso mean: 32.3693 Å2 / Biso min: 16.64 Å2
Refinement stepCycle: final / Resolution: 1.607→29.412 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2663 0 63 342 3068
Biso mean--48.23 44.02 -
Num. residues----327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122894
X-RAY DIFFRACTIONf_angle_d1.1063924
X-RAY DIFFRACTIONf_chiral_restr0.066388
X-RAY DIFFRACTIONf_plane_restr0.007511
X-RAY DIFFRACTIONf_dihedral_angle_d14.6181075
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 (%)
1.6071-1.64450.42251320.39416396652898
1.6445-1.68560.33511410.345465036644100
1.6856-1.73120.35551380.297865586696100
1.7312-1.78210.26591430.271865056648100
1.7821-1.83960.23141400.252565366676100
1.8396-1.90530.2961390.228965276666100
1.9053-1.98160.20811420.18865146656100
1.9816-2.07180.2111430.163465306673100
2.0718-2.1810.18841340.14665436677100
2.181-2.31760.16511390.141765356674100
2.3176-2.49640.20451440.141565256669100
2.4964-2.74750.1761430.144665206663100
2.7475-3.14470.14781440.146565176661100
3.1447-3.96040.14771340.1446509664399
3.9604-29.41720.20461380.165165086646100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.72270.40710.01372.1205-0.43211.5094-0.01730.00020.01960.0987-0.0331-0.2041-0.17070.2070.05270.14890.00210.03650.2088-0.01160.18835.3512-1.6298-18.5173
21.8523-0.82011.43911.9897-0.39943.65240.03470.1321-0.154-0.086-0.042-0.01380.24540.08320.00410.1688-0.00640.01490.1453-0.02980.20361.3233-23.5525-23.4876
30.7894-0.6576-0.10870.710.090.597-0.068-0.11270.00640.13360.02890.0142-0.00860.03550.04470.1784-0.01030.00850.19850.00120.1672-1.9572-5.1055-10.3086
40.62350.26120.44970.85410.39451.3728-0.00710.04510.0269-0.0165-0.02050.0924-0.0398-0.05370.03170.1544-0.00170.01980.14990.00740.1543-7.1165-5.8484-24.0898
51.40951.3715-0.08185.67573.8573.7669-0.1002-0.0421-0.36630.30470.05170.1580.6849-0.25690.02140.2778-0.03330.03210.26250.00560.2925-22.0478-2.2403-9.661
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 82 )A11 - 82
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 131 )A83 - 131
3X-RAY DIFFRACTION3chain 'A' and (resid 132 through 194 )A132 - 194
4X-RAY DIFFRACTION4chain 'A' and (resid 195 through 306 )A195 - 306
5X-RAY DIFFRACTION5chain 'A' and (resid 307 through 337 )A307 - 337

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