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- PDB-6kgo: LSD1-S2157 five-membered ring adduct model -

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Basic information

Entry
Database: PDB / ID: 6kgo
TitleLSD1-S2157 five-membered ring adduct model
ComponentsLysine-specific histone demethylase 1A
KeywordsOXIDOREDUCTASE / DEMETHYLASE / AMINE OXIDASE / CHROMATIN / HISTONE / FAD / MECHANISM-BASED INHIBITOR
Function / homology
Function and homology information


guanine metabolic process / negative regulation of transcription initiation-coupled chromatin remodeling / protein demethylase activity / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / neuron maturation / muscle cell development / positive regulation of neural precursor cell proliferation ...guanine metabolic process / negative regulation of transcription initiation-coupled chromatin remodeling / protein demethylase activity / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / neuron maturation / muscle cell development / positive regulation of neural precursor cell proliferation / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / MRF binding / regulation of androgen receptor signaling pathway / DNA repair complex / nuclear androgen receptor binding / regulation of double-strand break repair via homologous recombination / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of neuroblast proliferation / DNA repair-dependent chromatin remodeling / positive regulation of stem cell proliferation / histone H3K9 demethylase activity / negative regulation of DNA damage response, signal transduction by p53 class mediator / histone methyltransferase complex / histone demethylase activity / positive regulation of cell size / positive regulation of epithelial to mesenchymal transition / response to fungicide / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / cellular response to cAMP / epigenetic regulation of gene expression / positive regulation of protein ubiquitination / Regulation of PTEN gene transcription / HDACs deacetylate histones / promoter-specific chromatin binding / cellular response to gamma radiation / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / positive regulation of neuron projection development / HDMs demethylate histones / cerebral cortex development / protein modification process / cellular response to UV / p53 binding / transcription corepressor activity / flavin adenine dinucleotide binding / regulation of protein localization / positive regulation of cold-induced thermogenesis / Factors involved in megakaryocyte development and platelet production / transcription regulator complex / DNA-binding transcription factor binding / Estrogen-dependent gene expression / Potential therapeutics for SARS / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / chromosome, telomeric region / oxidoreductase activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Histone lysine-specific demethylase / ATP synthase, gamma subunit, helix hairpin domain / SWIRM domain / SWIRM domain / SWIRM domain profile. / : / Amine oxidase / Flavin containing amine oxidoreductase / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Homeobox-like domain superfamily ...Histone lysine-specific demethylase / ATP synthase, gamma subunit, helix hairpin domain / SWIRM domain / SWIRM domain / SWIRM domain profile. / : / Amine oxidase / Flavin containing amine oxidoreductase / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Homeobox-like domain superfamily / FAD/NAD(P)-binding domain superfamily / Helix Hairpins / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-DJ0 / FLAVIN-ADENINE DINUCLEOTIDE / L(+)-TARTARIC ACID / Lysine-specific histone demethylase 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsNiwa, H. / Sato, S. / Umehara, T.
CitationJournal: Chemmedchem / Year: 2020
Title: Development and Structural Evaluation of N-Alkylated trans-2-Phenylcyclopropylamine-Based LSD1 Inhibitors.
Authors: Niwa, H. / Sato, S. / Handa, N. / Sengoku, T. / Umehara, T. / Yokoyama, S.
History
DepositionJul 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysine-specific histone demethylase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,09810
Polymers74,3331
Non-polymers1,7649
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-10 kcal/mol
Surface area29910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.703, 185.703, 108.500
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lysine-specific histone demethylase 1A / BRAF35-HDAC complex protein BHC110 / Flavin-containing amine oxidase domain-containing protein 2


Mass: 74333.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / Source: (gene. exp.) Homo sapiens (human) / Gene: KDM1A, AOF2, KDM1, KIAA0601, LSD1 / Plasmid: PETDUET-1 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2(DE3) / References: UniProt: O60341, Oxidoreductases

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Non-polymers , 5 types, 199 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-DJ0 / 3-[3,5-bis(fluoranyl)-2-phenylmethoxy-phenyl]propanal


Mass: 276.278 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C16H14F2O2
#5: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C27H33N9O15P2 / Comment: FAD*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Nonpolymer details6KGO and 6KGP use the same data but have ligand models with possible different configurations.

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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: 3.75 Å3/Da / Density % sol: 67.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M MES (pH 6.2-6.3), 0.2M diammonium tartrate, 0.0005M TCEP, 10% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→48.06 Å / Num. obs: 52531 / % possible obs: 100 % / Redundancy: 14.8 % / Biso Wilson estimate: 46.81 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.028 / Rrim(I) all: 0.11 / Rsym value: 0.107 / Net I/σ(I): 22.5
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 14.9 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4503 / CC1/2: 0.773 / Rpim(I) all: 0.653 / Rrim(I) all: 2.56 / Rsym value: 2.474 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.13_2998+SVNrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→44.6 Å / SU ML: 0.2877 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.3751
RfactorNum. reflection% reflection
Rfree0.2043 5004 5.04 %
Rwork0.1733 --
obs0.1749 52484 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 63.15 Å2
Refinement stepCycle: LAST / Resolution: 2.25→44.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5066 0 119 190 5375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00725304
X-RAY DIFFRACTIONf_angle_d0.87257194
X-RAY DIFFRACTIONf_chiral_restr0.0568802
X-RAY DIFFRACTIONf_plane_restr0.0056963
X-RAY DIFFRACTIONf_dihedral_angle_d13.86373210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.280.37161810.32423111X-RAY DIFFRACTION99.76
2.28-2.30.34351660.30943138X-RAY DIFFRACTION99.73
2.3-2.330.36111500.30173169X-RAY DIFFRACTION99.94
2.33-2.360.32741820.28933152X-RAY DIFFRACTION99.94
2.36-2.390.31421960.273097X-RAY DIFFRACTION99.94
2.39-2.420.30781660.26263140X-RAY DIFFRACTION99.94
2.42-2.460.33441370.2573152X-RAY DIFFRACTION99.91
2.46-2.50.27091680.2453139X-RAY DIFFRACTION99.85
2.5-2.530.28221760.23653158X-RAY DIFFRACTION100
2.53-2.580.311230.23143172X-RAY DIFFRACTION99.91
2.58-2.620.27031980.2133134X-RAY DIFFRACTION99.97
2.62-2.670.24931780.21133097X-RAY DIFFRACTION100
2.67-2.720.26561360.2033201X-RAY DIFFRACTION100
2.72-2.770.24161470.19633150X-RAY DIFFRACTION99.94
2.77-2.830.191430.19083158X-RAY DIFFRACTION100
2.83-2.90.251490.19283165X-RAY DIFFRACTION100
2.9-2.970.22141780.19863125X-RAY DIFFRACTION100
2.97-3.050.23381410.20493172X-RAY DIFFRACTION100
3.05-3.140.26061800.1883144X-RAY DIFFRACTION100
3.14-3.240.22541970.18663106X-RAY DIFFRACTION100
3.24-3.360.23231570.17393169X-RAY DIFFRACTION99.97
3.36-3.50.22161560.17333140X-RAY DIFFRACTION100
3.5-3.650.17271920.17013125X-RAY DIFFRACTION99.97
3.65-3.850.21441570.15643149X-RAY DIFFRACTION100
3.85-4.090.18441690.13653133X-RAY DIFFRACTION100
4.09-4.40.14332060.13263128X-RAY DIFFRACTION99.91
4.4-4.850.1641890.12853103X-RAY DIFFRACTION99.91
4.85-5.550.1481780.14513123X-RAY DIFFRACTION99.91
5.55-6.980.19821780.15983135X-RAY DIFFRACTION99.76
6.98-44.60.1341300.13933155X-RAY DIFFRACTION98.8
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)
11.90551414137-1.47241323539-0.4219319798642.921792958860.3364507639710.959690838249-0.05689046762780.07198870899320.045663724630.1958397769550.0711263496854-0.30995558650.1512645725460.167847139978-0.01591454466680.428449614003-0.052385512529-0.03222878451790.384104557698-0.02442589131710.32077304559144.480689270838.1676557591-22.2185238375
20.5336338840630.6301120999380.6028744449264.482786406675.7914643397.06379859580.088016526255-0.1239060173430.272111939249-0.02212263138190.160902224333-0.179300278691-0.5812282636640.54982846501-0.169187048590.897486155308-0.178188488430.02495864160470.571073366703-0.09279162688990.6019961439735.328160899881.794755067729.5215371601
31.1560234079-0.4481671690120.03715887725522.182246123810.7420197529972.089021203580.0167049379278-0.0206075891989-0.03095803830080.206688250751-0.02602960711590.06940964416140.0815507225185-0.1841598733670.004879998960630.320696320565-0.08256207443620.01623971096150.352575969584-0.006506564698620.29809820595125.579184080247.2819014622-14.5271459989
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 172 through 371 )
2X-RAY DIFFRACTION2chain 'A' and (resid 372 through 513 )
3X-RAY DIFFRACTION3chain 'A' and (resid 514 through 832 )

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