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- PDB-6bgv: LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR 2-((2-chlorophenyl... -

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Basic information

Entry
Database: PDB / ID: 6bgv
TitleLINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR 2-((2-chlorophenyl)(2-(piperidin-1-yl)ethoxy)methyl)-1l2-pyrrolo[3,2-b]pyridine-7-carboxylic acid (Compound N40)
ComponentsLysine-specific demethylase 5A, linked KDM5A JMJ domain
KeywordsOXIDOREDUCTASE/INHIBITOR / DEMETHYLASE INHIBITION / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR COMPLEX / OXIDOREDUCTASE / OXIDOREDUCTASE-INHIBITOR complex
Function / homology
Function and homology information


[histone H3]-trimethyl-L-lysine4 demethylase / facultative heterochromatin formation / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / enzyme inhibitor activity / regulation of DNA-binding transcription factor activity / histone demethylase activity / methylated histone binding / Chromatin modifications during the maternal to zygotic transition (MZT) / circadian regulation of gene expression / HDMs demethylate histones ...[histone H3]-trimethyl-L-lysine4 demethylase / facultative heterochromatin formation / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / enzyme inhibitor activity / regulation of DNA-binding transcription factor activity / histone demethylase activity / methylated histone binding / Chromatin modifications during the maternal to zygotic transition (MZT) / circadian regulation of gene expression / HDMs demethylate histones / chromatin DNA binding / histone binding / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / chromatin / nucleolus / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
: / : / : / : / : / Lysine-specific demethylase 5, C-terminal helical domain / Lysine-specific demethylase-like domain / PLU-1-like protein / Zinc finger, C5HC2-type / C5HC2 zinc finger ...: / : / : / : / : / Lysine-specific demethylase 5, C-terminal helical domain / Lysine-specific demethylase-like domain / PLU-1-like protein / Zinc finger, C5HC2-type / C5HC2 zinc finger / ARID/BRIGHT DNA binding domain / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain / 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. / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-DQG / : / Lysine-specific demethylase 5A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.592 Å
AuthorsHorton, J.R. / Cheng, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245-23 United States
Citation
Journal: J. Med. Chem. / Year: 2018
Title: Insights into the Action of Inhibitor Enantiomers against Histone Lysine Demethylase 5A.
Authors: Horton, J.R. / Liu, X. / Wu, L. / Zhang, K. / Shanks, J. / Zhang, X. / Rai, G. / Mott, B.T. / Jansen, D.J. / Kales, S.C. / Henderson, M.J. / Pohida, K. / Fang, Y. / Hu, X. / Jadhav, A. / ...Authors: Horton, J.R. / Liu, X. / Wu, L. / Zhang, K. / Shanks, J. / Zhang, X. / Rai, G. / Mott, B.T. / Jansen, D.J. / Kales, S.C. / Henderson, M.J. / Pohida, K. / Fang, Y. / Hu, X. / Jadhav, A. / Maloney, D.J. / Hall, M.D. / Simeonov, A. / Fu, H. / Vertino, P.M. / Yan, Q. / Cheng, X.
#1: Journal: Cell Chem Biol / Year: 2016
Title: Structural Basis for KDM5A Histone Lysine Demethylase Inhibition by Diverse Compounds.
Authors: Horton, J.R. / Liu, X. / Gale, M. / Wu, L. / Shanks, J.R. / Zhang, X. / Webber, P.J. / Bell, J.S. / Kales, S.C. / Mott, B.T. / Rai, G. / Jansen, D.J. / Henderson, M.J. / Urban, D.J. / Hall, ...Authors: Horton, J.R. / Liu, X. / Gale, M. / Wu, L. / Shanks, J.R. / Zhang, X. / Webber, P.J. / Bell, J.S. / Kales, S.C. / Mott, B.T. / Rai, G. / Jansen, D.J. / Henderson, M.J. / Urban, D.J. / Hall, M.D. / Simeonov, A. / Maloney, D.J. / Johns, M.A. / Fu, H. / Jadhav, A. / Vertino, P.M. / Yan, Q. / Cheng, X.
#2: Journal: J. Biol. Chem. / Year: 2016
Title: Characterization of a Linked Jumonji Domain of the KDM5/JARID1 Family of Histone H3 Lysine 4 Demethylases.
Authors: Horton, J.R. / Engstrom, A. / Zoeller, E.L. / Liu, X. / Shanks, J.R. / Zhang, X. / Johns, M.A. / Vertino, P.M. / Fu, H. / Cheng, X.
History
DepositionOct 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysine-specific demethylase 5A, linked KDM5A JMJ domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,18713
Polymers37,9451
Non-polymers1,24212
Water4,360242
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint7 kcal/mol
Surface area15150 Å2
Unit cell
Length a, b, c (Å)116.289, 61.883, 46.735
Angle α, β, γ (deg.)90.00, 92.32, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-910-

HOH

21A-915-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lysine-specific demethylase 5A, linked KDM5A JMJ domain / Histone demethylase JARID1A / Jumonji/ARID domain-containing protein 1A / Retinoblastoma-binding ...Histone demethylase JARID1A / Jumonji/ARID domain-containing protein 1A / Retinoblastoma-binding protein 2 / RBBP-2


Mass: 37944.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM5A, JARID1A, RBBP2, RBP2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): Gold C-PLUS
References: UniProt: P29375, 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, 254 molecules

#2: Chemical ChemComp-DQG / 2-{(S)-(2-chlorophenyl)[2-(piperidin-1-yl)ethoxy]methyl}-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid


Mass: 413.897 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H24ClN3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.21 Å3/Da / Density % sol: 44.45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2), 0-20% glycerol, 25 mM (Na/K) dibasic/monobasic phosphate
PH range: 8.6-9.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Dec 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.59→30.942 Å / Num. obs: 43550 / % possible obs: 98.4 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.061 / Net I/σ(I): 15
Reflection shellResolution: 1.59→1.65 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.743 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 4247 / CC1/2: 0.645 / Rpim(I) all: 0.408 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIXdev_2863refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E6H

5e6h


Resolution: 1.592→30.942 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.184 2014 4.62 %
Rwork0.1677 --
obs0.1685 43547 97.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.592→30.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2425 0 78 242 2745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022606
X-RAY DIFFRACTIONf_angle_d0.5543555
X-RAY DIFFRACTIONf_dihedral_angle_d10.5751496
X-RAY DIFFRACTIONf_chiral_restr0.046366
X-RAY DIFFRACTIONf_plane_restr0.005461
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5922-1.63210.24591440.22152680X-RAY DIFFRACTION90
1.6321-1.67620.23761340.21442946X-RAY DIFFRACTION97
1.6762-1.72550.22061390.19742958X-RAY DIFFRACTION98
1.7255-1.78120.22051450.19392932X-RAY DIFFRACTION98
1.7812-1.84480.18641420.17532958X-RAY DIFFRACTION98
1.8448-1.91870.18351500.17042930X-RAY DIFFRACTION98
1.9187-2.0060.20711420.17063005X-RAY DIFFRACTION98
2.006-2.11170.17511430.16492968X-RAY DIFFRACTION99
2.1117-2.2440.20491500.16092988X-RAY DIFFRACTION99
2.244-2.41720.17541390.16053001X-RAY DIFFRACTION99
2.4172-2.66030.19491450.17673007X-RAY DIFFRACTION99
2.6603-3.0450.18351410.17053016X-RAY DIFFRACTION99
3.045-3.83530.18361440.15143053X-RAY DIFFRACTION100
3.8353-30.94730.14931560.15763091X-RAY DIFFRACTION100
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)
15.272-0.072-0.21141.59320.26931.3619-0.0532-0.0486-0.00510.16150.096-0.28080.20140.2152-0.04960.15550.0226-0.01870.12070.00140.1813-18.25222.68768.6108
27.24362.8193-0.6482.45370.19061.71070.10490.3301-0.1543-0.17420.0394-0.1792-0.05840.1463-0.10170.1517-0.0059-0.00230.1415-0.01190.1703-15.61371.9371-2.1845
31.2809-0.4702-0.14361.72080.38030.60590.0256-0.11530.10610.05390.0241-0.3123-0.11060.1259-0.04150.1581-0.0309-0.02730.16030.01680.1446-14.866219.524212.5575
40.6945-0.485-0.54652.2306-0.2460.8242-0.0215-0.12070.8046-0.1932-0.19790.2271-0.6217-0.22970.11640.36490.0526-0.03880.3257-0.03640.4577-41.104331.042611.3888
53.43662.3112-0.91424.2046-1.30842.15440.0139-0.30820.09690.4754-0.0488-0.0801-0.28120.04690.01650.23360.0195-0.01430.1344-0.02120.1022-25.361226.031423.7078
60.54020.85640.5791.44620.67262.8548-0.0026-0.17360.06090.2345-0.09980.12120.25-0.36790.07430.1757-0.00790.06240.1724-0.00140.1411-35.420915.451120.7839
72.9135-0.7896-0.30410.79260.33750.2879-0.0985-0.10250.49480.09310.1898-0.3727-0.15560.3198-0.08440.1784-0.04410.00010.2764-0.03430.2561-7.5924.044910.2087
81.0432-0.35530.63231.20170.33910.71760.04840.25440.0485-0.1425-0.0241-0.1572-0.16990.2108-0.03360.141-0.02210.02260.15070.02660.1155-16.873619.7538-0.4741
91.17720.25790.53620.41420.80561.6643-0.03630.01840.03280.004-0.0034-0.0099-0.08410.07210.05530.1064-0.0020.00110.07210.01580.0969-20.933613.97725.5467
100.6964-0.70480.07621.2453-0.49560.23920.07260.1834-0.0573-0.1053-0.11620.2977-0.1012-0.19120.03540.21060.0192-0.00180.2215-0.02210.2267-38.083416.4443-3.2548
110.97990.11520.20461.24760.62221.53230.00830.01-0.06290.0196-0.01160.00840.0177-0.0420.00310.09440.00120.00740.0760.01140.0916-24.90511.35495.6883
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 46 )
3X-RAY DIFFRACTION3chain 'A' and (resid 47 through 76 )
4X-RAY DIFFRACTION4chain 'A' and (resid 77 through 359 )
5X-RAY DIFFRACTION5chain 'A' and (resid 360 through 378 )
6X-RAY DIFFRACTION6chain 'A' and (resid 379 through 405 )
7X-RAY DIFFRACTION7chain 'A' and (resid 406 through 440 )
8X-RAY DIFFRACTION8chain 'A' and (resid 441 through 485 )
9X-RAY DIFFRACTION9chain 'A' and (resid 486 through 507 )
10X-RAY DIFFRACTION10chain 'A' and (resid 508 through 541 )
11X-RAY DIFFRACTION11chain 'A' and (resid 542 through 588 )

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