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- PDB-5f5i: Crystal Structure of human JMJD2A complexed with KDOOA011340 -

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Basic information

Entry
Database: PDB / ID: 5f5i
TitleCrystal Structure of human JMJD2A complexed with KDOOA011340
ComponentsLysine-specific demethylase 4A
KeywordsOXIDOREDUCTASE / DOUBLE-STRANDED BETA HELIX / DEMETHYLASE / OXYGENASE / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / negative regulation of astrocyte differentiation / histone demethylase activity ...[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / negative regulation of astrocyte differentiation / histone demethylase activity / pericentric heterochromatin / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / methylated histone binding / positive regulation of neuron differentiation / response to nutrient levels / negative regulation of autophagy / HDMs demethylate histones / fibrillar center / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of gene expression / chromatin remodeling / negative regulation of gene expression / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / chromatin / positive regulation of gene expression / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / : / : / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / PHD-finger / PHD-zinc-finger like domain / JmjN domain ...: / : / : / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / PHD-finger / PHD-zinc-finger like domain / JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / 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-5V1 / NICKEL (II) ION / Lysine-specific demethylase 4A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.63 Å
AuthorsKrojer, T. / Vollmar, M. / Crawley, L. / Szykowska, A. / Gileadi, C. / Johansson, C. / England, K. / Yang, H. / Burgess-Brown, N. / Brennan, P. ...Krojer, T. / Vollmar, M. / Crawley, L. / Szykowska, A. / Gileadi, C. / Johansson, C. / England, K. / Yang, H. / Burgess-Brown, N. / Brennan, P. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Oppermann, U. / von Delft, F. / Structural Genomics Consortium (SGC)
CitationJournal: J.Med.Chem. / Year: 2016
Title: 8-Substituted Pyrido[3,4-d]pyrimidin-4(3H)-one Derivatives As Potent, Cell Permeable, KDM4 (JMJD2) and KDM5 (JARID1) Histone Lysine Demethylase Inhibitors.
Authors: Bavetsias, V. / Lanigan, R.M. / Ruda, G.F. / Atrash, B. / McLaughlin, M.G. / Tumber, A. / Mok, N.Y. / Le Bihan, Y.V. / Dempster, S. / Boxall, K.J. / Jeganathan, F. / Hatch, S.B. / Savitsky, ...Authors: Bavetsias, V. / Lanigan, R.M. / Ruda, G.F. / Atrash, B. / McLaughlin, M.G. / Tumber, A. / Mok, N.Y. / Le Bihan, Y.V. / Dempster, S. / Boxall, K.J. / Jeganathan, F. / Hatch, S.B. / Savitsky, P. / Velupillai, S. / Krojer, T. / England, K.S. / Sejberg, J. / Thai, C. / Donovan, A. / Pal, A. / Scozzafava, G. / Bennett, J.M. / Kawamura, A. / Johansson, C. / Szykowska, A. / Gileadi, C. / Burgess-Brown, N.A. / von Delft, F. / Oppermann, U. / Walters, Z. / Shipley, J. / Raynaud, F.I. / Westaway, S.M. / Prinjha, R.K. / Fedorov, O. / Burke, R. / Schofield, C.J. / Westwood, I.M. / Bountra, C. / Muller, S. / van Montfort, R.L. / Brennan, P.E. / Blagg, J.
History
DepositionDec 4, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2Sep 14, 2016Group: Structure summary
Revision 1.3Jan 10, 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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 4A
B: Lysine-specific demethylase 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,51110
Polymers84,5862
Non-polymers9258
Water2,738152
1
A: Lysine-specific demethylase 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7565
Polymers42,2931
Non-polymers4624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysine-specific demethylase 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7565
Polymers42,2931
Non-polymers4624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.030, 149.580, 57.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 0 / Auth seq-ID: 8 - 352 / Label seq-ID: 12 - 356

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 42293.090 Da / Num. of mol.: 2 / Fragment: Oxidoreductase-2OG
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM4A, JHDM3A, JMJD2, JMJD2A, KIAA0677 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli)
References: UniProt: O75164, 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 , 5 types, 160 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-5V1 / 2-[[(phenylmethyl)amino]methyl]pyridine-4-carboxylic acid


Mass: 242.273 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H14N2O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.59 Å3/Da / Density % sol: 52.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 0.1M bis-tris pH 5.9 , 0.15M ammonium sulfate , 13% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.63→54.01 Å / Num. obs: 26629 / % possible obs: 99.2 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.043 / Net I/σ(I): 15.5 / Num. measured all: 176830
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.63-2.76.90.9072.31320919130.7280.36899.8
11.76-54.015.90.02852.6210835510.01398.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.1.29data scaling
REFMAC5.8.0131refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OQ7

2oq7


Resolution: 2.63→54.01 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.912 / SU B: 23.827 / SU ML: 0.256 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.922 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2433 1157 4.4 %RANDOM
Rwork0.2109 ---
obs0.2124 25432 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 124.95 Å2 / Biso mean: 53.513 Å2 / Biso min: 22.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å2-0 Å2
2---0.19 Å20 Å2
3---0.07 Å2
Refinement stepCycle: final / Resolution: 2.63→54.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5592 0 50 152 5794
Biso mean--60.81 38.79 -
Num. residues----689
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195832
X-RAY DIFFRACTIONr_bond_other_d0.0030.025320
X-RAY DIFFRACTIONr_angle_refined_deg1.2121.9377915
X-RAY DIFFRACTIONr_angle_other_deg1.0062.9912239
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9555692
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.11923.179280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.67415937
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8351537
X-RAY DIFFRACTIONr_chiral_restr0.0720.2812
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216586
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021453
X-RAY DIFFRACTIONr_mcbond_it0.832.7872762
X-RAY DIFFRACTIONr_mcbond_other0.832.7862761
X-RAY DIFFRACTIONr_mcangle_it1.5154.1733450
Refine LS restraints NCS

Ens-ID: 1 / Number: 39844 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.63→2.698 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 78 -
Rwork0.325 1830 -
all-1908 -
obs--99.43 %
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)
15.63083.31050.78352.00720.18271.58690.17030.37310.5079-0.03730.2790.44310.5969-0.486-0.44940.3393-0.0553-0.35510.39990.0070.4852-44.806-27.3364-31.3785
21.189-0.40910.46671.0765-0.13910.67370.33580.37160.0001-0.214-0.4176-0.0560.23460.27080.08180.17440.12190.08070.32360.07250.2429-25.949-21.3644-30.9631
33.4259-0.88021.01652.2329-0.03681.86120.40080.63110.06730.0397-0.423-0.3430.36580.52040.02220.14010.15230.09260.3580.12140.2831-12.9588-28.0045-26.191
42.1175-0.71330.57170.3934-0.24110.51780.13310.33370.232-0.1346-0.2471-0.0341-0.05580.2940.1140.13420.05020.06140.27040.05740.3409-27.7742-15.2021-26.7822
51.4773-0.95170.86970.7265-0.7921.50740.17650.1559-0.0683-0.0609-0.20610.0830.0370.0960.02960.1705-0.00160.05160.2151-0.03790.3404-29.4088-27.4539-18.6434
61.622-0.74891.7321.96790.28233.25890.0034-0.17350.16560.0868-0.05030.1074-0.1894-0.18450.04690.1252-0.01630.030.1409-0.06330.366-38.7667-14.1957-12.8146
70.9497-1.0574-0.78834.27691.65264.37350.0418-0.02660.14140.1601-0.16370.1565-0.0419-0.60930.12190.0320.03520.06040.2375-0.04130.4017-50.8569-14.0844-12.5441
81.61530.6245-0.522.3999-1.18681.76840.03480.12460.2413-0.4262-0.0512-0.4420.5265-0.0790.01650.3312-0.05840.05060.07970.01540.25-33.1923-55.0168-8.1817
92.2059-0.5798-2.05771.37-0.47144.3113-0.31470.09960.3622-0.16720.6959-0.13530.7129-1.082-0.38120.1545-0.2371-0.11420.54490.05790.1867-51.2125-53.3822-0.8723
100.69450.1841-0.74610.5892-0.76021.5694-0.1472-0.08680.0926-0.150.2351-0.17560.287-0.2229-0.08790.1955-0.1034-0.08680.177-0.0110.3628-38.8067-54.47414.6202
111.58080.6955-0.40660.5269-0.23581.6706-0.097-0.09470.1092-0.1240.1397-0.04190.1307-0.2061-0.04270.1668-0.0614-0.05990.21370.01330.3211-40.7431-48.61256.5611
122.0903-1.96571.47281.8702-1.39761.14170.0469-0.02730.0334-0.0636-0.0327-0.12840.15820.048-0.01420.13740.0401-0.04590.14440.09640.5839-23.1085-61.934112.9247
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 36
2X-RAY DIFFRACTION2A37 - 78
3X-RAY DIFFRACTION3A79 - 124
4X-RAY DIFFRACTION4A125 - 190
5X-RAY DIFFRACTION5A191 - 291
6X-RAY DIFFRACTION6A292 - 317
7X-RAY DIFFRACTION7A318 - 352
8X-RAY DIFFRACTION8B8 - 70
9X-RAY DIFFRACTION9B71 - 155
10X-RAY DIFFRACTION10B156 - 226
11X-RAY DIFFRACTION11B227 - 291
12X-RAY DIFFRACTION12B292 - 353

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