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- PDB-5fp3: Cell penetrant inhibitors of the JMJD2 (KDM4) and JARID1 (KDM5) f... -

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Basic information

Entry
Database: PDB / ID: 5fp3
TitleCell penetrant inhibitors of the JMJD2 (KDM4) and JARID1 (KDM5) families of histone lysine demethylases
ComponentsHUMAN LYSINE-SPECIFIC DEMETHYLASE 6B, JMJD3
KeywordsOXIDOREDUCTASE / INHIBITOR / JMJD3 / KDM6B / JUMONJI
Function / homology
Function and homology information


[histone H3]-trimethyl-L-lysine27 demethylase / histone H3K27me2/H3K27me3 demethylase activity / endothelial cell differentiation / cardiac muscle cell differentiation / MLL3/4 complex / inflammatory response to antigenic stimulus / mesodermal cell differentiation / histone demethylase activity / cell fate commitment / response to fungicide ...[histone H3]-trimethyl-L-lysine27 demethylase / histone H3K27me2/H3K27me3 demethylase activity / endothelial cell differentiation / cardiac muscle cell differentiation / MLL3/4 complex / inflammatory response to antigenic stimulus / mesodermal cell differentiation / histone demethylase activity / cell fate commitment / response to fungicide / Chromatin modifications during the maternal to zygotic transition (MZT) / hippocampus development / response to activity / HDMs demethylate histones / beta-catenin binding / chromatin DNA binding / cellular response to hydrogen peroxide / positive regulation of cold-induced thermogenesis / heart development / regulation of gene expression / Oxidative Stress Induced Senescence / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1370 / Cysteine Rich Protein - #20 / : / : / : / : / Lysine-specific demethylase 6/UTY, C-terminal helical domain / KDM6, GATA-like / Cysteine Rich Protein / Cupin ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1370 / Cysteine Rich Protein - #20 / : / : / : / : / Lysine-specific demethylase 6/UTY, C-terminal helical domain / KDM6, GATA-like / Cysteine Rich Protein / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Ribbon / Jelly Rolls / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / Chem-YC8 / Lysine-specific demethylase 6B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsChung, C.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Cell Penetrant Inhibitors of the Kdm4 and Kdm5 Families of Histone Lysine Demethylases. 1. 3-Amino-4-Pyridine Carboxylate Derivatives.
Authors: Westaway, S.M. / Preston, A.G.S. / Barker, M.D. / Brown, F. / Brown, J.A. / Campbell, M. / Chung, C. / Diallo, H. / Douault, C. / Drewes, G. / Eagle, R. / Gordon, L. / Haslam, C. / Hayhow, T. ...Authors: Westaway, S.M. / Preston, A.G.S. / Barker, M.D. / Brown, F. / Brown, J.A. / Campbell, M. / Chung, C. / Diallo, H. / Douault, C. / Drewes, G. / Eagle, R. / Gordon, L. / Haslam, C. / Hayhow, T.G. / Humphreys, P.G. / Joberty, G. / Katso, R. / Kruidenier, L. / Leveridge, M. / Liddle, J. / Mosley, J. / Muelbaier, M. / Randle, R. / Rioja, I. / Rueger, A. / Seal, G.A. / Sheppard, R.J. / Singh, O. / Taylor, J. / Thomas, P. / Thomson, D. / Wilson, D.M. / Lee, K. / Prinjha, R.K.
History
DepositionNov 27, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 2.0Mar 7, 2018Group: Atomic model / Derived calculations / Non-polymer description
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _chem_comp.formula / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr1_label_atom_id
Revision 3.0Oct 30, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 3.1May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_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_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HUMAN LYSINE-SPECIFIC DEMETHYLASE 6B, JMJD3
B: HUMAN LYSINE-SPECIFIC DEMETHYLASE 6B, JMJD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,66816
Polymers116,1012
Non-polymers1,56714
Water15,043835
1
A: HUMAN LYSINE-SPECIFIC DEMETHYLASE 6B, JMJD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8348
Polymers58,0501
Non-polymers7847
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HUMAN LYSINE-SPECIFIC DEMETHYLASE 6B, JMJD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8348
Polymers58,0501
Non-polymers7847
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.199, 65.552, 77.301
Angle α, β, γ (deg.)85.59, 67.65, 68.39
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein HUMAN LYSINE-SPECIFIC DEMETHYLASE 6B, JMJD3 / JMJC DOMAIN-CONTAINING PROTEIN 3 / JUMONJI DOMAIN-CONTAINING PROTEIN 3 / LYSINE DEMETHYLASE 6B / JMJD3


Mass: 58050.285 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, UNP RESIDUES 1141-1643
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: O15054, 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, 849 molecules

#2: Chemical ChemComp-YC8 / 3-(4-phenylbutanoylamino)pyridine-4-carboxylic acid


Mass: 284.310 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H16N2O3
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#6: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 835 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsC-TERMINAL PURIFICATION HIS6 TAG

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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: 2.29 Å3/Da / Density % sol: 46.3 % / Description: NONE
Crystal growpH: 8
Details: 0.1M TRIS HCL, BICINE PH 8.5, 37.5% MPD, PEG1K, PEG3350, 0.03M MGCL2, 0.03M CACL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Type: ESRF / Wavelength: 1.005
DetectorDate: Sep 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.005 Å / Relative weight: 1
ReflectionResolution: 2.05→40 Å / Num. obs: 61615 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.4
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 2 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.2 / % possible all: 90.3

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKLdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 2.05→71.3 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.912 / SU B: 10.109 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.23 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24322 2470 4 %RANDOM
Rwork0.20464 ---
obs0.20622 59141 95.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.083 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å2-2.17 Å2-1.27 Å2
2--1.89 Å23.03 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.05→71.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6836 0 94 835 7765
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.027189
X-RAY DIFFRACTIONr_bond_other_d0.0010.024813
X-RAY DIFFRACTIONr_angle_refined_deg0.8181.949792
X-RAY DIFFRACTIONr_angle_other_deg0.73311699
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4675873
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.37723.839336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.313151139
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.0361545
X-RAY DIFFRACTIONr_chiral_restr0.0470.21065
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0218029
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021526
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.053→2.106 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 158 -
Rwork0.275 3997 -
obs--86.85 %
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)
10.4391-0.18320.27810.0929-0.17410.3902-0.0056-0.01450.0167-0.00160.0116-0.007-0.0003-0.0177-0.0060.0664-0.0107-0.00120.0236-0.0270.03757.081616.8507-14.0377
20.4308-0.18580.25270.3706-0.26690.2537-0.00590.0158-0.0246-0.00830.0124-0.02710.0062-0.0167-0.00650.0514-0.00130.01840.0312-0.01850.050474.661646.341219.5202
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1177 - 1638
2X-RAY DIFFRACTION2B1180 - 1638

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