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- PDB-5kr7: KDM4C bound to pyrazolo-pyrimidine scaffold -

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Basic information

Entry
Database: PDB / ID: 5kr7
TitleKDM4C bound to pyrazolo-pyrimidine scaffold
ComponentsLysine-specific demethylase 4CKDM4C
KeywordsOXIDOREDUCTASE / inhibitor / histone / lysine demethylase
Function / homology
Function and homology information


H3K9me3 modified histone binding / histone H3K36 demethylase activity / regulation of stem cell differentiation / blastocyst formation / regulation of androgen receptor signaling pathway / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / nuclear androgen receptor binding / stem cell population maintenance / androgen receptor signaling pathway ...H3K9me3 modified histone binding / histone H3K36 demethylase activity / regulation of stem cell differentiation / blastocyst formation / regulation of androgen receptor signaling pathway / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / nuclear androgen receptor binding / stem cell population maintenance / androgen receptor signaling pathway / histone H3K9 demethylase activity / histone demethylase activity / pericentric heterochromatin / nuclear receptor coactivator activity / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / regulation of gene expression / chromatin remodeling / positive regulation of cell population proliferation / chromatin / enzyme binding / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
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 / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors ...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-6X9 / : / Lysine-specific demethylase 4C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBellon, S.F. / Poy, F. / Setser, J.W.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2016
Title: Identification of potent, selective KDM5 inhibitors.
Authors: Gehling, V.S. / Bellon, S.F. / Harmange, J.C. / LeBlanc, Y. / Poy, F. / Odate, S. / Buker, S. / Lan, F. / Arora, S. / Williamson, K.E. / Sandy, P. / Cummings, R.T. / Bailey, C.M. / Bergeron, ...Authors: Gehling, V.S. / Bellon, S.F. / Harmange, J.C. / LeBlanc, Y. / Poy, F. / Odate, S. / Buker, S. / Lan, F. / Arora, S. / Williamson, K.E. / Sandy, P. / Cummings, R.T. / Bailey, C.M. / Bergeron, L. / Mao, W. / Gustafson, A. / Liu, Y. / VanderPorten, E. / Audia, J.E. / Trojer, P. / Albrecht, B.K.
History
DepositionJul 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 1.2Oct 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _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 / _pdbx_struct_oper_list.symmetry_operation / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysine-specific demethylase 4C
B: Lysine-specific demethylase 4C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,42010
Polymers84,6752
Non-polymers7468
Water7,476415
1
A: Lysine-specific demethylase 4C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7105
Polymers42,3371
Non-polymers3734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lysine-specific demethylase 4C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7105
Polymers42,3371
Non-polymers3734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.817, 89.876, 100.011
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Lysine-specific demethylase 4C / KDM4C / Gene amplified in squamous cell carcinoma 1 protein / GASC-1 protein / JmjC domain-containing ...Gene amplified in squamous cell carcinoma 1 protein / GASC-1 protein / JmjC domain-containing histone demethylation protein 3C / Jumonji domain-containing protein 2C


Mass: 42337.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM4C, GASC1, JHDM3C, JMJD2C, KIAA0780 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H3R0, 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, 423 molecules

#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-6X9 / 6-ethyl-2,5-dimethyl-7-oxidanylidene-4~{H}-pyrazolo[1,5-a]pyrimidine-3-carbonitrile


Mass: 216.239 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N4O
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.55 Å3/Da / Density % sol: 51.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10-15% PEG 3350 0.2 magnesium chloride 0.1 HEPES pH 7.5
Temp details: cold room

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 4, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→66.82 Å / Num. obs: 64012 / % possible obs: 99.2 % / Redundancy: 4 % / Rsym value: 0.105 / Net I/σ(I): 13.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
PDB_EXTRACT3.2data extraction
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3dxu

3dxu


Resolution: 1.9→66.82 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / SU B: 7.893 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.143
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2339 3241 5.1 %RANDOM
Rwork0.1924 ---
obs0.1945 60706 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 117.3 Å2 / Biso mean: 26.056 Å2 / Biso min: 9.61 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0 Å2
2--0.58 Å2-0 Å2
3----0.58 Å2
Refinement stepCycle: final / Resolution: 1.9→66.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5565 0 38 415 6018
Biso mean--19.81 30.78 -
Num. residues----679
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195777
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.9517806
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5765677
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.78223.741278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.71215979
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0361530
X-RAY DIFFRACTIONr_chiral_restr0.1250.2792
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.0214448
X-RAY DIFFRACTIONr_mcbond_it2.4031.4972714
X-RAY DIFFRACTIONr_mcangle_it3.5552.2273389
X-RAY DIFFRACTIONr_scbond_it4.1381.8573063
LS refinement shellResolution: 1.899→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 243 -
Rwork0.3 4217 -
all-4460 -
obs--94.39 %
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)
10.35260.0874-0.16330.0829-0.13540.3688-0.0301-0.0263-0.0361-0.0097-0.0001-0.029-0.0335-0.0430.03020.0210.00530.01010.22980.00270.012427.373243.432512.3616
20.37560.0935-0.17590.0844-0.13520.3771-0.0233-0.0145-0.0114-0.0020.0039-0.0155-0.0259-0.01960.01930.01930.00670.00370.22940.00640.00427.4233-1.186-18.1162
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 349
2X-RAY DIFFRACTION2B10 - 348

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