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- PDB-5fpb: Crystal structure of human KDM4D in complex with 2-1H-pyrazol-4-y... -

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Basic information

Entry
Database: PDB / ID: 5fpb
TitleCrystal structure of human KDM4D in complex with 2-1H-pyrazol-4-yloxy- 3H,4H-pyrido-3,4-d-pyrimidin-4-one
ComponentsLYSINE-SPECIFIC DEMETHYLASE 4D
KeywordsOXIDOREDUCTASE / INHIBITOR / LYSINE SPECIFIC HISTONE DEMETHYLASE / JMJD2D / KDM4D / JUMONJI
Function / homology
Function and homology information


immune system process / plasma membrane
Similarity search - Function
: / jmjN domain / Cupin / JmjC domain, hydroxylase / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Jelly Rolls ...: / jmjN domain / Cupin / JmjC domain, hydroxylase / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Jelly Rolls / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Chem-HA6 / T cell receptor beta variable 9
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.91 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 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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.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: LYSINE-SPECIFIC DEMETHYLASE 4D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,56111
Polymers38,5351
Non-polymers1,02610
Water8,503472
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.180, 71.180, 150.788
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1347-

SO4

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Components

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Protein , 1 types, 1 molecules A

#1: Protein LYSINE-SPECIFIC DEMETHYLASE 4D / JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3D / JU MONJI DOMAIN-CONTAINING PROTEIN 2D / ...JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3D / JU MONJI DOMAIN-CONTAINING PROTEIN 2D / HUMAN LYSINE-SPECIFIC DEMETHYL ASE 4D / JMJD2D


Mass: 38534.633 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 11-341
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q6B0I6, 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, 482 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-HA6 / 2-(1H-pyrazol-4-yloxy)-3H-pyrido[3,4-d]pyrimidin-4-one


Mass: 229.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H7N5O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 472 / 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: 2.48 Å3/Da / Density % sol: 50.37 % / Description: NONE
Crystal growpH: 7.4 / Details: 0.1M HEPES PH 7.4, 2.45M AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Feb 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.91→41.86 Å / Num. obs: 30844 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.8
Reflection shellResolution: 1.91→2.01 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.9 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 1.91→31.15 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.879 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20319 1550 5 %RANDOM
Rwork0.16035 ---
obs0.16243 29158 99.3 %-
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: 25.725 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å20 Å2
2--0.51 Å20 Å2
3----1.03 Å2
Refinement stepCycle: LAST / Resolution: 1.91→31.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2682 0 54 472 3208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0192898
X-RAY DIFFRACTIONr_bond_other_d0.0010.022643
X-RAY DIFFRACTIONr_angle_refined_deg1.0091.9453949
X-RAY DIFFRACTIONr_angle_other_deg0.71236094
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3675357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85623.63146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.27515477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0881518
X-RAY DIFFRACTIONr_chiral_restr0.0630.2401
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213313
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02737
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_it1.162.7281352
X-RAY DIFFRACTIONr_mcbond_other1.1582.7231351
X-RAY DIFFRACTIONr_mcangle_it1.9386.1171697
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6373.11546
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: 1.91→1.96 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 115 -
Rwork0.212 2112 -
obs--99.51 %
Refinement TLS params.Method: refined / Origin x: 7.2651 Å / Origin y: 3.3909 Å / Origin z: 18.5305 Å
111213212223313233
T0.0074 Å2-0.0075 Å2-0.0051 Å2-0.0132 Å20.0112 Å2--0.0104 Å2
L0.2766 °2-0.0261 °20.0761 °2-0.1111 °20.0621 °2--0.3792 °2
S0.0145 Å °-0.0159 Å °-0.0017 Å °0.0171 Å °-0.0157 Å °-0.011 Å °0.0305 Å °-0.0145 Å °0.0012 Å °

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