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- PDB-5ear: Crystal structure of human WDR5 in complex with compound 9d -

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Basic information

Entry
Database: PDB / ID: 5ear
TitleCrystal structure of human WDR5 in complex with compound 9d
ComponentsWD repeat-containing protein 5
KeywordsTRANSCRIPTION / TRANSCRIPTION INHIBITOR / WDR5 / compound 9d / Structural Genomics / Structural Genomics Consortium / SGC / TRANSCRIPTION - TRANSCRIPTION INHIBITOR complex
Function / homology
Function and homology information


MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / histone methyltransferase complex / regulation of tubulin deacetylation / Formation of WDR5-containing histone-modifying complexes ...MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / histone methyltransferase complex / regulation of tubulin deacetylation / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / regulation of embryonic development / MLL1 complex / histone acetyltransferase complex / positive regulation of gluconeogenesis / methylated histone binding / transcription initiation-coupled chromatin remodeling / skeletal system development / gluconeogenesis / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / mitotic spindle / PKMTs methylate histone lysines / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Neddylation / HATs acetylate histones / histone binding / regulation of cell cycle / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats ...YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Chem-5MQ / WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDONG, A. / DOMBROVSKI, L. / SMIL, D. / GETLIK, M. / BOLSHAN, Y. / WALKER, J.R. / SENISTERRA, G. / PODA, G. / AL-AWAR, R. / SCHAPIRA, M. ...DONG, A. / DOMBROVSKI, L. / SMIL, D. / GETLIK, M. / BOLSHAN, Y. / WALKER, J.R. / SENISTERRA, G. / PODA, G. / AL-AWAR, R. / SCHAPIRA, M. / VEDADI, M. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / BROWN, P.J. / WU, H. / Structural Genomics Consortium (SGC)
CitationJournal: J. Med. Chem. / Year: 2016
Title: Structure-Based Optimization of a Small Molecule Antagonist of the Interaction Between WD Repeat-Containing Protein 5 (WDR5) and Mixed-Lineage Leukemia 1 (MLL1).
Authors: Getlik, M. / Smil, D. / Zepeda-Velazquez, C. / Bolshan, Y. / Poda, G. / Wu, H. / Dong, A. / Kuznetsova, E. / Marcellus, R. / Senisterra, G. / Dombrovski, L. / Hajian, T. / Kiyota, T. / ...Authors: Getlik, M. / Smil, D. / Zepeda-Velazquez, C. / Bolshan, Y. / Poda, G. / Wu, H. / Dong, A. / Kuznetsova, E. / Marcellus, R. / Senisterra, G. / Dombrovski, L. / Hajian, T. / Kiyota, T. / Schapira, M. / Arrowsmith, C.H. / Brown, P.J. / Vedadi, M. / Al-Awar, R.
History
DepositionOct 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Non-polymer description
Revision 1.2May 23, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: WD repeat-containing protein 5
B: WD repeat-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,71028
Polymers68,5802
Non-polymers2,13026
Water9,692538
1
A: WD repeat-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,27613
Polymers34,2901
Non-polymers98612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: WD repeat-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,43415
Polymers34,2901
Non-polymers1,14414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.640, 53.615, 64.707
Angle α, β, γ (deg.)107.920, 90.950, 109.660
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 WD repeat-containing protein 5 / BMP2-induced 3-kb gene protein


Mass: 34289.887 Da / Num. of mol.: 2 / Fragment: UNP residues 23-334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR5, BIG3 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)V2RpRARE / References: UniProt: P61964

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Non-polymers , 5 types, 564 molecules

#2: Chemical ChemComp-5MQ / N-[5-(2,3-dihydro-1-benzofuran-7-yl)-2-(4-methylpiperazin-1-yl)phenyl]-3-methylbenzamide


Mass: 427.538 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H29N3O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 4 / Source method: obtained synthetically
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 538 / 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: 2.09 Å3/Da / Density % sol: 41.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 22% PEG 3350, 0.1M NH4SO4, 0.1 M BisTris pH5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jan 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 48569 / % possible obs: 94.1 % / Redundancy: 4 % / Rmerge(I) obs: 0.042 / Χ2: 1.054 / Net I/av σ(I): 31.543 / Net I/σ(I): 17 / Num. measured all: 192066
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.8340.20722950.92589.8
1.83-1.8640.17123790.9590.6
1.86-1.940.14523281.02291
1.9-1.9440.13123611.16191.5
1.94-1.9840.10523561.03491.9
1.98-2.0340.09123941.0292.3
2.03-2.083.90.08823861.1792.3
2.08-2.1340.07524141.0593.1
2.13-2.240.06723771.04193
2.2-2.2740.07224141.22993.5
2.27-2.3540.06424351.05493.9
2.35-2.4440.0624591.06694.4
2.44-2.5540.05524371.08295.1
2.55-2.6940.04824551.08895.4
2.69-2.8640.04124591.00295.7
2.86-3.0840.03625111.0196.5
3.08-3.3940.03225101.03297.1
3.39-3.8840.02825191.00397.6
3.88-4.883.90.02725300.97598.2
4.88-503.90.0325501.15998.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0131refinement
PDB_EXTRACT3.15data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UR4

3ur4


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.1896 / WRfactor Rwork: 0.1538 / FOM work R set: 0.8873 / SU B: 2.284 / SU ML: 0.073 / SU R Cruickshank DPI: 0.1274 / SU Rfree: 0.1146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.185 1005 2.1 %RANDOM
Rwork0.1527 ---
obs0.1534 47564 93.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.44 Å2 / Biso mean: 19.754 Å2 / Biso min: 6.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20.25 Å2-0.55 Å2
2--0.98 Å20.1 Å2
3----0.73 Å2
Refinement stepCycle: final / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4615 0 149 550 5314
Biso mean--24 30.61 -
Num. residues----602
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194886
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.9366609
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3835608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.00924.972179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.58515796
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.389157
X-RAY DIFFRACTIONr_chiral_restr0.0890.2737
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213733
X-RAY DIFFRACTIONr_mcbond_it0.8591.7712416
X-RAY DIFFRACTIONr_mcangle_it1.3372.6473013
X-RAY DIFFRACTIONr_scbond_it1.2461.9322470
LS refinement shellResolution: 1.798→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 68 -
Rwork0.191 3285 -
all-3353 -
obs--87.73 %

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