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- PDB-6uhy: WDR5 in complex with Myc site fragment inhibitor -

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Basic information

Entry
Database: PDB / ID: 6uhy
TitleWDR5 in complex with Myc site fragment inhibitor
ComponentsWDR5
KeywordsTRANSCRIPTION / WDR5 / Myc / 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 ...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 / regulation of cell division / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / regulation of embryonic development / histone acetyltransferase complex / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / methylated histone binding / 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. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. ...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. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
1-cyclohexyl-1H-benzimidazole-5-carboxylic acid / WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsWang, F. / Fesik, S.W.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: J.Med.Chem. / Year: 2020
Title: Discovery of WD Repeat-Containing Protein 5 (WDR5)-MYC Inhibitors Using Fragment-Based Methods and Structure-Based Design.
Authors: Chacon Simon, S. / Wang, F. / Thomas, L.R. / Phan, J. / Zhao, B. / Olejniczak, E.T. / Macdonald, J.D. / Shaw, J.G. / Schlund, C. / Payne, W. / Creighton, J. / Stauffer, S.R. / Waterson, A.G. ...Authors: Chacon Simon, S. / Wang, F. / Thomas, L.R. / Phan, J. / Zhao, B. / Olejniczak, E.T. / Macdonald, J.D. / Shaw, J.G. / Schlund, C. / Payne, W. / Creighton, J. / Stauffer, S.R. / Waterson, A.G. / Tansey, W.P. / Fesik, S.W.
History
DepositionSep 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WDR5
B: WDR5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4734
Polymers66,9842
Non-polymers4892
Water11,385632
1
A: WDR5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7362
Polymers33,4921
Non-polymers2441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: WDR5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7362
Polymers33,4921
Non-polymers2441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)134.464, 46.955, 112.770
Angle α, β, γ (deg.)90.000, 117.630, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein WDR5 /


Mass: 33492.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P61964
#2: Chemical ChemComp-Q8G / 1-cyclohexyl-1H-benzimidazole-5-carboxylic acid


Mass: 244.289 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H16N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 632 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.34 Å3/Da / Density % sol: 47.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris pH 6.0, 0.2 M ammonium acetate, 28% to 32% PEG3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.26→50 Å / Num. obs: 162176 / % possible obs: 96.24 % / Redundancy: 4.1 % / Rpim(I) all: 0.035 / Net I/σ(I): 33.4
Reflection shellResolution: 1.26→1.28 Å / Num. unique obs: 7904 / CC1/2: 0.905

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.26→31.297 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.59
RfactorNum. reflection% reflection
Rfree0.1814 8121 5.01 %
Rwork0.1541 --
obs0.1554 162176 96.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.98 Å2 / Biso mean: 18.7451 Å2 / Biso min: 9.56 Å2
Refinement stepCycle: final / Resolution: 1.26→31.297 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4694 0 0 632 5326
Biso mean---27.16 -
Num. residues----607
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054986
X-RAY DIFFRACTIONf_angle_d0.8556808
X-RAY DIFFRACTIONf_chiral_restr0.091766
X-RAY DIFFRACTIONf_plane_restr0.005855
X-RAY DIFFRACTIONf_dihedral_angle_d12.8411762
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.26-1.27420.25722320.2173458986
1.2742-1.28910.24612560.2009498195
1.2891-1.30490.22332490.1842506095
1.3049-1.32140.20612460.1692508995
1.3214-1.33880.21052630.1691505995
1.3388-1.35710.19152740.1598503095
1.3571-1.37650.19252620.1606508596
1.3765-1.3970.19752580.1577508796
1.397-1.41890.20582790.1609508396
1.4189-1.44210.19242680.1546503596
1.4421-1.4670.17252740.1503516796
1.467-1.49370.18222610.1407507896
1.4937-1.52240.17042920.1429514097
1.5224-1.55350.17062550.1375510497
1.5535-1.58730.16082520.1328517197
1.5873-1.62420.172710.1318521197
1.6242-1.66480.17522880.131513797
1.6648-1.70980.16352730.1339516097
1.7098-1.76010.1682680.1388518397
1.7601-1.81690.182590.1426524398
1.8169-1.88180.17232830.1486520498
1.8818-1.95720.16342840.1451521998
1.9572-2.04620.18492810.1529521798
2.0462-2.15410.18172800.1502528598
2.1541-2.2890.1772870.158521298
2.289-2.46570.16532770.1595533299
2.4657-2.71370.18793080.1681527799
2.7137-3.10610.19332990.1678530199
3.1061-3.91210.18582860.1589525897
3.91210.17522560.1471505891

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