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- PDB-9ncw: Crystal Structure of WDR5 in complex with Triazole-Based Inhibitors -

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Basic information

Entry
Database: PDB / ID: 9ncw
TitleCrystal Structure of WDR5 in complex with Triazole-Based Inhibitors
ComponentsWD repeat-containing protein 5
KeywordsSTRUCTURAL PROTEIN/INHIBITOR / WDR5 / Inhibitor / STRUCTURAL PROTEIN / STRUCTURAL PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


histone H3Q5ser reader activity / histone H3K4me1 reader activity / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis ...histone H3Q5ser reader activity / histone H3K4me1 reader activity / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / Formation of WDR5-containing histone-modifying complexes / histone methyltransferase complex / regulation of cell division / MLL1 complex / regulation of embryonic development / histone acetyltransferase complex / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / gluconeogenesis / skeletal system development / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / PKMTs methylate histone lysines / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / mitotic spindle / Neddylation / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / 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
WDR5 beta-propeller domain / 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. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
: / WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsGoins, C.M. / Stauffer, S.R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biorxiv / Year: 2025
Title: Development and Characterization of Triazole-Based WDR5 Inhibitors for the Treatment of Glioblastoma
Authors: Coker, J.A. / Martinez, S.R. / Han, S.H. / Sloan, A.R. / Gupta, A.K. / Bukenya, G. / Polzer, P. / Ramos, J.H. / Rico, E. / Rico, A. / Lindsey, A.A. / Navadgi, T. / Reitz, N. / Romigh, T. / ...Authors: Coker, J.A. / Martinez, S.R. / Han, S.H. / Sloan, A.R. / Gupta, A.K. / Bukenya, G. / Polzer, P. / Ramos, J.H. / Rico, E. / Rico, A. / Lindsey, A.A. / Navadgi, T. / Reitz, N. / Romigh, T. / Goins, C.M. / Hubert, C.G. / Wang, N.S. / Cheng, F.R. / Alvarado, J. / Sprowls, S.A. / Lathia, J.D. / Stauffer, S.R.
History
DepositionFeb 17, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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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
C: WD repeat-containing protein 5
D: WD repeat-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,3746
Polymers188,2964
Non-polymers1,0772
Water20,7351151
1
A: WD repeat-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6132
Polymers47,0741
Non-polymers5391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: WD repeat-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6132
Polymers47,0741
Non-polymers5391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: WD repeat-containing protein 5


Theoretical massNumber of molelcules
Total (without water)47,0741
Polymers47,0741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: WD repeat-containing protein 5


Theoretical massNumber of molelcules
Total (without water)47,0741
Polymers47,0741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.534, 68.696, 93.018
Angle α, β, γ (deg.)91.293, 103.260, 90.383
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
WD repeat-containing protein 5 / BMP2-induced 3-kb gene protein


Mass: 47074.078 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR5, BIG3 / Production host: Escherichia coli (E. coli) / References: UniProt: P61964
#2: Chemical ChemComp-A1BW9 / 1-{[(6P)-3-[(3,5-dimethoxyphenyl)methyl]-6-(4-fluoro-2-methylphenyl)-4,5-dihydro-3H-naphtho[1,2-d][1,2,3]triazol-8-yl]methyl}-3-methyl-1,3-dihydro-2H-imidazol-2-imine


Mass: 538.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H31FN6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1151 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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

Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: ammonium acetate, PEG 3350, Bis-TRIS, HEPES, TRIS / PH range: 6.0-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.58→38.23 Å / Num. obs: 144679 / % possible obs: 94.95 % / Redundancy: 3.8 % / Biso Wilson estimate: 14.52 Å2 / CC1/2: 0.981 / Net I/σ(I): 11.04
Reflection shellResolution: 1.58→1.6 Å / Num. unique obs: 3473 / CC1/2: 0.836

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→38.23 Å / SU ML: 0.1944 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 43.8715
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2751 7044 4.87 %
Rwork0.2494 137630 -
obs0.2506 144674 94.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.97 Å2
Refinement stepCycle: LAST / Resolution: 1.58→38.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9062 0 80 1151 10293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00559388
X-RAY DIFFRACTIONf_angle_d0.835912778
X-RAY DIFFRACTIONf_chiral_restr0.05911440
X-RAY DIFFRACTIONf_plane_restr0.00591578
X-RAY DIFFRACTIONf_dihedral_angle_d14.80383232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.60.4251820.43293291X-RAY DIFFRACTION67.2
1.6-1.620.4172140.40344267X-RAY DIFFRACTION88.91
1.62-1.640.40131990.39324562X-RAY DIFFRACTION93.85
1.64-1.660.38122370.38074530X-RAY DIFFRACTION92.94
1.66-1.680.38312340.3724578X-RAY DIFFRACTION96.03
1.68-1.710.40732360.36024596X-RAY DIFFRACTION94.73
1.71-1.730.37552490.34544541X-RAY DIFFRACTION94.24
1.73-1.760.36342490.3284617X-RAY DIFFRACTION96.19
1.76-1.780.32522070.31044585X-RAY DIFFRACTION94.09
1.78-1.810.34452190.30274613X-RAY DIFFRACTION95.93
1.81-1.850.35342500.29394640X-RAY DIFFRACTION95.53
1.85-1.880.30432720.28124532X-RAY DIFFRACTION95.13
1.88-1.910.29182380.28054645X-RAY DIFFRACTION95.97
1.91-1.950.29642290.27154619X-RAY DIFFRACTION95.25
1.95-20.28612140.26064611X-RAY DIFFRACTION95.89
2-2.040.27922290.24584653X-RAY DIFFRACTION95.74
2.04-2.090.33642150.25054693X-RAY DIFFRACTION96.42
2.09-2.150.25092280.23864632X-RAY DIFFRACTION96.39
2.15-2.210.27942230.23414719X-RAY DIFFRACTION96.02
2.21-2.290.28312710.24054632X-RAY DIFFRACTION97.57
2.29-2.370.24342740.224648X-RAY DIFFRACTION96.91
2.37-2.460.23472540.2254725X-RAY DIFFRACTION96.94
2.46-2.570.23752360.22934688X-RAY DIFFRACTION97.78
2.57-2.710.28582110.23584747X-RAY DIFFRACTION97.93
2.71-2.880.27242900.23744700X-RAY DIFFRACTION98.07
2.88-3.10.23652450.22284765X-RAY DIFFRACTION97.85
3.1-3.410.25111790.21384779X-RAY DIFFRACTION98.51
3.41-3.910.21892390.20564776X-RAY DIFFRACTION98.45
3.91-4.920.19853010.1864669X-RAY DIFFRACTION98.3
4.92-38.230.2742200.23644577X-RAY DIFFRACTION94.41

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