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- PDB-5vfc: WDR5 bound to inhibitor MM-589 -

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Basic information

Entry
Database: PDB / ID: 5vfc
TitleWDR5 bound to inhibitor MM-589
ComponentsWD repeat-containing protein 5
KeywordsTRANSCRIPTION/INHIBITOR / inhibitor / complex / WD repeat / 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 / regulation of tubulin deacetylation / histone methyltransferase complex / 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 / regulation of tubulin deacetylation / histone methyltransferase complex / 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 / PKMTs methylate histone lysines / RMTs methylate histone arginines / mitotic spindle / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Neddylation / HATs acetylate histones / histone binding / regulation of cell cycle / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / 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
inhibitor MM-589 / Chem-9BA / WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.64 Å
AuthorsStuckey, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA177307 United States
CitationJournal: J. Med. Chem. / Year: 2017
Title: Discovery of a Highly Potent, Cell-Permeable Macrocyclic Peptidomimetic (MM-589) Targeting the WD Repeat Domain 5 Protein (WDR5)-Mixed Lineage Leukemia (MLL) Protein-Protein Interaction.
Authors: Karatas, H. / Li, Y. / Liu, L. / Ji, J. / Lee, S. / Chen, Y. / Yang, J. / Huang, L. / Bernard, D. / Xu, J. / Townsend, E.C. / Cao, F. / Ran, X. / Li, X. / Wen, B. / Sun, D. / Stuckey, J.A. / ...Authors: Karatas, H. / Li, Y. / Liu, L. / Ji, J. / Lee, S. / Chen, Y. / Yang, J. / Huang, L. / Bernard, D. / Xu, J. / Townsend, E.C. / Cao, F. / Ran, X. / Li, X. / Wen, B. / Sun, D. / Stuckey, J.A. / Lei, M. / Dou, Y. / Wang, S.
History
DepositionApr 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 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: WD repeat-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,33610
Polymers34,2331
Non-polymers1,1039
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint8 kcal/mol
Surface area11460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.348, 58.559, 56.801
Angle α, β, γ (deg.)90.00, 96.16, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 34232.840 Da / Num. of mol.: 1
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-9BA / N-{(3R,6S,9S,12R)-6-ethyl-12-methyl-9-[3-(N'-methylcarbamimidamido)propyl]-2,5,8,11-tetraoxo-3-phenyl-1,4,7,10-tetraazacyclotetradecan-12-yl}-2-methylpropanamide


Type: peptide-like, Cyclic peptide / Class: Inhibitor / Mass: 572.700 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H44N8O5 / References: inhibitor MM-589
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.13 Å3/Da / Density % sol: 42.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Na Bis-Tris pH 6.5, 26% PEG 8000 and 0.1 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.64→15.55 Å / Num. obs: 35269 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 14.98 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 10

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 1.64→15.55 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.081 / SU Rfree Blow DPI: 0.078 / SU Rfree Cruickshank DPI: 0.078
RfactorNum. reflection% reflectionSelection details
Rfree0.174 1807 5.12 %RANDOM
Rwork0.148 ---
obs0.149 35269 99.7 %-
Displacement parametersBiso mean: 15.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.4853 Å20 Å2-0.4561 Å2
2--0.0745 Å20 Å2
3----0.5598 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å
Refinement stepCycle: 1 / Resolution: 1.64→15.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2327 0 74 215 2616
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012509HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.143440HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d837SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes54HARMONIC2
X-RAY DIFFRACTIONt_gen_planes378HARMONIC5
X-RAY DIFFRACTIONt_it2509HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion5.23
X-RAY DIFFRACTIONt_other_torsion13.58
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion328SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3116SEMIHARMONIC4
LS refinement shellResolution: 1.64→1.69 Å / Rfactor Rfree error: 0 / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.174 153 5.43 %
Rwork0.136 2664 -
all0.138 2817 -
obs--97.34 %
Refinement TLS params.Method: refined / Origin x: 23.2505 Å / Origin y: 0.3083 Å / Origin z: 15.4169 Å
111213212223313233
T-0.0184 Å20.0014 Å2-0.0006 Å2--0.0231 Å20.0158 Å2---0.0435 Å2
L0.6087 °2-0.1684 °20.0366 °2-0.5516 °20.197 °2--0.4763 °2
S0.0406 Å °0.0983 Å °0.0074 Å °-0.0686 Å °-0.0039 Å °0.017 Å °-0.0185 Å °0.0113 Å °-0.0367 Å °
Refinement TLS groupSelection details: { A|* }

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