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- PDB-8pji: MLLT1 in complex with compound 10a -

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Basic information

Entry
Database: PDB / ID: 8pji
TitleMLLT1 in complex with compound 10a
ComponentsProtein ENL
KeywordsPEPTIDE BINDING PROTEIN / complex inhibitor
Function / homology
Function and homology information


RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / : / RNA Polymerase II Pre-transcription Events / transcription elongation factor complex / fibrillar center / chromatin binding / positive regulation of DNA-templated transcription / nucleoplasm / cytosol
Similarity search - Function
AF-9, ANC1 homology domain / : / ANC1 homology domain (AHD) / : / YEATS superfamily / YEATS family / YEATS domain profile.
Similarity search - Domain/homology
Chem-ZJF / Protein ENL
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsRaux, B. / Diaz-Saez, L. / Huber, K.V.M. / Fedorov, O. / Owen, D.R. / Londregan, A.T. / Bountra, C. / Edwards, A. / Arrowsmith, C.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Innovative Medicines Initiative875510 Switzerland
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2023
Title: Discovery of PFI-6, a small-molecule chemical probe for the YEATS domain of MLLT1 and MLLT3.
Authors: Raux, B. / Buchan, K.A. / Bennett, J. / Christott, T. / Dowling, M.S. / Farnie, G. / Fedorov, O. / Gamble, V. / Gileadi, C. / Giroud, C. / Huber, K.V.M. / Korczynska, M. / Limberakis, C. / ...Authors: Raux, B. / Buchan, K.A. / Bennett, J. / Christott, T. / Dowling, M.S. / Farnie, G. / Fedorov, O. / Gamble, V. / Gileadi, C. / Giroud, C. / Huber, K.V.M. / Korczynska, M. / Limberakis, C. / Narayanan, A. / Owen, D.R. / Saez, L.D. / Stock, I.A. / Londregan, A.T.
History
DepositionJun 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein ENL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7956
Polymers18,2251
Non-polymers5705
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.532, 49.532, 132.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Protein ENL / YEATS domain-containing protein 1


Mass: 18225.002 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLLT1, ENL, LTG19, YEATS1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q03111

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Non-polymers , 5 types, 51 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-ZJF / ~{N}-cyclopentyl-1-(3-hydroxyphenyl)imidazole-4-carboxamide


Mass: 271.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H17N3O2 / Feature type: SUBJECT OF INVESTIGATION
#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.: 46 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.22 Å3/Da / Density % sol: 44.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM Bis-Tris pH=7.0 150 mM AmSO4 Gradient 20-30% PEG3350

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.7→39.66 Å / Num. obs: 18898 / % possible obs: 99.86 % / Redundancy: 2 % / CC1/2: 0.983 / Rmerge(I) obs: 0.06371 / Rrim(I) all: 0.0901 / Net I/σ(I): 6.37
Reflection shellResolution: 1.7→1.761 Å / Num. unique obs: 1838 / CC1/2: 0.392 / % possible all: 99.29

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→39.66 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.659 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27665 936 4.9 %RANDOM
Rwork0.24295 ---
obs0.24453 18068 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.633 Å2
Baniso -1Baniso -2Baniso -3
1--2.34 Å2-0 Å2-0 Å2
2---2.34 Å2-0 Å2
3---4.67 Å2
Refinement stepCycle: 1 / Resolution: 1.7→39.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1161 0 37 46 1244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131234
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151150
X-RAY DIFFRACTIONr_angle_refined_deg1.5751.6621672
X-RAY DIFFRACTIONr_angle_other_deg1.3221.582657
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6895143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.69820.95973
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.0615209
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9941510
X-RAY DIFFRACTIONr_chiral_restr0.0670.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021382
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02307
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_it2.4752.864566
X-RAY DIFFRACTIONr_mcbond_other2.4772.861565
X-RAY DIFFRACTIONr_mcangle_it3.5944.279708
X-RAY DIFFRACTIONr_mcangle_other3.5934.283709
X-RAY DIFFRACTIONr_scbond_it3.4963.289668
X-RAY DIFFRACTIONr_scbond_other3.4943.289669
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5454.764964
X-RAY DIFFRACTIONr_long_range_B_refined6.90131.9811250
X-RAY DIFFRACTIONr_long_range_B_other6.88531.9041248
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.741 Å
RfactorNum. reflection% reflection
Rfree0.501 74 -
Rwork0.494 1299 -
obs--99.85 %

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