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- PDB-9qiu: Crystal structure of YTHDF2 in complex with compound 13 (AI-DF2-56) -

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Basic information

Entry
Database: PDB / ID: 9qiu
TitleCrystal structure of YTHDF2 in complex with compound 13 (AI-DF2-56)
ComponentsYTH domain-containing family protein 2
KeywordsRNA BINDING PROTEIN / Inhibitor / m6A reader
Function / homology
Function and homology information


C5-methylcytidine-containing RNA reader activity / organelle assembly / spermatogonial cell division / regulation of meiotic cell cycle process involved in oocyte maturation / regulation of rRNA processing / positive regulation of cap-independent translational initiation / gamete generation / endothelial to hematopoietic transition / embryonic morphogenesis / N6-methyladenosine-containing RNA reader activity ...C5-methylcytidine-containing RNA reader activity / organelle assembly / spermatogonial cell division / regulation of meiotic cell cycle process involved in oocyte maturation / regulation of rRNA processing / positive regulation of cap-independent translational initiation / gamete generation / endothelial to hematopoietic transition / embryonic morphogenesis / N6-methyladenosine-containing RNA reader activity / negative regulation of stem cell differentiation / regulation of hematopoietic stem cell differentiation / oocyte maturation / negative regulation of type I interferon-mediated signaling pathway / hematopoietic stem cell proliferation / mRNA destabilization / mRNA catabolic process / humoral immune response / regulation of neurogenesis / negative regulation of Notch signaling pathway / regulation of cell adhesion / regulation of mRNA stability / stress granule assembly / P-body / centriolar satellite / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / innate immune response / mRNA binding / RNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
YTH domain containing protein / YTH domain / YT521-B-like domain / YTH domain profile.
Similarity search - Domain/homology
: / YTH domain-containing family protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsNai, F. / Invernizzi, A. / Caflisch, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030-212195 Switzerland
CitationJournal: Acs Bio Med Chem Au / Year: 2025
Title: Discovery of YTHDF2 Ligands by Fragment-Based Design
Authors: Invernizzi, A. / Nai, F. / Bedi, R.K. / Vargas-Rosales, P.A. / Li, Y. / Bochenkova, E. / Herok, M. / Zalesak, F. / Caflisch, A.
History
DepositionMar 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YTH domain-containing family protein 2
B: YTH domain-containing family protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,56610
Polymers38,7362
Non-polymers8318
Water95553
1
A: YTH domain-containing family protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7815
Polymers19,3681
Non-polymers4134
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YTH domain-containing family protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7855
Polymers19,3681
Non-polymers4174
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.440, 79.440, 115.800
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

#1: Protein YTH domain-containing family protein 2 / CLL-associated antigen KW-14 / High-glucose-regulated protein 8 / Renal carcinoma antigen NY-REN-2


Mass: 19367.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YTHDF2, HGRG8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5A9
#2: Chemical ChemComp-A1IR4 / 3-sulfanyl-1,2,4-triazin-5-ol


Mass: 129.140 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H3N3OS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.83 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 2.025 M Ammonium sulfate, 0.1 M Sodium citrate tribasic pH 5.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 15021 / % possible obs: 99.7 % / Redundancy: 6.85 % / Biso Wilson estimate: 50.93 Å2 / CC1/2: 0.994 / Net I/σ(I): 9.48
Reflection shellResolution: 2.46→2.61 Å / Num. unique obs: 2375 / CC1/2: 0.834

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Processing

Software
NameVersionClassification
PHENIX1.21.1.5286refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.46→44.3 Å / SU ML: 0.3507 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.0492
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.279 746 4.99 %
Rwork0.2224 14189 -
obs0.2252 14935 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.98 Å2
Refinement stepCycle: LAST / Resolution: 2.46→44.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 47 53 2428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812465
X-RAY DIFFRACTIONf_angle_d0.89253347
X-RAY DIFFRACTIONf_chiral_restr0.0545348
X-RAY DIFFRACTIONf_plane_restr0.0079427
X-RAY DIFFRACTIONf_dihedral_angle_d15.1975858
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.650.3641480.27192821X-RAY DIFFRACTION98.8
2.65-2.920.36361490.27792822X-RAY DIFFRACTION99.6
2.92-3.340.33431480.26312825X-RAY DIFFRACTION99.53
3.34-4.210.2661480.21982845X-RAY DIFFRACTION99.14
4.21-44.30.23421530.18712876X-RAY DIFFRACTION99.8

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