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- PDB-8q4v: Crystal structure of YTHDC1 in complex with Compound 37 (ZA_356) -

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Basic information

Entry
Database: PDB / ID: 8q4v
TitleCrystal structure of YTHDC1 in complex with Compound 37 (ZA_356)
ComponentsYTH domain-containing protein 1
KeywordsRNA BINDING PROTEIN / YTHDC1 / inhibitor / complex / reader
Function / homology
Function and homology information


primary follicle stage / mRNA alternative polyadenylation / dosage compensation by inactivation of X chromosome / mRNA splice site recognition / N6-methyladenosine-containing RNA reader activity / regulation of mRNA splicing, via spliceosome / post-transcriptional regulation of gene expression / regulation of alternative mRNA splicing, via spliceosome / mRNA export from nucleus / mRNA splicing, via spliceosome ...primary follicle stage / mRNA alternative polyadenylation / dosage compensation by inactivation of X chromosome / mRNA splice site recognition / N6-methyladenosine-containing RNA reader activity / regulation of mRNA splicing, via spliceosome / post-transcriptional regulation of gene expression / regulation of alternative mRNA splicing, via spliceosome / mRNA export from nucleus / mRNA splicing, via spliceosome / spermatogenesis / in utero embryonic development / nuclear speck / mRNA binding / RNA binding / nucleoplasm / nucleus / plasma membrane
Similarity search - Function
YTH domain containing protein / YTH domain / YT521-B-like domain / YTH domain profile.
Similarity search - Domain/homology
Chem-JO0 / YTH domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsBedi, R.K. / Zalesak, F. / Caflisch, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_189363 Switzerland
CitationJournal: J.Med.Chem. / Year: 2024
Title: Structure-Based Design of a Potent and Selective YTHDC1 Ligand.
Authors: Zalesak, F. / Nai, F. / Herok, M. / Bochenkova, E. / Bedi, R.K. / Li, Y. / Errani, F. / Caflisch, A.
History
DepositionAug 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YTH domain-containing protein 1
B: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,99311
Polymers37,6482
Non-polymers1,3459
Water5,188288
1
A: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5446
Polymers18,8241
Non-polymers7205
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4485
Polymers18,8241
Non-polymers6244
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.800, 103.840, 41.910
Angle α, β, γ (deg.)90.000, 104.850, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein YTH domain-containing protein 1 / Splicing factor YT521 / YT521-B


Mass: 18823.826 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YTHDC1, KIAA1966, YT521 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96MU7
#2: Chemical ChemComp-JO0 / 2-chloranyl-9-[(3-chlorophenyl)methyl]-~{N}-cyclopropyl-7,8-dihydropurin-6-amine


Mass: 336.219 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H15Cl2N5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.22 Å3/Da / Density % sol: 44.68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 25% PEG 3350, 0.2M Ammonium Sulphate, 0.1M Bis-Tris pH 6.5

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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: Sep 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.36→40.514 Å / Num. obs: 67659 / % possible obs: 97 % / Redundancy: 3.42 % / CC1/2: 0.998 / Net I/σ(I): 13.51
Reflection shellResolution: 1.36→1.45 Å / Num. unique obs: 10701 / CC1/2: 0.511

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.36→40.51 Å / SU ML: 0.197 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.7801
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2211 3373 5 %
Rwork0.2073 64101 -
obs0.208 67474 96.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.37 Å2
Refinement stepCycle: LAST / Resolution: 1.36→40.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2513 0 73 288 2874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612655
X-RAY DIFFRACTIONf_angle_d0.90043606
X-RAY DIFFRACTIONf_chiral_restr0.0837390
X-RAY DIFFRACTIONf_plane_restr0.0152448
X-RAY DIFFRACTIONf_dihedral_angle_d7.4004347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.380.40091370.46122616X-RAY DIFFRACTION94.22
1.38-1.410.40961400.4012653X-RAY DIFFRACTION96.98
1.41-1.430.42951370.38032637X-RAY DIFFRACTION95.69
1.43-1.450.37151340.34812536X-RAY DIFFRACTION92.36
1.45-1.480.32771400.31062669X-RAY DIFFRACTION96.83
1.48-1.50.27951440.28222728X-RAY DIFFRACTION99.34
1.5-1.530.28511430.25522725X-RAY DIFFRACTION99.48
1.53-1.560.24451440.24522737X-RAY DIFFRACTION99.45
1.56-1.60.2551450.23882747X-RAY DIFFRACTION99.04
1.6-1.630.25311420.23892695X-RAY DIFFRACTION99.37
1.63-1.670.29061450.23242758X-RAY DIFFRACTION99.25
1.67-1.720.31481440.23542721X-RAY DIFFRACTION99.2
1.72-1.770.26941430.23492717X-RAY DIFFRACTION98.89
1.77-1.830.26821410.22622690X-RAY DIFFRACTION97.89
1.83-1.890.25531400.22652658X-RAY DIFFRACTION96.28
1.89-1.970.22481180.2282241X-RAY DIFFRACTION82.11
1.97-2.060.21841420.21472711X-RAY DIFFRACTION98.45
2.06-2.170.24331450.20372756X-RAY DIFFRACTION99.38
2.17-2.30.21431390.20512633X-RAY DIFFRACTION95.49
2.3-2.480.21171460.20722758X-RAY DIFFRACTION99.28
2.48-2.730.22441430.21122718X-RAY DIFFRACTION99.13
2.73-3.120.22231430.20852710X-RAY DIFFRACTION97.71
3.13-3.940.19451360.18012594X-RAY DIFFRACTION93.85
3.94-40.510.18221420.1782693X-RAY DIFFRACTION95.71

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