8Q4T

Crystal structure of YTHDC1 in complex with Compound 31 (ZA_400)

PDB DOI: https://doi.org/10.2210/pdb8Q4T/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-08-07 Released: 2023-12-06
Deposition Author(s): Bedi, R.K., Zalesak, F., Caflisch, A.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.51 Å
R-Value Free: 0.237
R-Value Work: 0.208
R-Value Observed: 0.210

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of YTHDC1 in complex with Compound 31 (ZA_400)

Bedi, R.K., Zalesak, F., Caflisch, A.

To be published.

Macromolecule Content

Total Structure Weight: 39.22 kDa
Atom Count: 2,820
Modelled Residue Count: 328
Deposited Residue Count: 332
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YTH domain-containing protein 1	A, B	166	Homo sapiens	Mutation(s): 0 Gene Names: YTHDC1, KIAA1966, YT521
UniProt & NIH Common Fund Data Resources
Find proteins for Q96MU7 (Homo sapiens) Explore Q96MU7 Go to UniProtKB: Q96MU7
PHAROS: Q96MU7 GTEx: ENSG00000083896
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96MU7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JBD (Subject of Investigation/LOI) Query on JBD Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B]	C [auth A], H [auth B]	~{N}-[4-chloranyl-2-[[2-chloranyl-6-(methylamino)purin-9-yl]methyl]phenyl]methanesulfonamide C₁₄ H₁₄ Cl₂ N₆ O₂ S VFTMKZXKNIRBJR-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] I [auth B] D [auth A], E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B], L [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]