9V84 | pdb_00009v84

Crystal structure of complex Hit-1 with YTHDC1

PDB DOI: https://doi.org/10.2210/pdb9V84/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-05-29 Released: 2025-12-24
Deposition Author(s): Zhang, H., Yang, S.Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.267 (Depositor), 0.267 (DCC)
R-Value Work:
0.228 (Depositor), 0.229 (DCC)
R-Value Observed:
0.230 (Depositor)

Starting Model: experimental
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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 with compound Hit-1

Zhang, H.

To be published.

Macromolecule Content

Total Structure Weight: 153.18 kDa
Atom Count: 10,419
Modeled Residue Count: 1,294
Deposited Residue Count: 1,304
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YTH domain-containing protein 1	A [auth B] B [auth A] C D E A [auth B], B [auth A], C, D, E, F, G, H	163	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
9N8 (Subject of Investigation/LOI) Query on 9N8 Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain FA [auth F] SDF format, chain I [auth B] SDF format, chain JA [auth G] SDF format, chain M [auth A] SDF format, chain MA [auth H] SDF format, chain S [auth C] SDF format, chain W [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain I [auth B] MOL2 format, chain JA [auth G] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth H] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] mmCIF format, chain AA [auth E] mmCIF format, chain FA [auth F] mmCIF format, chain I [auth B] mmCIF format, chain JA [auth G] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth H] mmCIF format, chain S [auth C] mmCIF format, chain W [auth D]	AA [auth E] FA [auth F] I [auth B] JA [auth G] M [auth A] AA [auth E], FA [auth F], I [auth B], JA [auth G], M [auth A], MA [auth H], S [auth C], W [auth D]	4-(2-bromanyl-6-fluoranyl-phenyl)carbonyl-~{N}-pyridin-3-yl-1~{H}-pyrrole-2-carboxamide C₁₇ H₁₁ Br F N₃ O₂ ATKCERYALDNMPL-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain FA [auth F] Focus chain I [auth B] Focus chain JA [auth G] Focus chain M [auth A] Focus chain MA [auth H] Focus chain S [auth C] Focus chain W [auth D] Interactions & Density Focus chain AA [auth E] Focus chain FA [auth F] Focus chain I [auth B] Focus chain JA [auth G] Focus chain M [auth A] Focus chain MA [auth H] Focus chain S [auth C] Focus chain W [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain CA [auth E] SDF format, chain DA [auth E] SDF format, chain EA [auth E] SDF format, chain GA [auth F] SDF format, chain HA [auth F] SDF format, chain IA [auth F] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain KA [auth G] SDF format, chain L [auth B] SDF format, chain LA [auth G] SDF format, chain N [auth A] SDF format, chain NA [auth H] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain EA [auth E] MOL2 format, chain GA [auth F] MOL2 format, chain HA [auth F] MOL2 format, chain IA [auth F] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain KA [auth G] MOL2 format, chain L [auth B] MOL2 format, chain LA [auth G] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth H] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain BA [auth E] mmCIF format, chain CA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain EA [auth E] mmCIF format, chain GA [auth F] mmCIF format, chain HA [auth F] mmCIF format, chain IA [auth F] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain KA [auth G] mmCIF format, chain L [auth B] mmCIF format, chain LA [auth G] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth H] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D]	BA [auth E] CA [auth E] DA [auth E] EA [auth E] GA [auth F] BA [auth E], CA [auth E], DA [auth E], EA [auth E], GA [auth F], HA [auth F], IA [auth F], J [auth B], K [auth B], KA [auth G], L [auth B], LA [auth G], N [auth A], NA [auth H], O [auth A], P [auth A], Q [auth A], R [auth A], T [auth C], U [auth C], V [auth C], X [auth D], Y [auth D], Z [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain J [auth B] Focus chain K [auth B] Focus chain KA [auth G] Focus chain L [auth B] Focus chain LA [auth G] Focus chain N [auth A] Focus chain NA [auth H] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain J [auth B] Focus chain K [auth B] Focus chain KA [auth G] Focus chain L [auth B] Focus chain LA [auth G] Focus chain N [auth A] Focus chain NA [auth H] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]