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Crystal structure of YTHDF2 with compound YLI_DC1_015

Analyse Crystal structure of YTHDF2 with compound YLI_DC1_015 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7R5L
Type: protein
Length: 148 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Yth domain-containing family protein 2
UniProt: Q9Y5A9
Ligands: I4S, SO4
Pockets: 1 · best druggability 0.46

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Yth domain-containing family protein 2	protein	148	32% helix, 30% strand	Q9Y5A9

Ligands and binding sites

I4S · 3,6-dimethyl-2~{H}-1,2,4-triazin-5-one · ligand · chains A
SO4 · Sulfate ion · ion · 5 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	65	0.46	0.83	17	I4S, SO4

Compared structures

7R5L · Crystal structure of YTHDF2 with compound YLI_DC1_015 · the same entry in another collection · chain A against A, TM-score 1.00
Q9Y5A9 · AlphaFold monomer V2.0 prediction for yth domain-containing family protein 2 (Q9Y5A9) · a predicted model of the same protein · chain A against A, TM-score 0.95

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q9Y5A9
Elsewhere: RCSB PDB 7R5L · PDBe 7R5L · UniProt Q9Y5A9

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