MolNFT v2 · #217386 · protein

Crystal structure of YTHDC1 in complex with Compound 22 (ZA_393)

8Q3A · YTH domain-containing protein 1: “Crystal structure of YTHDC1 in complex with Compound 22 (ZA_393)”. X-ray diffraction at 1.43, 2 ligands (IYQ, SO4), 4 pockets (best druggability 0.70). MolNFT v2 #217386 on GenesisL1: 3D structure…

PDB: 8Q3A
Type: protein
Length: 328 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.43
Source: Homo sapiens
Molecule: YTH domain-containing protein 1
UniProt: Q96MU7
Ligands: IYQ, SO4
Pockets: 4 · best druggability 0.70

Structure

x-ray diffraction · resolution 1.43 · 1 distinct chain · 32% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	YTH domain-containing protein 1	protein	164	32% helix, 24% strand	Q96MU7

Ligands and binding sites

IYQ · 3-[[2-chloranyl-6-(methylamino)purin-9-yl]methyl]benzamide · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 8 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	217	0.70	0.87	31	SO4
2	78	0.55	0.86	17	IYQ
3	63	0.49	0.85	15	IYQ
4	82	0.38	0.76	16	empty

Interfaces

1 interface between chains.

A–B · 558 Å² buried · 6 hydrogen bonds · protein-protein

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 Q96MU7
Elsewhere: RCSB PDB 8Q3A · PDBe 8Q3A · UniProt Q96MU7

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