MolNFT v1 · #170886 · protein

Crystal structure of YTHDC1 with compound ADO_AC_25

6YM2: “Crystal structure of YTHDC1 with compound ADO_AC_25”. X-ray diffraction, 2 ligands (OYK, SO4), 6 pockets (best druggability 0.54). MolNFT v1 #170886 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6YM2
Type: protein
Length: 328 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: YTHDC1
UniProt: Q96MU7
Ligands: OYK, SO4
Pockets: 6 · best druggability 0.54

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	YTHDC1	protein	164	32% helix, 25% strand	Q96MU7

Ligands and binding sites

OYK · ~{N},9-dimethylpurin-6-amine · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 11 copies · chains A, B

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

Pockets

6 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	63	0.54	0.87	16	OYK
2	66	0.53	0.87	16	OYK
3	135	0.47	0.78	19	empty
4	66	0.46	0.83	23	empty
5	93	0.45	0.79	18	empty

Interfaces

1 interface between chains.

A–B · 314 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6YM2 · Crystal structure of YTHDC1 with compound ADO_AC_25 · the same entry in another collection · chain A against A, TM-score 1.00

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 6YM2 · PDBe 6YM2 · UniProt Q96MU7

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