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Crystal structure of YTHDC1 with compound DHU_DC1_046

Analyse Crystal structure of YTHDC1 with compound DHU_DC1_046 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6YNJ
Type: protein
Length: 329 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: YTHDC1
UniProt: Q96MU7
Ligands: P0N, SO4
Pockets: 7 · best druggability 0.62

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	YTHDC1	protein	164	34% helix, 24% strand	Q96MU7
B	YTHDC1	protein	165	33% helix, 25% strand	Q96MU7

Ligands and binding sites

P0N · (2~{R})-2-(2-chlorophenyl)-5,5-dimethyl-morpholine · ligand · 3 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

7 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	177	0.62	0.83	20	P0N, SO4
2	191	0.60	0.82	19	P0N, SO4
3	102	0.48	0.80	15	empty
4	88	0.46	0.80	18	empty
5	99	0.41	0.77	16	empty

Interfaces

1 interface between chains.

A–B · 307 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6YNJ · Crystal structure of YTHDC1 with compound DHU_DC1_046 · 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 6YNJ · PDBe 6YNJ · UniProt Q96MU7

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