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Crystal structure of YTHDC1 with compound DHU_DC1_085

Analyse Crystal structure of YTHDC1 with compound DHU_DC1_085 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6YL9
Type: protein
Length: 321 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: YTHDC1
UniProt: Q96MU7
Ligands: OXB, SO4
Pockets: 7 · best druggability 0.59

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	YTHDC1	protein	156	33% helix, 26% strand	Q96MU7
B	YTHDC1	protein	165	33% helix, 25% strand	Q96MU7

Ligands and binding sites

OXB · 3-[(2~{R},5~{S})-2-(2,5-dimethylphenyl)-5-methyl-morpholin-4-yl]propane-1-sulfonamide · ligand · chains B
SO4 · Sulfate ion · ion · 7 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	233	0.59	0.79	21	OXB
2	87	0.45	0.80	17	empty
3	107	0.42	0.77	17	empty
4	75	0.40	0.78	14	empty
5	92	0.35	0.75	15	SO4

Interfaces

1 interface between chains.

A–B · 245 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6YL9 · Crystal structure of YTHDC1 with compound DHU_DC1_085 · the same entry in another collection · chain B against B, 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 6YL9 · PDBe 6YL9 · UniProt Q96MU7

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