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Crystal structure of YTHDC1 with compound DHU_DC1_139

Analyse Crystal structure of YTHDC1 with compound DHU_DC1_139 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6YNO
Type: protein
Length: 326 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: YTHDC1
UniProt: Q96MU7
Ligands: P0W, SO4
Pockets: 8 · best druggability 0.57

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	YTHDC1	protein	162	33% helix, 25% strand	Q96MU7
B	YTHDC1	protein	164	34% helix, 26% strand	Q96MU7

Ligands and binding sites

P0W · 6-[[methyl-[(1-phenylpyrazol-3-yl)methyl]amino]methyl]-1~{H}-pyrimidine-2,4-dione · 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

8 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	102	0.57	0.85	17	P0W
2	125	0.51	0.80	18	SO4
3	87	0.46	0.81	18	SO4
4	107	0.40	0.76	15	empty
5	86	0.39	0.77	17	empty

Interfaces

1 interface between chains.

A–B · 249 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6YNO · Crystal structure of YTHDC1 with compound DHU_DC1_139 · 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 6YNO · PDBe 6YNO · UniProt Q96MU7

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