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Crystal structure of YTHDC1 with compound YLI_DC1_006

Analyse Crystal structure of YTHDC1 with compound YLI_DC1_006 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7P8B
Type: protein
Length: 328 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Yth domain-containing protein 1
UniProt: Q96MU7
Ligands: OYT, SO4
Pockets: 4 · best druggability 0.69

Structure

x-ray diffraction · 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

OYT · 9-cyclopropyl-~{N}-methyl-purin-6-amine · 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

4 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	243	0.69	0.85	33	SO4
2	79	0.50	0.83	16	OYT
3	72	0.47	0.83	15	OYT
4	108	0.40	0.76	17	empty

Interfaces

1 interface between chains.

A–B · 580 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

7P8B · Crystal structure of YTHDC1 with compound YLI_DC1_006 · 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 7P8B · PDBe 7P8B · UniProt Q96MU7

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