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Crystal structure of YTHDC1 with compound DHU_DC1_222

Analyse Crystal structure of YTHDC1 with compound DHU_DC1_222 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7PJ7
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: 7RN, SO4
Pockets: 7 · best druggability 0.52

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Yth domain-containing protein 1	protein	164	34% helix, 25% strand	Q96MU7

Ligands and binding sites

7RN · N-methyl-3-(5-methylthiophen-2-yl)-1H-pyrazole-5-carboxamide · ligand · 2 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	124	0.52	0.81	22	7RN
2	83	0.52	0.84	20	7RN
3	107	0.44	0.78	15	empty
4	78	0.44	0.80	17	empty
5	109	0.42	0.76	17	empty

Interfaces

1 interface between chains.

A–B · 255 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

7PJ7 · Crystal structure of YTHDC1 with compound DHU_DC1_222 · 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 7PJ7 · PDBe 7PJ7 · UniProt Q96MU7

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