MolNFT v1 · #170839 · protein

Crystal structure of YTHDC1 with compound DHU_DC1_125

6YKJ: “Crystal structure of YTHDC1 with compound DHU_DC1_125”. X-ray diffraction, 2 ligands (OUW, SO4), 6 pockets (best druggability 0.58). MolNFT v1 #170839 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6YKJ
Type: protein
Length: 322 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: YTHDC1
UniProt: Q96MU7
Ligands: OUW, SO4
Pockets: 6 · best druggability 0.58

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	YTHDC1	protein	158	33% helix, 28% strand	Q96MU7
B	YTHDC1	protein	164	33% helix, 26% strand	Q96MU7

Ligands and binding sites

OUW · ~{N}-methyl-4-(methylamino)pyridine-2-carboxamide · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 5 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 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	224	0.58	0.80	34	OUW
2	84	0.46	0.81	17	empty
3	136	0.46	0.77	17	empty
4	96	0.46	0.80	16	OUW
5	104	0.41	0.76	16	empty

Interfaces

1 interface between chains.

A–B · 261 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6YKJ · Crystal structure of YTHDC1 with compound DHU_DC1_125 · 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 6YKJ · PDBe 6YKJ · UniProt Q96MU7

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