MolNFT v1 · #170938 · protein

Crystal structure of YTHDC1 with compound DHU_DC1_135

6YNN: “Crystal structure of YTHDC1 with compound DHU_DC1_135”. X-ray diffraction, 2 ligands (P0B, SO4), 8 pockets (best druggability 0.61). MolNFT v1 #170938 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6YNN
Type: protein
Length: 328 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: YTHDC1
UniProt: Q96MU7
Ligands: P0B, SO4
Pockets: 8 · best druggability 0.61

Structure

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

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

Ligands and binding sites

P0B · 6-[[(2-chloranyl-6-fluoranyl-phenyl)methyl-methyl-amino]methyl]-1~{H}-pyrimidine-2,4-dione · ligand · 2 copies · chains A, 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	118	0.61	0.86	18	P0B
2	122	0.58	0.84	17	P0B
3	89	0.45	0.80	18	empty
4	119	0.42	0.76	15	empty
5	109	0.41	0.76	16	empty

Interfaces

1 interface between chains.

A–B · 239 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6YNN · Crystal structure of YTHDC1 with compound DHU_DC1_135 · 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 6YNN · PDBe 6YNN · UniProt Q96MU7

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