MolNFT v1 · #170972 · protein

Crystal structure of YTHDC1 with compound VVR_DC1_002

6YOQ: “Crystal structure of YTHDC1 with compound VVR_DC1_002”. X-ray diffraction, 2 ligands (P5H, SO4), 6 pockets (best druggability 0.70). MolNFT v1 #170972 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6YOQ
Type: protein
Length: 329 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: YTHDC1
UniProt: Q96MU7
Ligands: P5H, SO4
Pockets: 6 · best druggability 0.70

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	YTHDC1	protein	165	35% helix, 25% strand	Q96MU7
B	YTHDC1	protein	164	32% helix, 24% strand	Q96MU7

Ligands and binding sites

P5H · 6-methyl-~{N}-[2-(methylsulfonylamino)ethyl]-2-oxidanylidene-3~{H}-pyridine-3-carboxamide · 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

6 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	184	0.70	0.88	30	SO4
2	59	0.51	0.86	15	P5H
3	64	0.48	0.84	14	P5H
4	87	0.40	0.77	16	empty
5	58	0.30	0.75	16	empty

Interfaces

1 interface between chains.

A–B · 582 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

6YOQ · Crystal structure of YTHDC1 with compound VVR_DC1_002 · 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 6YOQ · PDBe 6YOQ · UniProt Q96MU7

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