MolNFT v1 · #171668 · protein

Crystal structure of YTHDC1 with compound DHU_DC1_180

6ZCM: “Crystal structure of YTHDC1 with compound DHU_DC1_180”. X-ray diffraction, 2 ligands (QF2, SO4), 5 pockets (best druggability 0.70). MolNFT v1 #171668 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6ZCM
Type: protein
Length: 328 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: YTHDC1
UniProt: Q96MU7
Ligands: QF2, SO4
Pockets: 5 · best druggability 0.70

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

QF2 · 6-[[cyclopropyl-[(7-methoxy-1,3-benzodioxol-5-yl) methyl]amino]methyl]-1~{H}-pyrimidine-2,4-dione · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 9 copies · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	214	0.70	0.87	31	SO4
2	114	0.58	0.85	16	QF2
3	113	0.55	0.83	15	QF2
4	100	0.41	0.77	16	empty
5	56	0.28	0.74	14	empty

Interfaces

1 interface between chains.

A–B · 586 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

6ZCM · Crystal structure of YTHDC1 with compound DHU_DC1_180 · 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 6ZCM · PDBe 6ZCM · UniProt Q96MU7

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