MolNFT v1 · #184934 · protein

Crystal structure of YTHDC1 with compound YLI_DC1_002

7P88 · Yth domain-containing protein 1: “Crystal structure of YTHDC1 with compound YLI_DC1_002”. X-ray diffraction, 2 ligands (OYN, SO4), 4 pockets (best druggability 0.71). MolNFT v1 #184934 on GenesisL1: 3D structure, binding sites and…

PDB: 7P88
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: OYN, SO4
Pockets: 4 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Yth domain-containing protein 1	protein	164	34% helix, 24% strand	Q96MU7

Ligands and binding sites

OYN · 2-chloranyl-~{N}-methyl-9~{H}-purin-6-amine · 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

4 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	0.71	0.87	34	SO4
2	54	0.53	0.88	16	OYN
3	53	0.52	0.88	16	OYN
4	102	0.42	0.77	16	empty

Interfaces

1 interface between chains.

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

Compared structures

7P88 · Crystal structure of YTHDC1 with compound YLI_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 7P88 · PDBe 7P88 · UniProt Q96MU7

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