MolNFT v1 · #185204 · protein

Crystal structure of YTHDC1 with compound DHU_DC1_226

7PJP · Yth domain-containing protein 1: “Crystal structure of YTHDC1 with compound DHU_DC1_226”. X-ray diffraction, 2 ligands (7SL, SO4), 7 pockets (best druggability 0.58). MolNFT v1 #185204 on GenesisL1: 3D structure, binding sites and…

PDB: 7PJP
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: 7SL, SO4
Pockets: 7 · best druggability 0.58

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Yth domain-containing protein 1	protein	164	32% helix, 25% strand	Q96MU7

Ligands and binding sites

7SL · 5-(furan-2-yl)-N-methyl-1H-pyrazole-3-carboxamide · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 8 copies · chains A, B

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

Pockets

7 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	79	0.58	0.87	17	7SL
2	72	0.49	0.84	18	7SL
3	83	0.48	0.82	18	empty
4	123	0.42	0.76	15	empty
5	102	0.42	0.77	17	empty

Interfaces

1 interface between chains.

A–B · 258 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

7PJP · Crystal structure of YTHDC1 with compound DHU_DC1_226 · 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 7PJP · PDBe 7PJP · UniProt Q96MU7

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