MolNFT v1 · #126604 · protein

Structure of human O-glcnac hydrolase with new iminocyclitol type inhibitor

5M7U · Protein O-glcnacase: “Structure of human O-glcnac hydrolase with new iminocyclitol type inhibitor”. X-ray diffraction, 1 ligand (XHA), 6 pockets (best druggability 0.79). MolNFT v1 #126604 on GenesisL1: 3D structure, binding sites…

PDB: 5M7U
Type: protein
Length: 896 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein O-glcnacase
EC: 3.2.1.169, 3.2.1.-
UniProt: O60502
Ligands: XHA
Pockets: 6 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 49% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein O-glcnacase (EC 3.2.1.169, 3.2.1.-)	protein	448	49% helix, 9% strand	O60502
B	Protein O-glcnacase (EC 3.2.1.169, 3.2.1.-)	protein	448	49% helix, 9% strand	O60502

Ligands and binding sites

XHA · 2-[(2~{R},3~{S},4~{R},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)-1-[3-[3-(trifluoromethyl) phenyl]propyl]pyrrolidin-2-yl]-~{N}-methyl-ethanamide · ligand · 2 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1100	0.79	0.81	86	empty
2	581	0.69	0.78	76	XHA
3	412	0.64	0.78	53	XHA
4	69	0.61	0.91	16	empty
5	51	0.29	0.76	11	empty

Interfaces

1 interface between chains.

A–B · 4515 Å² buried · 43 hydrogen bonds · protein-protein

Compared structures

5M7U · Structure of human O-GlcNAc hydrolase with new iminocyclitol type inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
O60502 · AlphaFold monomer V2.0 prediction for protein O-glcnacase (O60502) · a predicted model of the same protein · chain B against A, TM-score 0.94

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 O60502
Elsewhere: RCSB PDB 5M7U · PDBe 5M7U · UniProt O60502

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