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WDR5DELTA23 bound to N-(4-(5-(hydroxymethyl)-1H-imidazol-2-YL)BUTYL) benzamide

Analyse WDR5DELTA23 bound to N-(4-(5-(hydroxymethyl)-1H-imidazol-2-YL)BUTYL) benzamide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6PG9
Type: protein
Length: 608 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Wd repeat-containing protein 5
UniProt: P61964
Ligands: OH1
Pockets: 3 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 0% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Wd repeat-containing protein 5	protein	304	0% helix, 51% strand	P61964

Ligands and binding sites

OH1 · N-{4-[4-(hydroxymethyl)-1H-imidazol-2-yl]butyl}benzamide · ligand · 2 copies · chains A, B

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

Pockets

3 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	1082	0.83	0.84	91	OH1
2	633	0.75	0.81	69	OH1
3	203	0.55	0.79	29	empty

Interfaces

1 interface between chains.

A–B · 506 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6PG9 · WDR5delta23 bound to N-(4-(5-(hydroxymethyl)-1H-imidazol-2-yl)butyl)benzamide · 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 P61964
Elsewhere: RCSB PDB 6PG9 · PDBe 6PG9 · UniProt P61964

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