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Human chymase in complex with 7-oxo-3-(phenoxyimino)-1,4-diazepane derivative

Analyse Human chymase in complex with 7-oxo-3-(phenoxyimino)-1,4-diazepane derivative in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5YJM
Type: protein
Length: 218 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Human chymase
Ligands: 8W3, NAG, ZN
Pockets: 1 · best druggability 0.46

Structure

x-ray diffraction · 1 distinct chain · 9% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Human chymase	protein	218	9% helix, 39% strand	—

Ligands and binding sites

8W3 · 2-amino-4-((R)-1-((R,Z)-6-(5-chloro-2-methoxybenzyl)-7-oxo-3-(phenoxyimino)-1,4-diazepane-1-carboxamido) propyl)benzoic acid · ligand · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
ZN · Zinc ion · metal · chains A

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	126	0.46	0.78	29	8W3

Modifications

Observed in the structure: 3 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

5YJM · Human chymase in complex with 7-oxo-3-(phenoxyimino)-1,4-diazepane derivative · 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
Elsewhere: RCSB PDB 5YJM · PDBe 5YJM

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