MolNFT v1 · #123525 · protein

Neprilysin complexed with LBQ657

5JMY: “Neprilysin complexed with LBQ657”. X-ray diffraction, 3 ligands (6LD, NAG, ZN), 20 pockets (best druggability 0.83). MolNFT v1 #123525 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5JMY
Type: protein
Length: 1,392 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Neprilysin
EC: 3.4.24.11
UniProt: P08473
Ligands: 6LD, NAG, ZN
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 59% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Neprilysin (EC 3.4.24.11)	protein	696	59% helix, 8% strand	P08473

Ligands and binding sites

6LD · Sacubitrilat · ligand · 2 copies · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B
ZN · Zinc ion · metal · 2 copies · chains A, B

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

Pockets

20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1143	0.83	0.84	98	empty
2	171	0.68	0.87	31	ZN, 6LD
3	148	0.67	0.88	29	6LD
4	364	0.65	0.80	53	empty
5	156	0.56	0.81	25	empty

Interfaces

1 interface between chains.

A–B · 1004 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 8 glycan (disulfide, N-glycosylation).

Compared structures

5JMY · Neprilysin complexed with LBQ657 · the same entry in another collection · chain A against A, TM-score 1.00
P08473 · AlphaFold monomer V2.0 prediction for neprilysin (P08473) · a predicted model of the same protein · 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 P08473
Elsewhere: RCSB PDB 5JMY · PDBe 5JMY · UniProt P08473

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