MolNFT v1 · #102458 · protein

X-ray structure of human furin in complex with the competitive inhibitor phac-rvr-amba

4OMD: “X-ray structure of human furin in complex with the competitive inhibitor phac-rvr-amba”. X-ray diffraction, 4 ligands (HY1, 00S, CA), 20 pockets (best druggability 0.79). MolNFT v1 #102458 on GenesisL1: 3D structure, binding sites…

PDB: 4OMD
Type: protein
Length: 2,810 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Furin; Phenylacetyl-arg-val-arg-(AMIDOMETHYL)BENZAMIDINE
EC: 3.4.21.75
UniProt: P09958
Ligands: HY1, 00S, CA, NA
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 20% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Furin (EC 3.4.21.75)	protein	466	20% helix, 28% strand	P09958
B, D, E, F	Furin (EC 3.4.21.75)	protein	465	20% helix, 28% strand	P09958
H, I, J, K, L, N	Phenylacetyl-arg-val-arg-(AMIDOMETHYL)BENZAMIDINE	protein	3	0% helix, 33% strand	—

Ligands and binding sites

HY1 · Phenylacetaldehyde · ligand · 6 copies · chains A, H, B, I, C, J, D, K, E, L, F, N
00S · 4-(aminomethyl)benzenecarboximidamide · ligand · 6 copies · chains A, H, B, I, C, J, D, K, E, L, F, N
CA · Calcium ion · metal · 18 copies · chains A, B, C, D, E, F
NA · Sodium ion · metal · 6 copies · chains A, B, C, D, E, F
FMT · Formic acid · additive · 12 copies · chains A, B, C, D, E, F

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

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	970	0.79	0.81	124	empty
2	669	0.79	0.84	83	empty
3	514	0.79	0.86	63	empty
4	738	0.78	0.82	94	FMT
5	695	0.78	0.82	94	FMT

Interfaces

11 interfaces between chains.

A–B · 1330 Å² buried · 12 hydrogen bonds · protein-protein
E–F · 1324 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 1307 Å² buried · 10 hydrogen bonds · protein-protein
C–F · 1084 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 436 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 disulfide, 12 covalent (disulfide, covalent ligand).

Compared structures

4OMD · X-ray structure of human furin in complex with the competitive inhibitor Phac-RVR-Amba · the same entry in another collection · chain N against N, 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 P09958
Elsewhere: RCSB PDB 4OMD · PDBe 4OMD · UniProt P09958

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