MolNFT v1 · #106413 · protein
X-ray structure of human furin in complex with the competitive inhibitor para-guanidinomethyl-phac-R-tle-R-amba
4RYD: “X-ray structure of human furin in complex with the competitive inhibitor…”. X-ray diffraction, 4 ligands (2UE, 00S, CA), 20 pockets (best druggability 0.81). MolNFT v1 #106413 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4RYD
- Type
- protein
- Length
- 2,810 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Furin; Para-guanidinomethyl-phenylacetyl-arg-(3-methylvaline)-arg…
- EC
- 3.4.21.75
- UniProt
- P09958
- Ligands
- 2UE, 00S, CA, NA
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Furin (EC 3.4.21.75) | protein | 466 | 21% helix, 28% strand | P09958 |
| B, D, E, F | Furin (EC 3.4.21.75) | protein | 465 | 22% helix, 28% strand | P09958 |
| H, I, J, K, L, N | Para-guanidinomethyl-phenylacetyl-arg-(3-methylvaline)-arg- (AMIDOMETHYL)BENZAMIDINE | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- 2UE · 1-[4-(2-oxoethyl)benzyl]guanidine · 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 · 18 copies · chains A, B, C, F, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 439 | 0.81 | 0.89 | 42 | empty |
| 2 | 493 | 0.80 | 0.87 | 45 | empty |
| 3 | 689 | 0.79 | 0.83 | 106 | FMT |
| 4 | 811 | 0.79 | 0.82 | 93 | 2UE |
| 5 | 878 | 0.78 | 0.81 | 116 | FMT |
Interfaces
11 interfaces between chains.
- A–B · 1356 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 1345 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1341 Ų buried · 8 hydrogen bonds · protein-protein
- C–F · 1118 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 437 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 12 covalent, 6 modified (disulfide, covalent ligand, nonstandard).
Compared structures
- 4RYD · X-ray structure of human furin in complex with the competitive inhibitor… · the same entry in another collection · chain I against I, 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 4RYD · PDBe 4RYD · UniProt P09958
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