6YD2 | pdb_00006yd2

X-ray structure of furin in complex with the canavanine-based inhibitor 4-aminomethyl-phenylacetyl-canavanine-Tle-Arg-Amba

• PDB DOI: https://doi.org/10.2210/pdb6YD2/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2020-03-20 Released: 2021-02-17 
• Deposition Author(s): Dahms, S.O.
• Funding Organization(s): Austrian Science Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.177 (Depositor), 0.178 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

The Basicity Makes the Difference: Improved Canavanine-Derived Inhibitors of the Proprotein Convertase Furin.

Lam van, T.V., Heindl, M.R., Schlutt, C., Bottcher-Friebertshauser, E., Bartenschlager, R., Klebe, G., Brandstetter, H., Dahms, S.O., Steinmetzer, T.

(2021) ACS Med Chem Lett 12: 426-432

• PubMed: 33732412 
• DOI: https://doi.org/10.1021/acsmedchemlett.0c00651
• Primary Citation Related Structures: 
  6YD2, 6YD3, 6YD4, 6YD7


• PubMed Abstract: 
  

  Furin activates numerous viral glycoproteins, and its inhibition prevents virus replication and spread. Through the replacement of arginine by the less basic canavanine, new inhibitors targeting furin in the trans-Golgi network were developed. These inhibitors exert potent antiviral activity in cell culture with much lower toxicity than arginine-derived analogues, most likely due to their reduced protonation in the blood circulation. Thus, despite its important physiological functions, furin might be a suitable antiviral drug target.

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Organizational Affiliation: 
• Institute of Pharmaceutical Chemistry, Philipps University, Marbacher Weg 6, 35032 Marburg, Germany.
Institute of Virology, Philipps University, Hans-Meerwein-Strasse 2, 35043 Marburg, Germany.
Department of Infectious Diseases, Molecular Virology, Heidelberg University and German Center for Infection Research, Heidelberg Partner Site, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany.
Department of Biosciences, University of Salzburg, Billrothstrasse 11, 5020 Salzburg, Austria.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 53.58 kDa 
• Atom Count: 4,179 
• Modeled Residue Count: 478 
• Deposited Residue Count: 487 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Furin	A	482	Homo sapiens	Mutation(s): 0  Gene Names: FURIN, FUR, PACE, PCSK3 EC: 3.4.21.75
UniProt & NIH Common Fund Data Resources
Find proteins for P09958 (Homo sapiens) Explore P09958  Go to UniProtKB:  P09958
PHAROS:  P09958 GTEx:  ENSG00000140564

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
4-aminomethyl-phenylacetyl-canavanine-Tle-Arg-Amba	B [auth 611]	5	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	J [auth A], K [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
DMS	L [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CA	C [auth A], D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	F [auth A], G [auth A], H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
GGB	B [auth 611]	L-PEPTIDE LINKING	C5 H12 N4 O3		--
TBG	B [auth 611]	L-PEPTIDE LINKING	C6 H13 N O2		VAL

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.177 (Depositor), 0.178 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.506	α = 90
b = 131.506	β = 90
c = 155.243	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
PHENIX	refinement
Coot	model building
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-02-17 
Deposition Author(s): Dahms, S.O.

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Funding Organization	Location	Grant Number
Austrian Science Fund	Austria	M 2730

Revision History  

• Version 1.0: 2021-02-17
  Type: Initial release
  
• Version 1.1: 2021-03-31
  Changes: Database references
• Version 2.0: 2022-10-19
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Other, Polymer sequence, Source and taxonomy, Structure summary
• Version 3.0: 2023-11-15
  Changes: Atomic model, Data collection
• Version 3.1: 2024-01-31
  Changes: Refinement description