6YD3

X-ray structure of furin in complex with the canavanine derived inhibitor 4-guanidinomethyl-phenylacetyl-Canavanine-Tle-Arg-Amba


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 3.1 of the entry. See complete history


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

  • DOI: https://doi.org/10.1021/acsmedchemlett.0c00651
  • Primary Citation of 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.


  • Organizational Affiliation

    Institute of Pharmaceutical Chemistry, Philipps University, Marbacher Weg 6, 35032 Marburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Furin480Homo sapiensMutation(s): 0 
Gene Names: FURINFURPACEPCSK3
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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09958
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
4-guanidinomethyl-phenylacetyl-Canavanine-Tle-Arg-AmbaB [auth 611]5synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
DMS
Query on DMS

Download Ideal Coordinates CCD File 
L [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TBG
Query on TBG
B [auth 611]L-PEPTIDE LINKINGC6 H13 N O2VAL
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.561α = 90
b = 131.561β = 90
c = 155.3γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
Cootmodel building
PHENIXrefinement
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

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

Funding OrganizationLocationGrant Number
Austrian Science FundAustriaM 2730

Revision History  (Full details and data files)

  • 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