6YD4

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

PDB DOI: https://doi.org/10.2210/pdb6YD4/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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.169
R-Value Work: 0.153
R-Value Observed: 0.154

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

PubMed: 33732412 Search on PubMedSearch on PubMed Central
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.

Macromolecule Content

Total Structure Weight: 53.37 kDa
Atom Count: 4,237
Modelled Residue Count: 478
Deposited Residue Count: 485
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Furin	A	480	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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P09958
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
4-guanidinomethyl-phenylacetyl-Canavanine-Tle-Canavanine-Amba	B	5	synthetic construct	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A]	J [auth A], K [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A]	L [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	C [auth A], D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A]	I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A]	F [auth A], G [auth A], H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TBG Query on TBG	B	L-PEPTIDE LINKING	C₆ H₁₃ N O₂		VAL

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.169
R-Value Work: 0.153
R-Value Observed: 0.154
Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.685	α = 90
b = 131.685	β = 90
c = 155.499	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-02-17

Deposition Author(s):

Dahms, S.O.

Funding Organization	Location	Grant Number
Austrian Science Fund	Austria	M 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, 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