8B4W | pdb_00008b4w

X-ray structure of furin (PCSK3) in complex with 1H-isoindol-3-amine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.179 (Depositor), 0.179 (DCC) 
  • R-Value Work: 
    0.166 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 
    0.167 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Fragment-Based Design, Synthesis, and Characterization of Aminoisoindole-Derived Furin Inhibitors.

Lange, R.W.Bloch, K.Heindl, M.R.Wollenhaupt, J.Weiss, M.S.Brandstetter, H.Klebe, G.Falcone, F.H.Bottcher-Friebertshauser, E.Dahms, S.O.Steinmetzer, T.

(2024) ChemMedChem 19: e202400057-e202400057

  • DOI: https://doi.org/10.1002/cmdc.202400057
  • Primary Citation Related Structures: 
    8B4V, 8B4W, 8B4X, 8OYH

  • PubMed Abstract: 

    A 1H-isoindol-3-amine was identified as suitable P1 group for the proprotein convertase furin using a crystallographic screening with a set of 20 fragments known to occupy the S1 pocket of trypsin-like serine proteases. Its binding mode is very similar to that observed for the P1 group of benzamidine-derived peptidic furin inhibitors suggesting an aminomethyl substitution of this fragment to obtain a couplable P1 residue for the synthesis of substrate-analogue furin inhibitors. The obtained inhibitors possess a slightly improved picomolar inhibitory potency compared to their benzamidine-derived analogues. The crystal structures of two inhibitors in complex with furin revealed that the new P1 group is perfectly suited for incorporation in peptidic furin inhibitors. Selected inhibitors were tested for antiviral activity against respiratory syncytial virus (RSV) and a furin-dependent influenza A virus (SC35M/H7N7) in A549 human lung cells and demonstrated an efficient inhibition of virus activation and replication at low micromolar or even submicromolar concentrations. First results suggest that the Mas-related G-protein coupled receptor GPCR-X2 could be a potential off-target for certain benzamidine-derived furin inhibitors.


  • Organizational Affiliation
    • Institute of Pharmaceutical Chemistry, Philipps University, Marbacher Weg 6-10, D-35032, Marburg, Germany Phone.

Macromolecule Content 

  • Total Structure Weight: 53.21 kDa 
  • Atom Count: 4,403 
  • Modeled Residue Count: 472 
  • Deposited Residue Count: 480 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P09958-1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
P [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
F05
(Subject of Investigation/LOI)

Query on F05



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A]
1H-isoindol-3-amine
C8 H8 N2
MTKKGHVQPVOXIL-UHFFFAOYSA-N
DMS

Query on DMS



Download:Ideal Coordinates CCD File
M [auth A],
N [auth A],
O [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
G [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
L [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
H [auth A],
I [auth A],
J [auth A],
K [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.179 (Depositor), 0.179 (DCC) 
  • R-Value Work:  0.166 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 0.167 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.959α = 90
b = 131.959β = 90
c = 155.34γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Austrian Science FundAustriaM 2730

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-04
    Type: Initial release
  • Version 1.1: 2024-03-13
    Changes: Database references
  • Version 1.2: 2024-05-15
    Changes: Database references
  • Version 1.3: 2024-11-13
    Changes: Structure summary