6HLB | pdb_00006hlb

X-ray structure of furin in complex with the cyclic peptide c[succinyl-Phe-2-Nal-(Arg)4-Lys]-Arg-4-Amba


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.187 (Depositor), 0.167 (DCC) 
  • R-Value Work: 
    0.169 (Depositor) 
  • R-Value Observed: 
    0.170 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6HLB

This is version 1.3 of the entry. See complete history

Literature

Design, Synthesis, and Characterization of Macrocyclic Inhibitors of the Proprotein Convertase Furin.

Van Lam van, T.Ivanova, T.Hardes, K.Heindl, M.R.Morty, R.E.Bottcher-Friebertshauser, E.Lindberg, I.Than, M.E.Dahms, S.O.Steinmetzer, T.

(2019) ChemMedChem 14: 673-685

  • DOI: https://doi.org/10.1002/cmdc.201800807
  • Primary Citation Related Structures: 
    6HLB, 6HLD, 6HLE, 6HZA, 6HZB, 6HZC, 6HZD

  • PubMed Abstract: 

    The activation of viral glycoproteins by the host protease furin is an essential step in the replication of numerous pathogenic viruses. Thus, effective inhibitors of furin could serve as broad-spectrum antiviral drugs. A crystal structure of an inhibitory hexapeptide derivative in complex with furin served as template for the rational design of various types of new cyclic inhibitors. Most of the prepared derivatives are relatively potent furin inhibitors with inhibition constants in the low nanomolar or even sub-nanomolar range. For seven derivatives the crystal structures in complex with furin could be determined. In three complexes, electron density was found for the entire inhibitor. In the other cases the structures could be determined only for the P6/P5-P1 segments, which directly interact with furin. The cyclic derivatives together with two non-cyclic reference compounds were tested as inhibitors of the proteolytic activation and replication of respiratory syncytial virus in cells. Significant antiviral activity was found for both linear reference inhibitors, whereas a negligible efficacy was determined for the cyclic derivatives.


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

Macromolecule Content 

  • Total Structure Weight: 54.39 kDa 
  • Atom Count: 4,028 
  • Modeled Residue Count: 474 
  • Deposited Residue Count: 491 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Furin482Homo 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
PHE-(ALN)-ARG-ARG-ARG-ARG-SLL-ARG-00S9synthetic constructMutation(s): 0 

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  2 Unique
IDChains TypeFormula2D DiagramParent
ALN
Query on ALN
B
L-PEPTIDE LINKINGC13 H13 N O2ALA
SLL
Query on SLL
B
L-PEPTIDE LINKINGC10 H18 N2 O5LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.187 (Depositor), 0.167 (DCC) 
  • R-Value Work:  0.169 (Depositor) 
  • R-Value Observed: 0.170 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.255α = 90
b = 133.255β = 90
c = 157.351γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2019-02-06 
  • Deposition Author(s): Dahms, S.O.

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-06
    Type: Initial release
  • Version 1.1: 2019-02-27
    Changes: Data collection, Database references
  • Version 1.2: 2019-04-03
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-24
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description