9QWD | pdb_00009qwd

X-ray structure of furin (PCSK3) in complex with the biphenyl-derived compound 34 (mi2470)

PDB DOI: https://doi.org/10.2210/pdb9QWD/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-04-14 Released: 2025-12-24
Deposition Author(s): Dahms, S.O., Brandstetter, H.
Funding Organization(s): Austrian Science Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.161 (Depositor), 0.167 (DCC)
R-Value Work:
0.135 (Depositor), 0.145 (DCC)
R-Value Observed:
0.136 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Design, Synthesis, and Characterization of Dichlorobiphenyl-Derived Inhibitors of the Proprotein Convertase Furin.

Lange, R.W., Boller, C., Loresch, M., Bloch, K., Bottcher-Friebertshauser, E., Brandstetter, H., Dahms, S.O., Steinmetzer, T.

(2025) J Med Chem 68: 25157-25170

PubMed: 41319212 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acs.jmedchem.5c02157
Primary Citation Related Structures:
9QWB, 9QWC, 9QWD, 9QWE, 9QWF, 9QWG

PubMed Abstract:
The proprotein convertase (PC) furin emerged as promising drug target for the treatment of numerous infectious diseases, cancer and cystic fibrosis. A recently described nonpeptidic lead structure served as template to develop a new series of PC inhibitors containing a dichlorobiphenyl-derived core segment decorated with a left and right inhibitor arm. The compounds were tested for their inhibitory potency against furin and the structurally related PC7. The most potent compounds inhibited furin with K _i values <5 nM, whereas most of them were significantly weaker inhibitors of PC7. Only for one compound, a significant potency with a K _i value of 7.3 nM against PC7 was found. Furthermore, crystal structures of six inhibitors in complex with furin were determined. Selected inhibitors were additionally tested for their antiviral potency against the furin-dependent H7N7 influenza A strain SC35M; a significant antiviral potency was found for compound 9 .

Organizational Affiliation

Institute of Pharmaceutical Chemistry, Philipps University, Marbacher Weg 10, D-35032 Marburg, Germany.

Macromolecule Content

Total Structure Weight: 53.9 kDa
Atom Count: 4,359
Modeled Residue Count: 472
Deposited Residue Count: 482
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09958
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A	Go to GlyGen: P09958-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1JA2 (Subject of Investigation/LOI) Query on A1JA2 Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain Q [auth A]	Q [auth A]	1-[[3-[3,5-bis(chloranyl)phenyl]-5-[(4-pyridin-4-ylpiperazin-1-yl)methyl]phenyl]methyl]-4-pyridin-4-yl-piperazine C₃₂ H₃₄ Cl₂ N₆ IFPHOKXTHCEYJO-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Interactions & Density Focus chain Q [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain P [auth A] MOL2 format, chain P [auth A] mmCIF format, chain P [auth A]	P [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain P [auth A] Interactions & Density Focus chain P [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A]	J [auth A] K [auth A] L [auth A] M [auth A] N [auth A] J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	B [auth A], C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF 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 E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	E [auth A], F [auth A], G [auth A], H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]