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- PDB-9qwe: X-ray structure of furin (PCSK3) in complex with the biphenyl-der... -

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Basic information

Entry
Database: PDB / ID: 9qwe
TitleX-ray structure of furin (PCSK3) in complex with the biphenyl-derived compound 27 (mi2471)
ComponentsFurin
KeywordsHYDROLASE / furin / proprotein convertase subtilisin/kexin type 3 / PCSK3 / antiviral / inhibitor / protease / complex
Function / homology
Function and homology information


furin / nerve growth factor production / dibasic protein processing / plasma lipoprotein particle remodeling / NGF processing / negative regulation of transforming growth factor beta1 production / Assembly of active LPL and LIPC lipase complexes / regulation of cholesterol transport / : / negative regulation of low-density lipoprotein particle receptor catabolic process ...furin / nerve growth factor production / dibasic protein processing / plasma lipoprotein particle remodeling / NGF processing / negative regulation of transforming growth factor beta1 production / Assembly of active LPL and LIPC lipase complexes / regulation of cholesterol transport / : / negative regulation of low-density lipoprotein particle receptor catabolic process / peptide biosynthetic process / cytokine precursor processing / Pre-NOTCH Processing in Golgi / nerve growth factor binding / Synthesis and processing of ENV and VPU / Formation of the cornified envelope / secretion by cell / Signaling by PDGF / trans-Golgi network transport vesicle / Signaling by NODAL / heparan sulfate binding / blastocyst formation / Elastic fibre formation / positive regulation of membrane protein ectodomain proteolysis / zymogen activation / peptide hormone processing / CD163 mediating an anti-inflammatory response / Activation of Matrix Metalloproteinases / regulation of protein catabolic process / Collagen degradation / Maturation of hRSV A proteins / TGF-beta receptor signaling activates SMADs / collagen catabolic process / viral translation / Respiratory syncytial virus (RSV) attachment and entry / Uptake and function of anthrax toxins / extracellular matrix disassembly / regulation of signal transduction / endopeptidase activator activity / Removal of aminoterminal propeptides from gamma-carboxylated proteins / viral life cycle / extracellular matrix organization / peptide binding / serine-type peptidase activity / transforming growth factor beta receptor signaling pathway / protein maturation / negative regulation of inflammatory response to antigenic stimulus / trans-Golgi network / serine-type endopeptidase inhibitor activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / protein processing / Golgi lumen / peptidase activity / heparin binding / protease binding / endopeptidase activity / amyloid fibril formation / Induction of Cell-Cell Fusion / Potential therapeutics for SARS / Attachment and Entry / positive regulation of viral entry into host cell / endosome membrane / viral protein processing / membrane raft / Amyloid fiber formation / Golgi membrane / serine-type endopeptidase activity / cell surface / endoplasmic reticulum / extracellular exosome / extracellular region / metal ion binding / membrane / plasma membrane
Similarity search - Function
Peptidase S8, pro-domain / Peptidase S8, pro-domain superfamily / Peptidase S8 pro-domain / Kexin/furin catalytic domain / P domain / Proprotein convertase P-domain / P/Homo B domain profile. / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. ...Peptidase S8, pro-domain / Peptidase S8, pro-domain superfamily / Peptidase S8 pro-domain / Kexin/furin catalytic domain / P domain / Proprotein convertase P-domain / P/Homo B domain profile. / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Furin-like repeat / Furin-like repeats / Growth factor receptor cysteine-rich domain superfamily / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDahms, S.O. / Brandstetter, H.
Funding support Austria, 2items
OrganizationGrant numberCountry
Austrian Science FundM 2730-B Austria
Austrian Science FundP26_P36648 Austria
CitationJournal: J.Med.Chem. / Year: 2025
Title: Design, Synthesis, and Characterization of Dichlorobiphenyl-Derived Inhibitors of the Proprotein Convertase Furin.
Authors: Lange, R.W. / Boller, C. / Loresch, M. / Bloch, K. / Bottcher-Friebertshauser, E. / Brandstetter, H. / Dahms, S.O. / Steinmetzer, T.
History
DepositionApr 14, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Furin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,89317
Polymers52,3891
Non-polymers1,50416
Water8,251458
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-56 kcal/mol
Surface area17620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.064, 131.064, 155.059
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-606-

NA

21A-1103-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Furin / Dibasic-processing enzyme / Paired basic amino acid residue-cleaving enzyme / PACE


Mass: 52388.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FURIN, FUR, PACE, PCSK3 / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P09958, furin
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 473 molecules

#2: Chemical ChemComp-A1JA3 / ~{N}-[[1-[[3-[3,5-bis(chloranyl)phenyl]-5-[(4-pyridin-4-ylpiperazin-1-yl)methyl]phenyl]methyl]piperidin-4-yl]methyl]ethanamide


Mass: 566.564 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H37Cl2N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.69 Å3/Da / Density % sol: 66.65 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: CRYSTALLIZATION SOLUTION: 100mM MES, 200mM K/NAH2PO4, PH 5.5, 2 M NACL; RESERVOIR SOLUTION: 3.0-3.2M NACL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.967697 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 26, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967697 Å / Relative weight: 1
ReflectionResolution: 1.6→42.9 Å / Num. obs: 103405 / % possible obs: 97.1 % / Redundancy: 20.4 % / Biso Wilson estimate: 17.24 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.0274 / Net I/σ(I): 13.19
Reflection shellResolution: 1.6→1.7 Å / Mean I/σ(I) obs: 1.16 / Num. unique obs: 15276 / CC1/2: 0.425 / Rrim(I) all: 4.812 / % possible all: 92.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487phasing
XDSVERSION Jun 30, 2024data reduction
XDSVERSION Jun 30, 2024data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→42.9 Å / SU ML: 0.1759 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.8009
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1854 4988 4.97 %
Rwork0.1511 95426 -
obs0.1528 100414 97.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.05 Å2
Refinement stepCycle: LAST / Resolution: 1.6→42.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3590 0 85 458 4133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00783995
X-RAY DIFFRACTIONf_angle_d0.92095474
X-RAY DIFFRACTIONf_chiral_restr0.0564581
X-RAY DIFFRACTIONf_plane_restr0.0107748
X-RAY DIFFRACTIONf_dihedral_angle_d12.75671480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.36751330.32212664X-RAY DIFFRACTION82.68
1.62-1.640.32771420.31982992X-RAY DIFFRACTION92.18
1.64-1.660.34661640.2873065X-RAY DIFFRACTION95.56
1.66-1.680.31491740.25873132X-RAY DIFFRACTION97.01
1.68-1.70.30331810.24163118X-RAY DIFFRACTION97.52
1.7-1.720.29961890.24233150X-RAY DIFFRACTION97.6
1.72-1.750.25151820.21653146X-RAY DIFFRACTION97.94
1.75-1.770.23381500.2113173X-RAY DIFFRACTION97.91
1.77-1.80.26151550.1993166X-RAY DIFFRACTION97.76
1.8-1.830.29232010.20643147X-RAY DIFFRACTION97.89
1.83-1.860.2441580.19413167X-RAY DIFFRACTION98.11
1.86-1.90.24871540.17753202X-RAY DIFFRACTION97.76
1.9-1.930.23161700.16813171X-RAY DIFFRACTION98.18
1.93-1.970.24331510.15713185X-RAY DIFFRACTION98.06
1.97-2.010.18181570.14723215X-RAY DIFFRACTION98.11
2.02-2.060.17491670.13843188X-RAY DIFFRACTION98.44
2.06-2.110.20751760.13363217X-RAY DIFFRACTION98.46
2.11-2.170.16661610.12543189X-RAY DIFFRACTION98.44
2.17-2.230.18971760.12053226X-RAY DIFFRACTION98.67
2.23-2.310.14341490.1213241X-RAY DIFFRACTION98.6
2.31-2.390.15321500.11453271X-RAY DIFFRACTION98.9
2.39-2.480.17931550.12073238X-RAY DIFFRACTION99.18
2.48-2.60.16321610.12053277X-RAY DIFFRACTION99.02
2.6-2.730.17971660.12283274X-RAY DIFFRACTION99.25
2.73-2.910.18251680.13172850X-RAY DIFFRACTION86.82
2.91-3.130.15091610.12823213X-RAY DIFFRACTION96.73
3.13-3.440.15531870.12953291X-RAY DIFFRACTION98.86
3.45-3.940.13721730.12473307X-RAY DIFFRACTION98.84
3.94-4.970.13361790.12243382X-RAY DIFFRACTION99.22
4.97-42.90.18331980.1933569X-RAY DIFFRACTION99.34

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