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

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Basic information

Entry
Database: PDB / ID: 9qwf
TitleX-ray structure of furin (PCSK3) in complex with the biphenyl-derived compound 13 (mi3102)
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: 1.65 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)53,95217
Polymers52,3891
Non-polymers1,56316
Water8,467470
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-57 kcal/mol
Surface area17700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.270, 131.270, 155.235
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-605-

NA

21A-1105-

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 / Production host: Homo sapiens (human) / References: UniProt: P09958, furin
#6: 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, 485 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


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


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


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


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Chemical ChemComp-A1JA5 / ~{N}-[[1-[[3-[3,5-bis(chloranyl)phenyl]-5-[(4-piperidin-4-ylpiperidin-1-yl)methyl]phenyl]methyl]piperidin-4-yl]methyl]-2,2,2-tris(fluoranyl)ethanamide


Mass: 625.595 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H41Cl2F3N4O / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 3.7 Å3/Da / Density % sol: 66.8 %
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 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967697 Å / Relative weight: 1
ReflectionResolution: 1.65→42.97 Å / Num. obs: 92367 / % possible obs: 97.5 % / Redundancy: 21.2 % / Biso Wilson estimate: 21.92 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.148 / Net I/σ(I): 16.33
Reflection shellResolution: 1.65→1.75 Å / Mean I/σ(I) obs: 1.53 / Num. unique obs: 14665 / CC1/2: 0.688 / Rrim(I) all: 2.305 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487phasing
XDSVERSION Jun 30, 2023data reduction
XDSVERSION Jun 30, 2023data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→42.97 Å / SU ML: 0.1791 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.6623
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1681 4590 4.97 %
Rwork0.1546 87750 -
obs0.1553 92340 97.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.23 Å2
Refinement stepCycle: LAST / Resolution: 1.65→42.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3601 0 82 470 4153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00793958
X-RAY DIFFRACTIONf_angle_d0.97545420
X-RAY DIFFRACTIONf_chiral_restr0.0586580
X-RAY DIFFRACTIONf_plane_restr0.0106731
X-RAY DIFFRACTIONf_dihedral_angle_d12.69381442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.31781590.30662859X-RAY DIFFRACTION96.98
1.67-1.690.29941570.2792849X-RAY DIFFRACTION96.97
1.69-1.710.29971590.26182868X-RAY DIFFRACTION97.3
1.71-1.730.24651820.25082836X-RAY DIFFRACTION97.23
1.73-1.750.27291530.24072904X-RAY DIFFRACTION97.36
1.75-1.780.2251390.2122867X-RAY DIFFRACTION97.44
1.78-1.80.22011370.20252892X-RAY DIFFRACTION97.3
1.8-1.830.24351860.19772857X-RAY DIFFRACTION97.63
1.83-1.860.21531420.18852894X-RAY DIFFRACTION97.62
1.86-1.890.19691520.17862876X-RAY DIFFRACTION97.68
1.89-1.920.21631540.16812917X-RAY DIFFRACTION97.8
1.92-1.960.19131430.16052929X-RAY DIFFRACTION98.02
1.96-1.990.18811310.15762939X-RAY DIFFRACTION97.77
1.99-2.030.16981490.15872905X-RAY DIFFRACTION98.23
2.03-2.080.17871530.14832918X-RAY DIFFRACTION98.15
2.08-2.130.15311530.13562919X-RAY DIFFRACTION98.18
2.13-2.180.16861560.12972919X-RAY DIFFRACTION98.27
2.18-2.240.15281580.12312942X-RAY DIFFRACTION98.41
2.24-2.310.1341390.12632968X-RAY DIFFRACTION98.48
2.31-2.380.15591360.12912968X-RAY DIFFRACTION98.63
2.38-2.460.15671410.13512962X-RAY DIFFRACTION98.63
2.46-2.560.1611490.1382969X-RAY DIFFRACTION99.02
2.56-2.680.1651450.15012932X-RAY DIFFRACTION96.61
2.68-2.820.17581320.15612440X-RAY DIFFRACTION81.42
2.82-30.16821620.15192912X-RAY DIFFRACTION96.3
3-3.230.13611490.14523016X-RAY DIFFRACTION99.34
3.23-3.550.14831660.14163045X-RAY DIFFRACTION99.38
3.55-4.070.13411610.12723064X-RAY DIFFRACTION99.57
4.07-5.120.13681670.12763101X-RAY DIFFRACTION99.73
5.12-42.970.1881800.23283X-RAY DIFFRACTION99.31
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2234352814510.00598705832245-0.06576614876820.4445008289710.150186522220.6443482761870.006097477892140.0123562470028-0.00114362619493-0.0369996057116-0.006913878699710.0331598712997-0.00407784060445-0.0710233686211-1.25702748644E-60.120781686525-0.001512239883230.002573033617170.1576457182590.003109328478430.15617683268635.1138010075-37.677805710.262105699037
20.03682146064520.0264602597725-0.01980250658870.06661590001570.00548605897690.0244010178410.0209124640143-0.06933937344910.0216840157906-0.001916093438840.03646872697470.00209181028707-0.117914619158-0.0391229002653-4.92937818148E-50.27067538689-0.00766439473670.01250774985460.2433756050180.01085711113140.22965451971340.292094043-37.4511313202-3.91800757911
31.99999977384-6.714979545487.286452156191.999999580331.999999598831.999999970710.2464731610080.142670734191-0.040027887903-0.553076968535-0.2024406786860.118294666640.2171278739660.445124213593-0.04984046576770.4244239636950.1272501563860.05064940632620.374505990206-0.07935847924010.4616160985818.301736234-19.6242208969.71505079522
40.191023187406-0.0990069875741-0.0223793607110.3298521122060.09106729129380.2985906890950.00669244182542-0.01684556931740.0154315286939-0.00535502593351-0.0061234309964-0.000426397790361-0.0262741822325-0.0392886599443-1.50909376082E-50.125254302637-0.0103095492770.009131190080860.141084570469-0.0002646705880990.13934016003437.3002841395-37.82350197060.937158026114
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain AAA110 - 5811 - 472
22chain CCB - O1 - 17
33chain DDP1
44chain SSQ702 - 1674

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