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- PDB-1owi: Substituted 2-Naphthamidine Inhibitors of Urokinase -

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Basic information

Entry
Database: PDB / ID: 1owi
TitleSubstituted 2-Naphthamidine Inhibitors of Urokinase
ComponentsUrokinase-type plasminogen activator
KeywordsHYDROLASE / Plasminogen activation / Serine protease / Glycoprotein / Kringle / EGF-like domain
Function / homology
Function and homology information


u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / regulation of wound healing / protein complex involved in cell-matrix adhesion / regulation of signaling receptor activity / negative regulation of plasminogen activation / regulation of smooth muscle cell migration ...u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / regulation of wound healing / protein complex involved in cell-matrix adhesion / regulation of signaling receptor activity / negative regulation of plasminogen activation / regulation of smooth muscle cell migration / serine-type endopeptidase complex / Dissolution of Fibrin Clot / smooth muscle cell migration / plasminogen activation / regulation of cell adhesion mediated by integrin / tertiary granule membrane / negative regulation of fibrinolysis / regulation of cell adhesion / specific granule membrane / serine protease inhibitor complex / fibrinolysis / chemotaxis / blood coagulation / regulation of cell population proliferation / response to hypoxia / positive regulation of cell migration / external side of plasma membrane / serine-type endopeptidase activity / focal adhesion / Neutrophil degranulation / cell surface / signal transduction / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / : / Kringle-like fold / EGF-like domain profile. ...Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / : / Kringle-like fold / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-426 / Urokinase-type plasminogen activator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.93 Å
AuthorsWendt, M.D. / Rockway, T.W. / Geyer, A. / McClellan, W. / Weitzberg, M. / Zhao, X. / Mantei, R. / Nienaber, V.L. / Stewart, K. / Klinghofer, V. / Giranda, V.L.
CitationJournal: J.Med.Chem. / Year: 2004
Title: Identification of Novel Binding Interactions in the Development of Potent, Selective 2-Naphthamidine Inhibitors of Urokinase. Synthesis, Structural Analysis, and SAR of N-Phenyl Amide 6-Substitution.
Authors: Wendt, M.D. / Rockway, T.W. / Geyer, A. / McClellan, W. / Weitzberg, M. / Zhao, X. / Mantei, R. / Nienaber, V.L. / Stewart, K. / Klinghofer, V. / Giranda, V.L.
History
DepositionMar 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Urokinase-type plasminogen activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9962
Polymers27,6221
Non-polymers3731
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.160, 53.000, 82.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Urokinase-type plasminogen activator / uPA / U-plasminogen activator


Mass: 27622.496 Da / Num. of mol.: 1 / Fragment: residues 179-423
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLAU / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P00749, u-plasminogen activator
#2: Chemical ChemComp-426 / 6-[(Z)-AMINO(IMINO)METHYL]-N-[3-(CYCLOPENTYLOXY)PHENYL]-2-NAPHTHAMIDE / 6-[N-(3-CYCLOPENTYLOXYPHENYL)CARBAMYL]-2-NAPHTHALENECARBOXAMIDINE


Mass: 373.448 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H23N3O2
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: 2.19 Å3/Da / Density % sol: 43.42 %
Crystal grow
*PLUS
Temperature: 18-24 ℃ / pH: 4 / Method: vapor diffusion, hanging drop / Details: Nienaber, V., (2000) J.Biol.Chem., 275, 7239.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.15 M1reservoirLi2SO4
220 %PEG40001reservoirpH4.8-6.0
36 mg/mlprotein1drop
410 mMcitrate1droppH4.0
53 mMepsilon-aminocaproic acid p-carbethoxyphenyl1drop
61 %1dropMe2SO

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Data collection

DiffractionMean temperature: 160 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.93→34.66 Å / Num. all: 4691 / Num. obs: 4691 / Observed criterion σ(I): 0 / Biso Wilson estimate: 117.3 Å2
Reflection
*PLUS

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Processing

Software
NameVersionClassification
X-PLOR98refinement
MAR345data collection
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.93→10 Å / Rfactor Rfree error: 0.018 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.349 358 10.3 %RANDOM
Rwork0.286 ---
all0.286 3480 --
obs0.286 3480 63 %-
Displacement parametersBiso mean: 12.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.93→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1933 0 28 0 1961
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.76
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.141.5
X-RAY DIFFRACTIONx_mcangle_it1.872
X-RAY DIFFRACTIONx_scbond_it1.712
X-RAY DIFFRACTIONx_scangle_it2.642.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.065 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.382 35 10.3 %
Rwork0.27 305 -
obs--37.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM11.WATTOPHCSDX.PRO
X-RAY DIFFRACTION2PARVICKI.PRO
X-RAY DIFFRACTION3PARAM19X.PRO
X-RAY DIFFRACTION4PARHCSDX.PRO
X-RAY DIFFRACTION5A276426.XPRM
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.76

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