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PDBsum entry 1f5l

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Hydrolase PDB id
1f5l
Jmol PyMol
Contents
Protein chain
245 a.a. *
Ligands
SO4 ×2
AMR
Waters ×48
* Residue conservation analysis
PDB id:
1f5l
Name: Hydrolase
Title: Urokinase plasminogen activator b-chain-amiloride complex
Structure: Urokinase-type plasminogen activator. Chain: a. Fragment: b chain. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.10Å     R-factor:   0.202     R-free:   0.250
Authors: E.Zeslawska,A.Schweinitz,A.Karcher,P.Sondermann,S.Sperl, J.Sturzebecher,U.Jacob
Key ref:
E.Zeslawska et al. (2000). Crystals of the urokinase type plasminogen activator variant beta(c)-uPAin complex with small molecule inhibitors open the way towards structure-based drug design. J Mol Biol, 301, 465-475. PubMed id: 10926521 DOI: 10.1006/jmbi.2000.3966
Date:
15-Jun-00     Release date:   15-Jun-01    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00749  (UROK_HUMAN) -  Urokinase-type plasminogen activator
Seq:
Struc:
431 a.a.
245 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.4.21.73  - U-plasminogen activator.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Specific cleavage of Arg-|-Val bond in plasminogen to form plasmin.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     proteolysis   1 term 
  Biochemical function     serine-type endopeptidase activity     1 term  

 

 
DOI no: 10.1006/jmbi.2000.3966 J Mol Biol 301:465-475 (2000)
PubMed id: 10926521  
 
 
Crystals of the urokinase type plasminogen activator variant beta(c)-uPAin complex with small molecule inhibitors open the way towards structure-based drug design.
E.Zeslawska, A.Schweinitz, A.Karcher, P.Sondermann, S.Sperl, J.Stürzebecher, U.Jacob.
 
  ABSTRACT  
 
Urokinase is a serine protease involved in cancer growth and metastasis. Here we present the first urokinase crystal structure in complex with reversible inhibitors at 2.1 and 2.6 A resolution. These inhibitor complex structures have been obtained from crystals of engineered urokinase type plasminogen activator designed to obtain a crystal form open for inhibitor soaking. The mutant C122S loses its flexible A-chain upon activation cleavage and crystallizes in the presence of benzamidine, which was later displaced by the desired inhibitor. This new soakable crystal form turned out to be of great value in the process of structure-based drug design. The evaluated binding mode of amiloride, and UKI-1D revealed a new subsite of the primary specificity pocket of urokinase that will be employed in the future ligand optimisation process.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Binding mode of the inhibitors (a) UKI-1D (b) amiloride and (c) WX293T (all in white) in complex with bc-uPA (in yellow) in ball-and-stick representation. Hydrogen bonds are drawn as thin white lines and the chlorine atom is depicted in green. The Figure was produced with MOLSCRIPT and Raster3D.
Figure 5.
Figure 5. Close-up of the active site of urokinase, in ball-and-stick representation, covered by a semi-transparent surface coloured according to the surface electrostatic potential from negative (red) to positive (blue). Also shown is a superposition of amiloride (magenta), EGR-cmk (yellow) and WX293T (cyan) in ball-and-stick representation occupying the different accessible subsites as indicated and discussed in the text. The Figure was produced with MOLSCRIPT, Raster3D and GRASP [Nicholls et al 1991].
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 301, 465-475) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  17261841 A.L.Brown, S.M.Fernandez-Illescas, Z.Liao, and M.B.Goodman (2007).
Gain-of-function mutations in the MEC-4 DEG/ENaC sensory mechanotransduction channel alter gating and drug blockade.
  J Gen Physiol, 129, 161-173.  
17388811 O.J.Kyrieleis, R.Huber, E.Ong, R.Oehler, M.Hunter, E.L.Madison, and U.Jacob (2007).
Crystal structure of the catalytic domain of DESC1, a new member of the type II transmembrane serine proteinase family.
  FEBS J, 274, 2148-2160.
PDB code: 2oq5
19003060 E.Atkins, S.Zamora, B.J.Candia, A.Baca, and R.A.Orlando (2005).
Development of a Mammalian suspension culture for expression of active recombinant human urokinase-type plasminogen activator.
  Cytotechnology, 49, 25-37.  
16141208 M.Hansen, T.Wind, G.E.Blouse, A.Christensen, H.H.Petersen, S.Kjelgaard, L.Mathiasen, T.L.Holtet, and P.A.Andreasen (2005).
A urokinase-type plasminogen activator-inhibiting cyclic peptide with an unusual P2 residue and an extended protease binding surface demonstrates new modalities for enzyme inhibition.
  J Biol Chem, 280, 38424-38437.  
15908426 O.B.Kashlan, S.Sheng, and T.R.Kleyman (2005).
On the interaction between amiloride and its putative alpha-subunit epithelial Na+ channel binding site.
  J Biol Chem, 280, 26206-26215.  
16231330 Z.Sun, and J.N.Liu (2005).
Mutagenesis at Pro309 of single-chain urokinase-type plasminogen activator alters its catalytic properties.
  Proteins, 61, 870-877.  
15150279 A.Schweinitz, T.Steinmetzer, I.J.Banke, M.J.Arlt, A.Stürzebecher, O.Schuster, A.Geissler, H.Giersiefen, E.Zeslawska, U.Jacob, A.Krüger, and J.Stürzebecher (2004).
Design of novel and selective inhibitors of urokinase-type plasminogen activator with improved pharmacokinetic properties for use as antimetastatic agents.
  J Biol Chem, 279, 33613-33622.
PDB codes: 1sc8 1vj9 1vja
12437104 M.M.Mueller, S.Sperl, J.Stürzebecher, W.Bode, and L.Moroder (2002).
(R)-3-Amidinophenylalanine-derived inhibitors of factor Xa with a novel active-site binding mode.
  Biol Chem, 383, 1185-1191.
PDB code: 3liw
11731301 B.A.Katz, P.A.Sprengeler, C.Luong, E.Verner, K.Elrod, M.Kirtley, J.Janc, J.R.Spencer, J.G.Breitenbucher, H.Hui, D.McGee, D.Allen, A.Martelli, and R.L.Mackman (2001).
Engineering inhibitors highly selective for the S1 sites of Ser190 trypsin-like serine protease drug targets.
  Chem Biol, 8, 1107-1121.
PDB codes: 1gj4 1gj5 1gj6 1gj7 1gj8 1gj9 1gja 1gjb 1gjc 1gjd
11727504 B.Muehlenweg, S.Sperl, V.Magdolen, M.Schmitt, and N.Harbeck (2001).
Interference with the urokinase plasminogen activator system: a promising therapy concept for solid tumours.
  Expert Opin Biol Ther, 1, 683-691.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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