PDBsum entry 1gj6

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Hydrolase PDB id
Jmol PyMol
Protein chain
223 a.a. *
Waters ×915
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Engineering inhibitors highly selective for the s1 sites of ser190 trypsin-like serine protease drug targets
Structure: Beta-trypsin. Chain: a. Ec:
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: pancreas
1.50Å     R-factor:   0.187     R-free:   0.206
Authors: B.A.Katz,P.A.Sprengeler,C.Luong,E.Verner,J.R.Spencer, J.G.Breitenbucher,H.Hui,D.Mcgee,D.Allen,A.Martelli, R.L.Mackman
Key ref:
B.A.Katz et al. (2001). Engineering inhibitors highly selective for the S1 sites of Ser190 trypsin-like serine protease drug targets. Chem Biol, 8, 1107-1121. PubMed id: 11731301 DOI: 10.1016/S1074-5521(01)00084-9
27-Apr-01     Release date:   27-Apr-02    
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Protein chain
Pfam   ArchSchema ?
P00760  (TRY1_BOVIN) -  Cationic trypsin
246 a.a.
223 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Trypsin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Preferential cleavage: Arg-|-Xaa, Lys-|-Xaa.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   2 terms 
  Biological process     digestion   2 terms 
  Biochemical function     protein binding     6 terms  


DOI no: 10.1016/S1074-5521(01)00084-9 Chem Biol 8:1107-1121 (2001)
PubMed id: 11731301  
Engineering inhibitors highly selective for the S1 sites of Ser190 trypsin-like serine protease drug targets.
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, R.L.Mackman.
BACKGROUND: Involved or implicated in a wide spectrum of diseases, trypsin-like serine proteases comprise well studied drug targets and anti-targets that can be subdivided into two major classes. In one class there is a serine at position 190 at the S1 site, as in urokinase type plasminogen activator (urokinase or uPA) and factor VIIa, and in the other there is an alanine at 190, as in tissue type plasminogen activator (tPA) and factor Xa. A hydrogen bond unique to Ser190 protease-arylamidine complexes between O gamma(Ser190) and the inhibitor amidine confers an intrinsic preference for such inhibitors toward Ser190 proteases over Ala190 counterparts. RESULTS: Based on the structural differences between the S1 sites of Ser190 and Ala190 protease-arylamidine complexes, we amplified the selectivity of amidine inhibitors toward uPA and against tPA, by factors as high as 220-fold, by incorporating a halo group ortho to the amidine of a lead inhibitor scaffold. Comparison of K(i) values of such halo-substituted and parent inhibitors toward a panel of Ser190 and Ala190 proteases demonstrates pronounced selectivity of the halo analogs for Ser190 proteases over Ala190 counterparts. Crystal structures of Ser190 proteases, uPA and trypsin, and of an Ala190 counterpart, thrombin, bound by a set of ortho (halo, amidino) aryl inhibitors and of non-halo parents reveal the structural basis of the exquisite selectivity and validate the design principle. CONCLUSIONS: Remarkable selectivity enhancements of exceptionally small inhibitors are achieved toward the uPA target over the highly similar tPA anti-target through a single atom substitution on an otherwise relatively non-selective scaffold. Overall selectivities for uPA over tPA as high as 980-fold at physiological pH were realized. The increase in selectivity results from the displacement of a single bound water molecule common to the S1 site of both the uPA target and the tPA anti-target because of the ensuing deficit in hydrogen bonding of the arylamidine inhibitor when bound in the Ala190 protease anti-target.
  Selected figure(s)  
Figure 6.
Fig. 6. a: Structure and (2|F[o]|−|F[c]|), α[c] map for uPA–APC-11092, 1.80 Å resolution. The long N1–Oδ2[Asp189] and N2–Oδ2[Asp189] interactions (3.17 Å and 3.40 Å, respectively, at pH 6.5) are shown in yellow and transparent light yellow, respectively. b: Structure and (2|F[o]|−|F[c]|), α[c] map for uPA–APC-10950, 1.64 Å resolution. The H[2]O1[S1]–F hydrogen bond (2.76 Å) is formed at the expense of the H[2]O1[S1]–O[Trp215] interaction, the length of which increases from 3.07 Å in uPA–APC-8696 to 3.52 Å in uPA–APC-10950 (Table 3c).
Figure 7.
Fig. 7. a: Structure and (2|F[o]|−|F[c]|), α[c] map of trypsin–APC-11922, 1.50 Å resolution. For the major inhibitor conformer (opaque sticks) there is a hydrogen bond between the inhibitor phenol (O6′) and Nε2[His57], and a short O6′–Oγ[Ser195] hydrogen bond. b: Structure and (2|F[o]|−|F[c]|), α[c] map of uPA–APC-11421, 1.75 Å resolution. In this and all other uPA complexes of the APC-7136 analogs in Fig. 2b, the phenol hydroxyl is at or near the oxyanion hole, receiving hydrogen bonds from N[Gly193] and from the inhibitor NH amide group. In many trypsin and thrombin complexes the inhibitor is discretely disordered between the two binding modes in (a) and (b).
  The above figures are reprinted by permission from Cell Press: Chem Biol (2001, 8, 1107-1121) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21136135 J.Schaller, and S.S.Gerber (2011).
The plasmin-antiplasmin system: structural and functional aspects.
  Cell Mol Life Sci, 68, 785-801.  
19104179 W.Dietrich, S.Nicklisch, A.Koster, M.Spannagl, H.Giersiefen, and A.van de Locht (2009).
CU-2010--a novel small molecule protease inhibitor with antifibrinolytic and anticoagulant properties.
  Anesthesiology, 110, 123-130.  
18653760 O.Khoruzhii, A.G.Donchev, N.Galkin, A.Illarionov, M.Olevanov, V.Ozrin, C.Queen, and V.Tarasov (2008).
Application of a polarizable force field to calculations of relative protein-ligand binding affinities.
  Proc Natl Acad Sci U S A, 105, 10378-10383.  
17001711 A.Hoffmann-Röder, E.Schweizer, J.Egger, P.Seiler, U.Obst-Sander, B.Wagner, M.Kansy, D.W.Banner, and F.Diederich (2006).
Mapping the fluorophilicity of a hydrophobic pocket: synthesis and biological evaluation of tricyclic thrombin inhibitors directing fluorinated alkyl groups into the p pocket.
  ChemMedChem, 1, 1205-1215.
PDB code: 2cn0
16700049 C.A.Bottoms, T.A.White, and J.J.Tanner (2006).
Exploring structurally conserved solvent sites in protein families.
  Proteins, 64, 404-421.  
16892401 E.Schweizer, A.Hoffmann-Röder, K.Schärer, J.A.Olsen, C.Fäh, P.Seiler, U.Obst-Sander, B.Wagner, M.Kansy, and F.Diederich (2006).
A fluorine scan at the catalytic center of thrombin: C--F, C--OH, and C--OMe bioisosterism and fluorine effects on pKa and log D values.
  ChemMedChem, 1, 611-621.  
16199530 J.Tang, C.L.Yu, S.R.Williams, E.Springman, D.Jeffery, P.A.Sprengeler, A.Estevez, J.Sampang, W.Shrader, J.Spencer, W.Young, M.McGrath, and B.A.Katz (2005).
Expression, crystallization, and three-dimensional structure of the catalytic domain of human plasma kallikrein.
  J Biol Chem, 280, 41077-41089.
PDB codes: 2anw 2any
15545266 L.Jin, P.Pandey, R.E.Babine, J.C.Gorga, K.J.Seidl, E.Gelfand, D.T.Weaver, S.S.Abdel-Meguid, and J.E.Strickler (2005).
Crystal structures of the FXIa catalytic domain in complex with ecotin mutants reveal substrate-like interactions.
  J Biol Chem, 280, 4704-4712.
PDB codes: 1xx9 1xxd 1xxf
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.  
12546953 S.F.Betz, S.M.Baxter, and J.S.Fetrow (2002).
Function first: a powerful approach to post-genomic drug discovery.
  Drug Discov Today, 7, 865-871.  
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.