PDBsum entry 1o32

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Hydrolase PDB id
Jmol PyMol
Protein chain
223 a.a. *
Waters ×387
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Elaborate manifold of short hydrogen bond arrays mediating binding of active site-directed serine protease inhibitors
Structure: Beta-trypsin. Chain: a. Ec:
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: pancreas
1.78Å     R-factor:   0.190     R-free:   0.209
Authors: B.A.Katz,K.Elrod,E.Verner,R.L.Mackman,C.Luong,W.D.Shrader, M.Sendzik,J.R.Spencer,P.A.Sprengeler,A.Kolesnikov,V.W.Tai, H.C.Hui,J.G.Breitenbucher,D.Allen,J.W.Janc
Key ref:
B.A.Katz et al. (2003). Elaborate manifold of short hydrogen bond arrays mediating binding of active site-directed serine protease inhibitors. J Mol Biol, 329, 93. PubMed id: 12742021 DOI: 10.1016/S0022-2836(03)00399-1
06-Mar-03     Release date:   02-Sep-03    
Go to PROCHECK summary

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/S0022-2836(03)00399-1 J Mol Biol 329:93 (2003)
PubMed id: 12742021  
Elaborate manifold of short hydrogen bond arrays mediating binding of active site-directed serine protease inhibitors.
B.A.Katz, K.Elrod, E.Verner, R.L.Mackman, C.Luong, W.D.Shrader, M.Sendzik, J.R.Spencer, P.A.Sprengeler, A.Kolesnikov, V.W.Tai, H.C.Hui, J.G.Breitenbucher, D.Allen, J.W.Janc.
An extensive structural manifold of short hydrogen bond-mediated, active site-directed, serine protease inhibition motifs is revealed in a set of over 300 crystal structures involving a large suite of small molecule inhibitors (2-(2-phenol)-indoles and 2-(2-phenol)-benzimidazoles) determined over a wide range of pH (3.5-11.4). The active site hydrogen-bonding mode was found to vary markedly with pH, with the steric and electronic properties of the inhibitor, and with the type of protease (trypsin, thrombin or urokinase type plasminogen activator (uPA)). The pH dependence of the active site hydrogen-bonding motif is often intricate, constituting a distinct fingerprint of each complex. Isosteric replacements or minor substitutions within the inhibitor that modulate the pK(a) of the phenol hydroxyl involved in short hydrogen bonding, or that affect steric interactions distal to the active site, can significantly shift the pH-dependent structural profile characteristic of the parent scaffold, or produce active site-binding motifs unique to the bound analog.Ionization equilibria at the active site associated with inhibitor binding are probed in a series of the protease-inhibitor complexes through analysis of the pH dependence of the structure and environment of the active site-binding groups involved in short hydrogen bond arrays. Structures determined at high pH (>11), suggest that the pK(a) of His57 is dramatically elevated, to a value as high as approximately 11 in certain complexes. K(i) values involving uPA and trypsin determined as a function of pH for a set of inhibitors show pronounced parabolic pH dependence, the pH for optimal inhibition governed by the pK(a) of the inhibitor phenol involved in short hydrogen bonds. Comparison of structures of trypsin, thrombin and uPA, each bound by the same inhibitor, highlights important structural variations in the S1 and active sites accessible for engineering notable selectivity into remarkably small molecules with low nanomolar K(i) values.
  Selected figure(s)  
Figure 4.
Figure 4. (a) Resonance forms (A, B) for the lowest energy (non-bind- ing) conformation of the benzi- midazole scaffold. Structure C represents the conformer and tauto- mer for bound benzimidazoles. (b1) Resonance forms for the lowest energy (non-binding) conformation of the 6-chlorobenzimidazole scaffold (D, E). Structure F rep- resents the conformer and tautomer for bound 6-chlorobenzimidazoles. (b2) Resonance forms for bound 6-chlorobenzimidazoles.
Figure 10.
Figure 10. (a) Structure and (2lF ol 2 lFc l); ac map for trypsin-CRA-18306, pH 7.2, 1.56 A resolution. The OSer195 g -- Ophenol hydrogen bond is short (2.35 ^ 05 A ) at pH , 7.7 and longer at pH . 7.8 (2.59 ^ 09 A , Table S1). (b) Structure and (2lF o l 2 lFcl); ac map for trypsin-CRA-18607, pH 7.9, 1.55 A resolution. Hydrogen bonds (short and ordinary) cor- responding to the (Ooxy, OSer195 (conformation 1) g , Ophenol) array are cyan, while those for the (OS2, OSer195 (conformation 2) g , Ophenol) array are yellow, (or olive green for NHis57 12 -- OS2).
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 329, 93-0) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19275144 C.Mulakala, and Y.N.Kaznessis (2009).
Path-integral method for predicting relative binding affinities of protein-ligand complexes.
  J Am Chem Soc, 131, 4521-4528.  
19152365 F.Fontaine, S.Cross, G.Plasencia, M.Pastor, and I.Zamora (2009).
SHOP: a method for structure-based fragment and scaffold hopping.
  ChemMedChem, 4, 427-439.  
19235177 M.I.Zavodszky, A.Rohatgi, J.R.Van Voorst, H.Yan, and L.A.Kuhn (2009).
Scoring ligand similarity in structure-based virtual screening.
  J Mol Recognit, 22, 280-292.  
18247345 D.Bandyopadhyay, and E.L.Mehler (2008).
Quantitative expression of protein heterogeneity: Response of amino acid side chains to their local environment.
  Proteins, 72, 646-659.  
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.  
17372355 M.Sherawat, P.Kaur, M.Perbandt, C.Betzel, W.A.Slusarchyk, G.S.Bisacchi, C.Chang, B.L.Jacobson, H.M.Einspahr, and T.P.Singh (2007).
Structure of the complex of trypsin with a highly potent synthetic inhibitor at 0.97 A resolution.
  Acta Crystallogr D Biol Crystallogr, 63, 500-507.
PDB code: 2ayw
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
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.  
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.