1O3D

Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Binding of Active Site-Directed Serine Protease Inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Elaborate manifold of short hydrogen bond arrays mediating binding of active site-directed serine protease inhibitors.

Katz, B.A.Elrod, K.Verner, E.Mackman, R.L.Luong, C.Shrader, W.D.Sendzik, M.Spencer, J.R.Sprengeler, P.A.Kolesnikov, A.Tai, V.W.Hui, H.C.Breitenbucher, J.G.Allen, D.Janc, J.W.

(2003) J.Mol.Biol. 329: 93-120

  • Primary Citation of Related Structures:  
    1O3P, 1O3O, 1O3N, 1O3M, 1O3L, 1O3K, 1O3J, 1O3I, 1O3H, 1O3G, 1O3F, 1O3E, 1O3C, 1O3B, 1O3A, 1O39, 1O38, 1O37, 1O36, 1O35, 1O34, 1O33, 1O32, 1O31, 1O30, 1O2Z, 1O2Y, 1O2X, 1O2W, 1O2V, 1O2U, 1O2T, 1O2S, 1O2R, 1O2Q, 1O2P, 1O2O, 1O2N, 1O2M, 1O2L, 1O2K, 1O2J, 1O2I, 1O2H, 1O2G

  • PubMed Abstract: 
  • 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 a ...

    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.


    Organizational Affiliation

    Celera, 180 Kimball Way, South San Francisco, CA 94080, USA. brad.katz@celera.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BETA-TRYPSIN
A
223Bos taurusEC: 3.4.21.4
Find proteins for P00760 (Bos taurus)
Go to UniProtKB:  P00760
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
780
Query on 780

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Download CCD File 
A
3-{5-[AMINO(IMINIO)METHYL]-1H-BENZIMIDAZOL-2-YL}-1,1'-BIPHENYL-2-OLATE
CRA_7806
C20 H16 N4 O
LMGQGPVCSYOMNS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
780Ki: 74 nM BINDINGMOAD
780Ki: 74 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.730α = 90.00
b = 63.290β = 90.00
c = 69.300γ = 90.00
Software Package:
Software NamePurpose
bioteXdata reduction
Quantamodel building
X-PLORrefinement
bioteXdata collection
bioteXdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-09-02
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description