human beta-II tryptase in complex with 4-(3-Aminomethyl-phenyl)- piperidin-1-yl-(5-phenethyl- pyridin-3-yl)-methanone

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 

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Ligand Structure Quality Assessment 

This is version 1.5 of the entry. See complete history


Structure Based Design of 4-(3-Aminomethylphenyl) Piperidinyl-1-Amides: Novel, Potent, Selective, and Orally Bioavailable Inhibitors of Bii Tryptase

Levell, J.Astles, P.Eastwood, P.Cairns, J.Houille, O.Aldous, S.Merriman, G.Whitley, B.Pribish, J.Czekaj, M.Liang, G.Maignan, S.Guilloteau, J.-P.Dupuy, A.Davidson, J.Harrison, T.Morley, A.Watson, S.Fenton, G.Mccarthy, C.Romano, J.Mathew, R.Engers, D.Gardyan, M.Sides, K.Kwong, J.Tsay, J.Rebello, S.Shen, L.Wang, J.Luo, Y.Giardino, O.Lim, H.-K.Smith, K.Pauls, H.

(2005) Bioorg Med Chem 13: 2859

  • DOI: https://doi.org/10.1016/j.bmc.2005.02.014
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Tryptase is a serine protease found almost exclusively in mast cells. It has trypsin-like specificity, favoring cleavage of substrates with an arginine (or lysine) at the P1 position, and has optimal catalytic activity at neutral pH. Current evidence suggests tryptase beta is the most important form released during mast cell activation in allergic diseases. It is shown to have numerous pro-inflammatory cellular activities in vitro, and in animal models tryptase provokes broncho-constriction and induces a cellular inflammatory infiltrate characteristic of human asthma. Screening of in-house inhibitors of factor Xa (a closely related serine protease) identified beta-amidoester benzamidines as potent inhibitors of recombinant human betaII tryptase. X-ray structure driven template modification and exchange of the benzamidine to optimize potency and pharmacokinetic properties gave selective, potent and orally bioavailable 4-(3-aminomethyl phenyl)piperidinyl-1-amides.

  • Organizational Affiliation

    Drug Innovation and Approval, Aventis Pharmaceuticals, 1041 Route 202-206, Mail Stop N-103A, Bridgewater, NJ 08807-6800, USA. julian.levell@aventis.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
245Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P20231 (Homo sapiens)
Explore P20231 
Go to UniProtKB:  P20231
PHAROS:  P20231
GTEx:  ENSG00000197253 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20231
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
PM2 Binding MOAD:  2BM2 Ki: 15 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82α = 90
b = 82β = 90
c = 171.19γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2005-03-22
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-08
    Changes: Advisory, Data collection, Experimental preparation, Other
  • Version 1.4: 2019-05-22
    Changes: Data collection, Refinement description
  • Version 1.5: 2023-12-13
    Changes: Advisory, Data collection, Database references, Other, Refinement description