2BM2

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

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: 10.1016/j.bmc.2005.02.014

  • 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 ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HUMAN BETA2 TRYPTASE
A, B, C, D
245Homo sapiensMutation(s): 0 
Gene Names: TPSB2 (TPS2)
EC: 3.4.21.59
Find proteins for P20231 (Homo sapiens)
Go to Gene View: TPSB2
Go to UniProtKB:  P20231
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PM2
Query on PM2

Download SDF File 
Download CCD File 
A, B, C, D
1-[3-(1-{[5-(2-PHENYLETHYL)PYRIDIN-3-YL]CARBONYL}PIPERIDIN-4-YL)PHENYL]METHANAMINE
[4-(3-AMINOMETHYL-PHENYL)-PIPERIDIN-1-YL]-(5-PHENETHYL- PYRIDIN-3-YL)-METHANONE
C26 H29 N3 O
CCLHROFBSWWOQO-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PM2Ki: 15 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.203 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 82.000α = 90.00
b = 82.000β = 90.00
c = 171.190γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
X-PLORrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

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