1OS0

Thermolysin with an alpha-amino phosphinic inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Interactions of a new alpha-aminophosphinic derivative inside the active site of TLN (thermolysin): a model for zinc-metalloendopeptidase inhibition.

Selkti, M.Tomas, A.Gaucher, J.F.Prange, T.Fournie-Zaluski, M.C.Chen, H.Roques, B.P.

(2003) Acta Crystallogr.,Sect.D 59: 1200-1205


  • PubMed Abstract: 
  • A new alpha-aminophosphinic compound able to inhibit both zinc-containing exopeptidases and endopeptidases has been crystallized with TLN as a model in order to investigate the mode of zinc recognition by the phosphinic moiety and to evaluate the pot ...

    A new alpha-aminophosphinic compound able to inhibit both zinc-containing exopeptidases and endopeptidases has been crystallized with TLN as a model in order to investigate the mode of zinc recognition by the phosphinic moiety and to evaluate the potential role of the free alpha-amino group in the formation of enzyme-inhibitor complexes. In addition to the main interactions between the backbone of the inhibitor and the enzyme active site, it is observed that the phosphinic group acts as a distorted bidentate ligand for the zinc ion, while the free alpha-amino function does not directly participate in interactions within the active site. Association of the present data and the K(i) values of various analogues of the inhibitor towards TLN and neprilysin suggests differences in the hydrophobicity of the S(1)-S(2) domains of the enzymes. This could be taken into account in the design of selective inhibitors.


    Related Citations: 
    • Crystal structures of alpha-mercaptoacyldipeptides in the Thermolysin active site: Structural parameters for a Zn Monodentation or bidentation in metalloendopeptidases
      Gaucher, J.F.,Selkti, M.,Tiraboschi, G.,Prange, T.,Roques, B.P.,Tomas, A.,Fournie-Zaluski, M.C.
      (1999) Biochemistry 38: 12569


    Organizational Affiliation

    Laboratoire de Cristallographie et RMN Biologiques (UMR 8015 CNRS), 4 Avenue de l'Observatoire, 75270 Paris CEDEX 06, France. selkti@pharmacie.univ-paris5.fr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thermolysin
A
316Bacillus thermoproteolyticusGene Names: npr
EC: 3.4.24.27
Find proteins for P00800 (Bacillus thermoproteolyticus)
Go to UniProtKB:  P00800
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
0PQ
Query on 0PQ

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Download CCD File 
A
N-{(2R)-3-[(S)-[(1R)-1-amino-2-phenylethyl](hydroxy)phosphoryl]-2-benzylpropanoyl}-L-phenylalanine
C27 H31 N2 O5 P
XNPYGVCNHOXQRJ-DSNGMDLFSA-N
 Ligand Interaction
DMS
Query on DMS

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Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0PQKi: 930 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.147 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 93.782α = 90.00
b = 93.782β = 90.00
c = 132.249γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SHELXL-97refinement
CCP4data scaling
TRUNCATEdata scaling
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-03-25
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description