1THL

Thermolysin complexed with a novel glutaramide derivative, n-(1-(2(r,s)-carboxy-4-phenylbutyl) cyclopentylcarbonyl)-(s)-tryptophan


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Inhibition of Thermolysin and Neutral Endopeptidase 24.11 By a Novel Glutaramide Derivative; X-Ray Structure Determination of the Thermolysin-Inhibitor Complex

Holland, D.R.Barclay, P.L.Danilewicz, J.C.Matthews, B.W.James, K.

(1994) Biochemistry 33: 51-56


  • PubMed Abstract: 
  • Determination of the X-ray structure of thermolysin-inhibitor complexes has proven useful in aiding our understanding of the mode of binding of inhibitors of related, physiologically important, mammalian zinc peptidases including neutral endopeptidas ...

    Determination of the X-ray structure of thermolysin-inhibitor complexes has proven useful in aiding our understanding of the mode of binding of inhibitors of related, physiologically important, mammalian zinc peptidases including neutral endopeptidase EC 3.4.24.11 and angiotensin-converting enzyme. Here we describe the mode of binding to crystalline thermolysin of N-[1-(2(R,S)-carboxy-4-phenylbutyl)-cyclopentylcarbonyl]-(S) -tryptophan (CCT). CCT is an analogue of both candoxatrilat, a potent inhibitor of neutral endopeptidase 24.11, and of the 5-indanyl ester prodrug candoxatril, which is under clinical evaluation as a potential therapy for congestive heart failure. CCT differs from the previously studied N-carboxyalkyl dipeptide CLT [N-(S)-(1-carboxy-3-phenylpropyl)-(S)-leucyl-(S)-tryptophan] in several important respects. It has a highly constrained gem-cyclopentyl P1' substituent and lacks the characteristic imino nitrogen substituent of CLT. The structure determination shows that, notwithstanding the conformational influence of the gem-cyclopentyl substituent, CCT binds within the active site of thermolysin in a similar manner to CLT. Although the characteristic hydrogen bond between the imino nitrogen of CLT and thermolysin is absent in CCT, the affinities of the two inhibitors for the enzyme are virtually identical. These results illustrate the importance of considering not only those hydrogen bonds that are formed in an enzyme-ligand complex but also the other hydrogen bonds that may be lost due to desolvation of the enzyme and ligand on formation of the complex. In addition, the overall conformational demands placed upon a ligand in order to achieve receptor interaction may be critically important.


    Related Citations: 
    • Structure of Thermolysin
      Matthews, B.W.,Colman, P.M.,Jansonius, J.N.,Titani, K.,Walsh, K.A.,Neura, H.
      (1972) Nature New Biol. 238: 41
    • Structure of Thermolysin Refined at 1.6 Angstroms Resolution
      Holmes, M.A.,Matthews, B.W.
      (1982) J.Mol.Biol. 160: 623
    • Three Dimensional Structure of Thermolysin
      Matthews, B.W.,Jansonius, J.N.,Colman, P.N.,Schoenborn, B.P.,Duporque, D.
      (1972) Nature New Biol. 238: 37
    • The Conformation of Thermolysin
      Matthews, B.W.,Weaver, L.H.,Kester, W.R.
      (1974) J.Biol.Chem. 249: 8030
    • Binding of N-Carboxymethyl Dipeptide Inhibitors to Thermolysin Determined by X-Ray Crystallography: A Novel Class of Transition-State Analogues for Zinc Peptidases
      Monzingo, A.F.,Matthews, B.W.
      (1984) Biochemistry 23: 5724


    Organizational Affiliation

    Howard Hughes Medical Institute, University of Oregon, Eugene 97403.




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 3 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

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

Download SDF File 
Download CCD File 
A
N-({1-[(2S)-2-carboxy-4-phenylbutyl]cyclopentyl}carbonyl)-L-tryptophan
CCT
C28 H32 N2 O5
MPZIROHQGMKFGS-YKSBVNFPSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000237 (0DB)
Query on PRD_000237
AN-({1-[(2S)-2-carboxy-4-phenylbutyl]cyclopentyl}carbonyl)-L-tryptophanPeptide-like / Inhibitor

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External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0DBKi: 380 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Work: 0.162 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 94.100α = 90.00
b = 94.100β = 90.00
c = 131.400γ = 120.00
Software Package:
Software NamePurpose
TNTphasing
XUONG-HAMLINdata scaling
Xuong-Hamlindata reduction
Xuong-Hamlindata collection
TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    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: 2012-12-12
    Type: Other