2HU6

Crystal structure of human MMP-12 in complex with acetohydroxamic acid and a bicyclic inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Synthesis of bicyclic molecular scaffolds (BTAa): an investigation towards new selective MMP-12 inhibitors.

Mannino, C.Nievo, M.Machetti, F.Papakyriakou, A.Calderone, V.Fragai, M.Guarna, A.

(2006) Bioorg.Med.Chem. 14: 7392-7403

  • DOI: 10.1016/j.bmc.2006.07.028

  • PubMed Abstract: 
  • Starting from 3-aza-6,8-dioxa-bicyclo[3.2.1]octane scaffold (BTAa) a virtual library of molecules was generated and screened in silico against the crystal structure of the Human Macrophage Metalloelastase (MMP-12). The molecules obtaining high score ...

    Starting from 3-aza-6,8-dioxa-bicyclo[3.2.1]octane scaffold (BTAa) a virtual library of molecules was generated and screened in silico against the crystal structure of the Human Macrophage Metalloelastase (MMP-12). The molecules obtaining high score were synthesized and the affinity for the catalytic domain of MMP-12 was experimentally proved by NMR experiments. A BTAa scaffold 20 having a N-hydroxyurea group in position 3 and a p-phenylbenzylcarboxy amide in position 7 showed a fair inhibition potency (IC50 = 149 microM) for MMP-12 and some selectivity towards five different MMPs. These results, taken together with the X-ray structure of the adduct between MMP-12, the inhibitor 20 and the acetohydroxamic acid (AHA), suggest that bicyclic scaffold derivatives may be exploited for the design of new selective matrix metalloproteinase inhibitors (MMPIs).


    Related Citations: 
    • Conformational variability of matrix metalloproteinases: beyond a single 3D structure.
      Bertini, I.,Calderone, V.,Cosenza, M.,Fragai, M.,Lee, Y.-M.,Luchinat, C.,Mangani, S.,Turano, P.
      (2005) Proc.Natl.Acad.Sci.USA 102: 5334


    Organizational Affiliation

    Department of Organic Chemistry U. Schiff, University of Florence, 50019 Sesto Fiorentino (FI), Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Macrophage metalloelastase
A
159Homo sapiensMutation(s): 1 
Gene Names: MMP12 (HME)
EC: 3.4.24.65
Find proteins for P39900 (Homo sapiens)
Go to Gene View: MMP12
Go to UniProtKB:  P39900
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HAE
Query on HAE

Download SDF File 
Download CCD File 
A
ACETOHYDROXAMIC ACID
C2 H5 N O2
RRUDCFGSUDOHDG-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
37A
Query on 37A

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Download CCD File 
A
(1S,5S,7R)-N~7~-(BIPHENYL-4-YLMETHYL)-N~3~-HYDROXY-6,8-DIOXA-3-AZABICYCLO[3.2.1]OCTANE-3,7-DICARBOXAMIDE
(1S,5S,7R)-3-AZA-6,8-DIOXA-BICYCLO[3.2.1]OCTANE-3,7-DICARBOXYLIC ACID 7-[(BIPHENYL-4-YLMETHYL)-AMIDE]-3-HYDROXYAMIDE
C20 H21 N3 O5
PPLDARNGJSQINK-OKZBNKHCSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
37AIC50: 149000 nM (99) BINDINGDB
37AKd: 154000 nM (99) BINDINGDB
37AKd: 154000 nM BINDINGMOAD
37AKd: 154000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.161 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 51.250α = 90.00
b = 60.179β = 114.59
c = 53.974γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
MOLREPphasing
MOSFLMdata reduction
REFMACrefinement
MAR345data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-12-19
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description
  • Version 1.4: 2018-01-24
    Type: Database references