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 
  • R-Value Observed: 0.163 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.6 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: https://doi.org/10.1016/j.bmc.2006.07.028
  • Primary Citation of Related Structures:  
    2HU6

  • 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 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).


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Macrophage metalloelastase159Homo sapiensMutation(s): 1 
Gene Names: MMP12HME
EC: 3.4.24.65
UniProt & NIH Common Fund Data Resources
Find proteins for P39900 (Homo sapiens)
Explore P39900 
Go to UniProtKB:  P39900
PHAROS:  P39900
GTEx:  ENSG00000262406 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39900
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
37A
Query on 37A

Download Ideal Coordinates CCD File 
G [auth A](1S,5S,7R)-N~7~-(BIPHENYL-4-YLMETHYL)-N~3~-HYDROXY-6,8-DIOXA-3-AZABICYCLO[3.2.1]OCTANE-3,7-DICARBOXAMIDE
C20 H21 N3 O5
PPLDARNGJSQINK-OKZBNKHCSA-N
HAE
Query on HAE

Download Ideal Coordinates CCD File 
H [auth A]ACETOHYDROXAMIC ACID
C2 H5 N O2
RRUDCFGSUDOHDG-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
37A PDBBind:  2HU6 Kd: 1.54e+5 (nM) from 1 assay(s)
BindingDB:  2HU6 Kd: 1.54e+5 (nM) from 1 assay(s)
IC50: 1.49e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.25α = 90
b = 60.179β = 114.59
c = 53.974γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-12-19
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2018-01-24
    Changes: Database references
  • Version 1.5: 2021-10-20
    Changes: Data collection, Database references, Derived calculations
  • Version 1.6: 2023-08-30
    Changes: Data collection, Refinement description