5I43

Crystal structure of the catalytic domain of MMP-12 in complex with a selective sugar-conjugated triazole-linked carboxylate chelator water-soluble inhibitor (DC32).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Sugar-Based Arylsulfonamide Carboxylates as Selective and Water-Soluble Matrix Metalloproteinase-12 Inhibitors.

Nuti, E.Cuffaro, D.D'Andrea, F.Rosalia, L.Tepshi, L.Fabbi, M.Carbotti, G.Ferrini, S.Santamaria, S.Camodeca, C.Ciccone, L.Orlandini, E.Nencetti, S.Stura, E.A.Dive, V.Rossello, A.

(2016) ChemMedChem 11: 1626-1637

  • DOI: 10.1002/cmdc.201600235
  • Primary Citation of Related Structures:  
    5I0L, 5I12, 5I2Z, 5I43, 5I3M, 5I4O

  • PubMed Abstract: 
  • Matrix metalloproteinase-12 (MMP-12) can be considered an attractive target to study selective inhibitors useful in the development of new therapies for lung and cardiovascular diseases. In this study, a new series of arylsulfonamide carboxylates, with increased hydrophilicity resulting from conjugation with a β-N-acetyl-d-glucosamine moiety, were designed and synthesized as MMP-12 selective inhibitors ...

    Matrix metalloproteinase-12 (MMP-12) can be considered an attractive target to study selective inhibitors useful in the development of new therapies for lung and cardiovascular diseases. In this study, a new series of arylsulfonamide carboxylates, with increased hydrophilicity resulting from conjugation with a β-N-acetyl-d-glucosamine moiety, were designed and synthesized as MMP-12 selective inhibitors. Their inhibitory activity was evaluated on human MMPs by using the fluorimetric assay, and a crystallographic analysis was performed to characterize their binding mode. Among these glycoconjugates, a nanomolar MMP-12 inhibitor with improved water solubility, compound 3 [(R)-2-(N-(2-(3-(2-acetamido-2-deoxy-β-d-glucopyranosyl)thioureido)ethyl)biphenyl-4-ylsulfonamido)-3-methylbutanoic acid], was identified.


    Organizational Affiliation

    Department of Pharmacy, University of Pisa, via Bonanno 6, 56126, Pisa, Italy. armando.rossello@farm.unipi.it.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Macrophage metalloelastaseA, B, C, D159Homo sapiensMutation(s): 2 
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
67M
Query on 67M

Download Ideal Coordinates CCD File 
HA [auth C], J [auth A], U [auth B], UA [auth D](2R)-2-[({1-[3-({(2R,3R,4R,5S,6R)-3-(acetylamino)-4,5-bis(acetyloxy)-6-[(acetyloxy)methyl]tetrahydro-2H-pyran-2-yl}oxy)propyl]-1H-1,2,3-triazol-4-yl}methyl)(biphenyl-4-ylsulfonyl)amino]-3-methylbutanoic acid (non-preferred name)
C37 H47 N5 O13 S
GRIPTHDAFNBNAB-HTJFLOPLSA-N
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
FA [auth B], PA [auth C]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
PGO
Query on PGO

Download Ideal Coordinates CCD File 
GA [auth B], GB [auth D], QA [auth C], RA [auth C], SA [auth C], TA [auth C]S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], IA [auth C], JA [auth C], V [auth B], VA [auth D], W [auth B], WA [auth D]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth B] , AB [auth D] , BA [auth B] , BB [auth D] , CA [auth B] , CB [auth D] , DA [auth B] , DB [auth D] , 
AA [auth B],  AB [auth D],  BA [auth B],  BB [auth D],  CA [auth B],  CB [auth D],  DA [auth B],  DB [auth D],  EA [auth B],  EB [auth D],  FB [auth D],  K [auth A],  L [auth A],  M [auth A],  N [auth A],  NA [auth C],  O [auth A],  OA [auth C],  P [auth A],  Q [auth A],  R [auth A],  S [auth A],  T [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
G [auth A] , H [auth A] , I [auth A] , KA [auth C] , LA [auth C] , MA [auth C] , X [auth B] , XA [auth D] , 
G [auth A],  H [auth A],  I [auth A],  KA [auth C],  LA [auth C],  MA [auth C],  X [auth B],  XA [auth D],  Y [auth B],  YA [auth D],  Z [auth B],  ZA [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.03α = 90
b = 63.66β = 103.03
c = 79.03γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-06
    Type: Initial release
  • Version 1.1: 2016-07-13
    Changes: Database references
  • Version 1.2: 2016-08-17
    Changes: Database references
  • Version 1.3: 2018-01-24
    Changes: Source and taxonomy