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


Ligand Structure Quality Assessment 


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:  
    5I2Z, 5I43, 5I3M, 5I4O, 5I0L, 5I12

  • 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 (Subject of Investigation/LOI)
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



Ligand Structure Quality Assessment  



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