5I4O | pdb_00005i4o

Crystal structure of the catalytic domain of MMP-12 in complex with a selective sugar-conjugated triazole-linked carboxylate zinc-chelator water-soluble inhibitor (DC28).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 
    0.249 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5I4O

Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1002/cmdc.201600235
  • Primary Citation Related Structures: 
    5I0L, 5I12, 5I2Z, 5I3M, 5I43, 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. 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.

Macromolecule Content 

  • Total Structure Weight: 73.93 kDa 
  • Atom Count: 5,591 
  • Modeled Residue Count: 624 
  • Deposited Residue Count: 636 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Macrophage metalloelastase
A, B, C, D
159Homo sapiensMutation(s): 0 
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
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
V28

Query on V28



Download:Ideal Coordinates CCD File
E [auth A],
K [auth B],
Q [auth C],
W [auth D]
N-({1-[2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl]-1H-1,2,3-triazol-4-yl}methyl)-N-[([1,1'-biphenyl]-4-yl)sulfonyl]-D-valine
C28 H35 N5 O9 S
KNBZJXWGCBPDHT-ZRRJEQDASA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
L [auth B]
M [auth B]
R [auth C]
F [auth A],
G [auth A],
L [auth B],
M [auth B],
R [auth C],
S [auth C],
X [auth D],
Y [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
AA [auth D]
BA [auth D]
H [auth A]
I [auth A]
J [auth A]
AA [auth D],
BA [auth D],
H [auth A],
I [auth A],
J [auth A],
N [auth B],
O [auth B],
P [auth B],
T [auth C],
U [auth C],
V [auth C],
Z [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free:  0.249 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.98α = 90
b = 63.51β = 102.31
c = 78.64γ = 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
  • Version 1.4: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description