5I3M | pdb_00005i3m

Crystal structure of the catalytic domain of MMP-12 in complex with a selective sugar-conjugated thiourea-linked carboxylate zinc-chelator water-soluble inhibitor (DC31).

• PDB DOI: https://doi.org/10.2210/pdb5I3M/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-02-10 Released: 2016-07-06 
• Deposition Author(s): Stura, E.A., Rosalia, L., Cuffaro, D., Tepshi, L., Ciccone, L., Rossello, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 
  0.253 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.206 (Depositor) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

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

• PubMed: 27356908 
• 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.

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Organizational Affiliation: 
• Department of Pharmacy, University of Pisa, via Bonanno 6, 56126, Pisa, Italy.
CEA-Saclay, Service d'Ingenierie Moleculaire des Proteines, CEA, iBiTec-S, 91191, Gif sur Yvette, France.
Biotherapy Unit, IRCCS AOU San Martino-IST, Largo R. Benzi 10, 16132, Genoa, Italy.
Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, OX3 7FY, Oxford, UK.
Division of Immunology, Transplants and Infectious Diseases, San Raffaele Scientific Institute, Via Olgettina, 20132, Milan, Italy.
Department of Pharmacy, University of Pisa, via Bonanno 6, 56126, Pisa, Italy. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 74.65 kDa 
• Atom Count: 5,646 
• Modeled Residue Count: 628 
• Deposited Residue Count: 636 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrophage metalloelastase	A, B, C, D	159	Homo sapiens	Mutation(s): 2  Gene Names: MMP12, HME 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

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
67F	DA [auth D], E [auth A], M [auth B], V [auth C]	(2S)-2-{[2-({[(2R,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]carbamothioyl}amino)ethyl](biphenyl-4-ylsulfonyl)amino}-3-methylbutanoic acid (non-preferred name) C28 H38 N4 O9 S2 NZFBENDBEOZJMI-DIVFVBEMSA-N
DIO	CA [auth C], T [auth B], U [auth B]	1,4-DIETHYLENE DIOXIDE C4 H8 O2 RYHBNJHYFVUHQT-UHFFFAOYSA-N
DMS	JA [auth D], K [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
PGO	L [auth A], S [auth B]	S-1,2-PROPANEDIOL C3 H8 O2 DNIAPMSPPWPWGF-VKHMYHEASA-N
ZN	EA [auth D], F [auth A], FA [auth D], G [auth A], N [auth B], O [auth B], W [auth C], X [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	BA [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	AA [auth C], GA [auth D], H [auth A], HA [auth D], I [auth A], IA [auth D], J [auth A], P [auth B], Q [auth B], R [auth B], Y [auth C], Z [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free:  0.253 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.206 (Depositor) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.72	α = 90
b = 63.14	β = 103.09
c = 78.92	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
PHENIX	refinement
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-07-06 
Deposition Author(s): Stura, E.A., Rosalia, L., Cuffaro, D., Tepshi, L., Ciccone, L., Rossello, A.

Revision History  

• 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: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description