5N5K

Human catalytic MMP-12 in complex with 5-(1,2-dithiolan-3-yl)-N-(3-hydroxypropyl)pentanamide

• PDB DOI: https://doi.org/10.2210/pdb5N5K/pdb

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


• Deposited: 2017-02-14 Released: 2017-11-01 
• Deposition Author(s): Calderone, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.227 
• R-Value Work: 0.167 
• R-Value Observed: 0.170 

Literature

Lipoyl-Homotaurine Derivative (ADM_12) Reverts Oxaliplatin-Induced Neuropathy and Reduces Cancer Cells Malignancy by Inhibiting Carbonic Anhydrase IX (CAIX).

Fragai, M., Comito, G., Di Cesare Mannelli, L., Gualdani, R., Calderone, V., Louka, A., Richichi, B., Francesconi, O., Angeli, A., Nocentini, A., Gratteri, P., Chiarugi, P., Ghelardini, C., Tadini-Buoninsegni, F., Supuran, C.T., Nativi, C.

(2017) J Med Chem 60: 9003-9011

• PubMed: 29048889 
• DOI: https://doi.org/10.1021/acs.jmedchem.7b01237
• Primary Citation of Related Structures:  
  5N5J, 5N5K


• PubMed Abstract: 
  

  Oxaliplatin (OXA) is a valuable and largely used cancer drug which induces a serious and intractable neuropathy. The lipoyl-homotaurine derivative (ADM_12) reverts in vivo OXA-induced neuropathy, and it is an effective antagonist of the nociceptive sensor channel TRPA1. Unprecedentedly, this safe analgesic showed a synergy with OXA in vitro and proved to inhibit CA IX, a relevant therapeutic target, clearly interfering with pancreatic cancer cells' aggressiveness.

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Organizational Affiliation: 

Department of Chemistry, University of Florence , via della Lastruccia 3-13, 50019 Sesto Fiorentino, Italy.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 17.92 kDa 
• Atom Count: 1,422 
• Modelled Residue Count: 156 
• Deposited Residue Count: 156 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrophage metalloelastase	A	156	Homo sapiens	Mutation(s): 1  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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8NW	H [auth A]	5-[(3~{S})-1,2-dithiolan-3-yl]-~{N}-(3-oxidanylpropyl)pentanamide C11 H21 N O2 S2 QPQPASXMSHOHIW-JTQLQIEISA-N
HAE	G [auth A]	ACETOHYDROXAMIC ACID C2 H5 N O2 RRUDCFGSUDOHDG-UHFFFAOYSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	D [auth A], E [auth A], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.227 
• R-Value Work: 0.167 
• R-Value Observed: 0.170 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.79	α = 90
b = 60.17	β = 114.61
c = 53.73	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-11-01 
Deposition Author(s): Calderone, V.

Revision History  

• Version 1.0: 2017-11-01
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description