3N2V

Crystal structure of the catalytic domain of human MMP12 complexed with the inhibitor N-hydroxy-2-(N-hydroxyethyl)biphenyl-4-ylsulfonamido)acetamide

• PDB DOI: https://doi.org/10.2210/pdb3N2V/pdb

• Classification: Hydrolase/Hydrolase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-05-19 Released: 2010-11-10 
• Deposition Author(s): Calderone, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.180 
• R-Value Work: 0.132 
• R-Value Observed: 0.136 

Starting Model: experimental

Literature

Structure-based approach to nanomolar, water soluble matrix metalloproteinases inhibitors (MMPIs).

Attolino, E., Calderone, V., Dragoni, E., Fragai, M., Richichi, B., Luchinat, C., Nativi, C.

(2010) Eur J Med Chem 45: 5919-5925

• PubMed: 20965620 
• DOI: https://doi.org/10.1016/j.ejmech.2010.09.057
• Primary Citation of Related Structures:  
  3N2U, 3N2V


• PubMed Abstract: 
  

  N-arylsulfonyl-based MMPs inhibitors (MMPIs) are among the most prominent inhibitors possessing nanomolar affinity. However, their poor bioavailability remains critical for the drug development of this family of molecules. The structural analysis of the complex of NNGH (the most representative member of the family) with MMP-12 provided us with the basis to effectively design simple NNGH analogues with enhanced solubility in water. Following this approach, the sec-butyl residue, not directly involved in the binding with MMP, has been replaced with hydrophilic residues thus yielding new potent inhibitors soluble in water.

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Organizational Affiliation: 

ProtEra s.r.l. viale delle Idee, 22 I-50019 Sesto F.no (FI), 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: 18.09 kDa 
• Atom Count: 1,530 
• Modelled Residue Count: 158 
• Deposited Residue Count: 158 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrophage metalloelastase	A	158	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JT5	G [auth A]	N~2~-(biphenyl-4-ylsulfonyl)-N-hydroxy-N~2~-(2-hydroxyethyl)glycinamide C16 H18 N2 O5 S QQDWEVONJRXVDB-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

Binding Affinity Annotations
ID	Source	Binding Affinity
JT5	PDBBind:  3N2V	Ki: 31 (nM) from 1 assay(s)
	BindingDB:  3N2V	Ki: 31 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.180 
• R-Value Work: 0.132 
• R-Value Observed: 0.136 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.614	α = 90
b = 60.277	β = 115.2
c = 54.186	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-10 
Deposition Author(s): Calderone, V.

Revision History  

• Version 1.0: 2010-11-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description