Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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: 1530 
• Residue Count: 158 
• Unique protein chains: 1

3N2V

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

• DOI: 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 

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: 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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Related Citations: 

• Exploring the subtleties of drug-receptor interactions: the case of matrix metalloproteinases.
  Bertini, I., Calderone, V., Fragai, M., Giachetti, A., Loconte, M., Luchinat, C., Maletta, M., Nativi, C., Yeo, K.J.
  (2007) J Am Chem Soc 129: 2466

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Organizational Affiliation: 

ProtEra s.r.l. viale delle Idee, 22 I-50019 Sesto F.no (FI), Italy.

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
Find proteins for P39900 (Homo sapiens) Explore P39900  Go to UniProtKB:  P39900
NIH Common Fund Data Resources
PHAROS:  P39900 GTEx:  ENSG00000262406

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JT5	A	N~2~-(biphenyl-4-ylsulfonyl)-N-hydroxy-N~2~-(2-hydroxyethyl)glycinamide C16 H18 N2 O5 S QQDWEVONJRXVDB-UHFFFAOYSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
JT5	Ki :  31   nM  PDBBind
JT5	Ki:  31   nM  BindingDB

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

• Deposited Date: 2010-05-19 
• 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