3EHY

Crystal structure of the catalytic domain of human MMP12 complexed with the inhibitor (R)-2-(4-methoxyphenylsulfonamido)propanoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Biotin-tagged probes for MMP expression and activation: design, synthesis, and binding properties

Dragoni, E.Calderone, V.Fragai, M.Jaiswal, R.Luchinat, C.Nativi, C.

(2009) Bioconjug.Chem. 20: 719-727

  • DOI: 10.1021/bc8003827
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The design and synthesis of biotin chain-terminated inhibitors (BTI) showing high affinity for matrix metalloproteinases (MMPs) on one side and high affinity for avidin through the biotinylated tag on the other are reported. The affinity of the desig ...

    The design and synthesis of biotin chain-terminated inhibitors (BTI) showing high affinity for matrix metalloproteinases (MMPs) on one side and high affinity for avidin through the biotinylated tag on the other are reported. The affinity of the designed BTI toward five different MMPs has been evaluated and the simultaneous formation of a highly stable ternary system Avidin-BTI-MMP clearly assessed. This system will permit the development of new approaches to detect, quantify, or collect MMPs in biological samples, with potential applications in vivo.


    Related Citations: 
    • X-ray structures of binary and ternary enzyme-product-inhibitor complexes of matrix metalloproteinases
      Bertini, I.,Calderone, V.,Fragai, M.,Luchinat, C.,Mangani, S.,Terni, B.
      (2003) Angew.Chem.Int.Ed.Engl. 42: 2673


    Organizational Affiliation

    Magnetic Resonance Center - University of Florence, Sesto Fiorentino, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Macrophage metalloelastase
A
158Homo sapiensMutation(s): 1 
Gene Names: MMP12 (HME)
EC: 3.4.24.65
Find proteins for P39900 (Homo sapiens)
Go to Gene View: MMP12
Go to UniProtKB:  P39900
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
TBL
Query on TBL

Download SDF File 
Download CCD File 
A
N-[(4-methoxyphenyl)sulfonyl]-D-alanine
(R)-2-(4-methoxyphenylsulfonamido)propanoic acid
C10 H13 N O5 S
XTCIPBHRVYICGT-SSDOTTSWSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TBLKi: 1400 nM BINDINGMOAD
TBLKi: 1400 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.155 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 51.256α = 90.00
b = 60.479β = 116.17
c = 54.598γ = 90.00
Software Package:
Software NamePurpose
CrysalisProdata collection
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-09-15 
  • Released Date: 2009-05-19 
  • Deposition Author(s): Calderone, V.

Revision History 

  • Version 1.0: 2009-05-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance