6ELA

Crystal structure of MMP12 in complex with inhibitor BE4.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.485 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Development of Thioaryl-Based Matrix Metalloproteinase-12 Inhibitors with Alternative Zinc-Binding Groups: Synthesis, Potentiometric, NMR, and Crystallographic Studies.

Nuti, E.Cuffaro, D.Bernardini, E.Camodeca, C.Panelli, L.Chaves, S.Ciccone, L.Tepshi, L.Vera, L.Orlandini, E.Nencetti, S.Stura, E.A.Santos, M.A.Dive, V.Rossello, A.

(2018) J. Med. Chem. 61: 4421-4435


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Macrophage metalloelastase
A, B, C, D
159Homo sapiensMutation(s): 2 
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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

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Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
B9Z
Query on B9Z

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Download CCD File 
A, B, C, D
(2~{S})-2-[2-[4-(4-methoxyphenyl)phenyl]sulfanylphenyl]pentanedioic acid
C24 H22 O5 S
KSEPBMMZVPGILK-NRFANRHFSA-N
 Ligand Interaction
DIO
Query on DIO

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Download CCD File 
A, B, C, D
1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.485 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 64.190α = 90.00
b = 63.320β = 103.73
c = 78.320γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
XDSdata reduction
PHENIXrefinement
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 1.1: 2018-06-06
    Type: Data collection, Database references