6ESM

Crystal structure of MMP9 in complex with inhibitor BE4.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.104 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.156 

wwPDB Validation 3D Report Full Report


This is version 2.0 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
Matrix metalloproteinase-9,Matrix metalloproteinase-9
A
160Homo sapiensMutation(s): 1 
Gene Names: MMP9 (CLG4B)
EC: 3.4.24.35
Find proteins for P14780 (Homo sapiens)
Go to Gene View: MMP9
Go to UniProtKB:  P14780
Small Molecules
Ligands 4 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
B9Z
Query on B9Z

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

Download SDF File 
Download CCD File 
A
piperazine
C4 H10 N2
GLUUGHFHXGJENI-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.104 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.156 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 39.690α = 90.00
b = 39.690β = 90.00
c = 163.660γ = 120.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
PHASERphasing
PHENIXrefinement

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 2.0: 2018-06-06
    Type: Atomic model, Data collection, Database references