4HMA

Crystal structure of an MMP twin carboxylate based inhibitor LC20 in complex with the MMP-9 catalytic domain

Structural Biology Knowledgebase: 4HMA SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.283
  • R-Value Work: 0.211

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4HMA

Classification: Hydrolase / Hydrolase Inhibitor

Total Structure Weight: 39045.02

Macromolecule Entities
Molecule Chains Length Organism Details
Matrix metalloproteinase-9 A, B 160 Homo sapiens EC#: 3.4.24.35 IUBMB
Fragment: MMP-9 catalytic domain 107-215,391-443
Mutation: E227Q
Gene Name(s): MMP9 Gene View CLG4B

Small Molecules
Ligands 7 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
0ZD
Query on 0ZD

A N,N'-bis(2-[(biphenyl-4ylsulfonyl)[(2R)-1- hydroxy-3-methyl-1-oxobutan-2-yl]-amino]ethyl)benzene- 1,3-dicarboxamide
C46 H50 N4 O10 S2
JEFGHXXQQOIPKU-NCRNUEESSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MLT
Query on MLT

B D-MALATE
(2R)-2-HYDROXYBUTANEDIOIC ACID; 2-HYDROXY- SUCCINIC ACID (Synonym)
C4 H6 O5
BJEPYKJPYRNKOW-UWTATZPHSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PEG
Query on PEG

A, B DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PGO
Query on PGO

A, B S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.283
  • R-Value Work: 0.211
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 73.87 α = 90.00
b = 98.24 β = 90.00
c = 47.44 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-10-18
  • Released Date: 2013-04-24
  • Deposition author(s): Stura, E.A., Antoni, C., Vera, L., Nuti, E., Carafa, L., Cassar-Lajeunesse, E., Dive, V., Rossello, A.

Revision History

  • 2015-08-12
    Type: Citation | Details: Citation update
  • 2014-10-08
    Type: Entry authorship | Details: --
  • 2013-05-01
    Type: Citation | Details: --