4H2E

Crystal structure of an MMP twin inhibitor complexing two MMP-9 catalytic domains

Structural Biology Knowledgebase: 4H2E SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.311
  • R-Value Work: 0.277

Literature

Macromolecules
Sequence Display for 4H2E

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 39934.97

Macromolecule Entities
Molecule Chains Length Organism Details
human MMP-9 catalytic domain wild-type A, B 164 Homo sapiens EC#: 3.4.24.35 IUBMB
Fragment: unp residues 110-214 and 391-444
Mutation: Q227E
Gene Name(s): MMP9 Gene View CLG4B
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
0Y3
Query on 0Y3

B N,N'-bis(4-{[(3R)-3-[(biphenyl-4-ylsulfonyl)(propan- 2-yloxy)amino]-4-(hydroxyamino)-4-oxobutyl]amino}- 4-oxobutyl)benzene-1,3-dicarboxamide
C54 H66 N8 O14 S2
QTGQZAQZBAEHLR-URZIEALYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BCN
Query on BCN

A, B BICINE
C6 H13 N O4
FSVCELGFZIQNCK-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PEG
Query on PEG

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

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

A, B ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
0Y3 IC50: 8.3 nM (90) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.311
  • R-Value Work: 0.277
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 40.18 α = 90.00
b = 97.40 β = 111.99
c = 45.69 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-09-12
  • Released Date: 2013-04-24
  • Deposition author(s): Stura, E.A., Vera, L., Cassar-Lajeunesse, E., Nuti, E., Catalani, M.P., 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: --