4H3X

Crystal structure of an MMP broad spectrum hydroxamate based inhibitor CC27 in complex with the MMP-9 catalytic domain

Structural Biology Knowledgebase: 4H3X SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.254
  • R-Value Work: 0.196

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4H3X

Classification: HYDROLASE / HYDROLASE Inhibitor

Total Structure Weight: 38840.80

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: human wild-type MMP-9 catalytic domain unp residues 107-215/391-443
Mutation: Q227E
Gene Name(s): MMP9 Gene View CLG4B

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
10B
Query on 10B

A, B N-2-(biphenyl-4-ylsulfonyl)-N-2-(isopropyloxy)- acetohydroxamic acid
N~2~-(biphenyl-4-ylsulfonyl)-N-hydroxy-N~2~- (propan-2-yloxy)glycinamide (Synonym)
C17 H20 N2 O5 S
PHGLPDURIUEELR-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PEG
Query on PEG

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 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)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
10B IC50: 200 nM (90) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.254
  • R-Value Work: 0.196
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 40.11 α = 90.00
b = 97.94 β = 111.73
c = 46.08 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-09-14
  • Released Date: 2013-04-24
  • Deposition author(s): Stura, E.A., Vera, L., Cassar-Lajeunesse, E., Nuti, E., Dive, V., Rossello, A.

Revision History

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