1D8F

CRYSTAL STRUCTURE OF MMP3 COMPLEXED WITH A PIPERAZINE BASED INHIBITOR.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.252
  • R-Value Work: 0.294

Literature

Macromolecules
Sequence Display for 1D8F

Classification: HYDROLASE

Total Structure Weight: 39784.64

Macromolecule Entities
Molecule Chains Length Organism Details
STROMELYSIN-1 PRECURSOR A, B 173 Homo sapiens EC#: 3.4.24.17 IUBMB
Fragment: CATALYTIC DOMAIN
Gene Name(s): MMP3 Gene View STMY1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

B N-HYDROXY-1-(4-METHOXYPHENYL)SULFONYL-4-BENZYLOXYCARBONYL- PIPERAZINE-2-CARBOXAMIDE
C20 H23 N3 O7 S
DNGGPLKVDUPXFN-GOSISDBHSA-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)
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 %)
SPI IC50: 18 nM (100) BindingDB

IC50: 18 nM  BindingMOAD
IC50: 18 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.252
  • R-Value Work: 0.294
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 38.27 α = 90.00
b = 78.54 β = 90.00
c = 106.58 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-10-22
  • Released Date: 2000-10-23
  • Deposition author(s): Cheng, M.Y., De, B., Pikul, S., Almstead, N.G., Natchus, M.G., Anastasio, M.V., McPhail, S.J., Snider, C.E., Taiwo, Y.O., Chen, L.Y.

Revision History

  • Version 1_0: 2000-10-23

    Type: Initial release

  • Version 1_1: 2008-04-27

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Version format compliance