1D5J

CRYSTAL STRUCTURE OF MMP3 COMPLEXED WITH A THIAZEPINE BASED INHIBITOR.

Structural Biology Knowledgebase: 1D5J SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.257
  • R-Value Work: 0.237

Literature

Macromolecules
Sequence Display for 1D5J

Classification: HYDROLASE

Total Structure Weight: 40084.35

Macromolecule Entities
Molecule Chains Length Organism Details
STROMELYSIN-1 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
MM3
Query on MM3

A, B N-HYDROXY-4-[(4-METHOXYLPHENYL)SULFONYL]- 2,2-DIMETHYL-HEXAHYDRO-1,4-THIAZEPINE-3(S)- CARBOXAMIDE
C15 H22 N2 O5 S2
CYYCSKFJEOSZTF-CYBMUJFWSA-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 %)
MM3 N/A in BindingDB
N/A in BindingMoad
IC50: 0.7 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.257
  • R-Value Work: 0.237
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 37.78 α = 90.00
b = 78.54 β = 90.00
c = 105.27 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-10-07
  • Released Date: 2000-10-09
  • Deposition author(s): Almstead, N.G., Bradley, R.S., Pikul, S., De, B., Natchus, M.G.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4