1SP4

Crystal structure of NS-134 in complex with bovine cathepsin B: a two headed epoxysuccinyl inhibitor extends along the whole active site cleft

Structural Biology Knowledgebase: 1SP4 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Work: 0.194

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1SP4

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 28118.40

Macromolecule Entities
Molecule Chains Length Organism Details
Cathepsin B A 48 Bos taurus EC#: 3.4.22.1 IUBMB
Fragment: light chain
Gene Name(s): CTSB Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cathepsin B B 205 Bos taurus EC#: 3.4.22.1 IUBMB
Fragment: heavy chain
Gene Name(s): CTSB Gene View

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
EP2
Query on EP2

B methyl N-[(2S)-4-{[(1S)-1-{[(2S)-2-carboxypyrrolidin- 1-yl]carbonyl}-3-methylbutyl]amino}-2-hydroxy- 4-oxobutanoyl]-L-leucylglycylglycinate
NS-134 (Synonym)
C26 H41 N5 O10
LLLKOFOBLVPXQZ-RNEDXHKXSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000444 (MEU,PRO,LEU,GLY,EPO) B NS-134 TWO HEADED EPOXYSUCCINYL INHIBITOR Peptide-like /
Inhibitor
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Observed:
  • Space Group: P 43 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 73.06 α = 90.00
b = 73.06 β = 90.00
c = 141.97 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-03-16
  • Released Date: 2004-05-04
  • Deposition author(s): Stern, I., Schaschke, N., Moroder, L., Turk, D.

Revision History

  • 2014-02-12
    Type: Refinement description | Details: added R factor
  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 2011-07-13
    Type: Atom nomenclature | Details: Atom nomenclature
  • 2011-07-13
    Type: Binding sites and description | Details: Binding sites and description
  • 2011-07-13
    Type: Non-polymer description | Details: Non-polymer description
  • 2011-07-13
    Type: Function and keywords | Details: Function and keywords
  • 2011-07-13
    Type: Linkage | Details: Linkage
  • 2011-07-13
    Type: Sequence database correspondence | Details: Sequence database correspondence
  • 2011-07-13
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4