1NMK

The Sanglifehrin-Cyclophilin Interaction: Degradation Work, Synthetic Macrocyclic Analogues, X-ray Crystal Structure and Binding Data

Structural Biology Knowledgebase: 1NMK SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.189
  • R-Value Work: 0.163

Literature

Macromolecules
Sequence Display for 1NMK

Classification: Isomerase

Total Structure Weight: 37555.06

Macromolecule Entities
Molecule Chains Length Organism Details
Peptidyl-prolyl cis-trans isomerase A A, B 165 Homo sapiens EC#: 5.2.1.8 IUBMB
Gene Name(s): PPIA Gene View CYPA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B (13E,15E)-(3S,6S,9R,10R,11S,12S,18S,21S)- 10,12-DIHYDROXY-3-(3-HYDROXYBEN-ZYL)-18-((E)- 3-HYDROXY-1-METHYLPROPENYL)-6-ISOPROPYL-11- METHYL-9-(3-OXO-BUTYL)-19-OXA-1,4,7,25-TETRAAZA- BICYCLO[19.3.1]PENTACOSA-13,15-DIENE-2,5,8,20- TETRAONE
ANALOGUE OF MACROLIDE FROM DEGRADED SANGLIFEHRIN A (Synonym)
C39 H56 N4 O10
WZVMDDRRINUPRQ-APBCKSDASA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
SFM N/A in BindingDB
IC50: 5.7 nM  BindingMOAD
IC50: 5.7 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.189
  • R-Value Work: 0.163
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 58.20 α = 90.00
b = 67.30 β = 90.00
c = 78.20 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-01-10
  • Released Date: 2003-04-01
  • Deposition author(s): Kallen, J., Sedrani, R., Wagner, J.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update