Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37.55 kDa 
• Atom Count: 2846 
• Residue Count: 330 
• Unique protein chains: 1

1NMK

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

• DOI: 10.2210/pdb1NMK/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli str. K-12 substr. W3110
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.189 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 

Literature

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

Sedrani, R., Kallen, J., Cabrejas, L.M.M., Papageorgiou, C.D., Senia, F., Rohrbach, S., Wagner, D., Thai, B., Eme, A.-M.J., France, J., Oberer, L., Rihs, G., Zenke, G., Wagner, J.

(2003) J Am Chem Soc 125: 3849-3859

• PubMed: 12656618 
• DOI: 10.1021/ja021327y
• Primary Citation of Related Structures:  
  1NMK


• PubMed Abstract: 
  

Sanglifehrin A (SFA) is a novel immunosuppressive natural product isolated from Streptomyces sp. A92-308110. SFA has a very strong affinity for cyclophilin A (IC(50) = 6.9 +/- 0.9 nM) but is structurally different from cyclosporin A (CsA) and exerts its immunosuppressive activity via a novel mechanism. SFA has a complex molecular structure consisting of a 22-membered macrocycle, bearing in position 23 a nine-carbon tether terminated by a highly substituted spirobicyclic moiety. Selective oxidative cleavage of the C(26)=C(27) exocyclic double bond affords the spirolactam containing fragment 1 and macrolide 2. The affinity of 2 for cyclophilin (IC(50) = 29 +/- 2.1 nM) is essentially identical to SFA, which indicates that the interaction between SFA and cyclophilin A is mediated exclusively by the macrocyclic portion of the molecule. This observation was confirmed by the X-ray crystal structure resolved at 2.1 A of cyclophilin A complexed to macrolide 16, a close analogue of 2. The X-ray crystal structure showed that macrolide 16 binds to the same deep hydrophobic pocket of cyclophilin A as CsA. Additional valuable details of the structure-activity relationship were obtained by two different chemical approaches: (1) degradation work on macrolide 2 or (2) synthesis of a library of macrolide analogues using the ring-closing metathesis reaction as the key step. Altogether, it appears that the complex macrocyclic fragment of SFA is a highly optimized combination of multiple functionalities including an (E,E)-diene, a short polypropionate fragment, and an unusual tripeptide unit, which together provide an extremely strong affinity for cyclophilin A.

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Organizational Affiliation: 

Transplantation Research, Novartis Pharma AG, S-507.312, CH-4002 Basel, Switzerland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase A	A, B	165	Homo sapiens	Mutation(s): 0  Gene Names: PPIA OR CYPA, PPIA, CYPA EC: 5.2.1.8
Find proteins for P62937 (Homo sapiens) Explore P62937  Go to UniProtKB:  P62937
NIH Common Fund Data Resources
PHAROS  P62937 GTEx  ENSG00000196262

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
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 C39 H56 N4 O10 WZVMDDRRINUPRQ-APBCKSDASA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
SFM	IC50:  5.699999809265137   nM  Binding MOAD
SFM	IC50 :  5.699999809265137   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.189 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.2	α = 90
b = 67.3	β = 90
c = 78.2	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

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 

• Version 1.0: 2003-04-01
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance