1MIK

THE ROLE OF WATER MOLECULES IN THE STRUCTURE-BASED DESIGN OF (5-HYDROXYNORVALINE)-2-CYCLOSPORIN: SYNTHESIS, BIOLOGICAL ACTIVITY, AND CRYSTALLOGRAPHIC ANALYSIS WITH CYCLOPHILIN A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Work: 0.175 
  • R-Value Observed: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The Role of Water Molecules in the Structure-Based Design of (5-Hydroxynorvaline)-2-Cyclosporin: Synthesis, Biological Activity, and Crystallographic Analysis with Cyclophilin A.

Mikol, V.Papageorgiou, C.Borer, X.

(1995) J Med Chem 38: 3361

  • DOI: 10.1021/jm00017a020
  • Primary Citation of Related Structures:  
    1MIK

  • PubMed Abstract: 
  • Analysis of the contact surface of the cyclophilin A (CypA)/cyclosporin A (CsA, 1) crystal structure delineates a unique cavity between both molecules in the vicinity of the Abu-2 side chain atoms of 1 (Abu pocket). Therefore, (5-hydroxynorvaline)-2- ...

    Analysis of the contact surface of the cyclophilin A (CypA)/cyclosporin A (CsA, 1) crystal structure delineates a unique cavity between both molecules in the vicinity of the Abu-2 side chain atoms of 1 (Abu pocket). Therefore, (5-hydroxynorvaline)-2-cyclosporin (2) was designed and prepared as a CsA derivative which could mediate additional interactions within the pocket. The X-ray crystal structure of the CypA/2 complex at 1.76 A resolution shows that 1 and 2 have identical backbone conformations and that the introduced hydroxypropyl chain makes indeed the expected supplemental interactions with CypA. However, 2 has 8-9-fold lower binding affinity than 1 for CypA. This results from a presumed unfavorable free energy change associated with the displacement of one of the tightly bound water molecules within the pocket and a change in prebinding equilibria. The role of the later was assessed by comparing the conformation distribution of 1 and 2 to that of norvaline-2-cyclosporin (3) and norvaline-2-(D-MeSer)-3-cyclosporin (4).


    Related Citations: 
    • Crystallization of the Complex between Cyclophilin a and Cyclosporin Derivatives: The Use of Cross- Seeding.
      Mikol, V., Duc, D.
      (1994) Acta Crystallogr D Biol Crystallogr 50: 543
    • X-Ray Structure of a Monomeric Cyclophilin A- Cyclosporin a Crystal Complex at 2.1 A Resolution.
      Mikol, V., Kallen, J., Pflugl, G., Walkinshaw, M.D.
      (1993) J Mol Biol 234: 1119

    Organizational Affiliation

    Sandoz Pharma Ltd., Preclinical Research, Basel, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PEPTIDYL-PROLYL CIS-TRANS ISOMERASE AA165Homo sapiensMutation(s): 0 
Gene Names: CYCLOPHILINPPIACYPA
EC: 5.2.1.8
Find proteins for P62937 (Homo sapiens)
Explore P62937 
Go to UniProtKB:  P62937
NIH Common Fund Data Resources
PHAROS  P62937
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CYCLOSPORIN AB11Tolypocladium inflatumMutation(s): 1 
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  5 Unique
IDChainsTypeFormula2D DiagramParent
AA4
Query on AA4
BL-PEPTIDE LINKINGC5 H11 N O3ALA
BMT
Query on BMT
BL-PEPTIDE LINKINGC10 H19 N O3THR
MLE
Query on MLE
BL-PEPTIDE LINKINGC7 H15 N O2LEU
MVA
Query on MVA
BL-PEPTIDE LINKINGC6 H13 N O2VAL
SAR
Query on SAR
BPEPTIDE LINKINGC3 H7 N O2GLY
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000766
Query on PRD_000766
BCYCLOSPORIN A, 6 mutationCyclic peptide /  Immunosuppressant

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Work: 0.175 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.439α = 90
b = 61.32β = 90
c = 72.575γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 1995-09-20 
  • Released Date: 1996-03-08 
  • Deposition Author(s): Mikol, V.

Revision History 

  • Version 1.0: 1996-03-08
    Type: Initial release
  • Version 1.1: 2011-06-14
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-07-27
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 1.4: 2012-12-12
    Changes: Other