6YF2

FKBP12 in complex with the BMP potentiator compound 6 at 1.03A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.03 Å
  • R-Value Free: 0.149 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.141 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Phenotypic screen identifies calcineurin-sparing FK506 analogs as BMP potentiators for treatment of acute kidney injury.

Larraufie, M.H.Gao, X.Xia, X.Devine, P.J.Kallen, J.Liu, D.Michaud, G.Harsch, A.Savage, N.Ding, J.Tan, K.Mihalic, M.Roggo, S.Canham, S.M.Bushell, S.M.Krastel, P.Gao, J.Izaac, A.Altinoglu, E.Lustenberger, P.Salcius, M.Harbinski, F.Williams, E.T.Zeng, L.Loureiro, J.Cong, F.Fryer, C.J.Klickstein, L.Tallarico, J.A.Jain, R.K.Rothman, D.M.Wang, S.

(2021) Cell Chem Biol 28: 1271

  • DOI: https://doi.org/10.1016/j.chembiol.2021.04.001
  • Primary Citation of Related Structures:  
    6YF0, 6YF1, 6YF2, 6YF3

  • PubMed Abstract: 

    Acute kidney injury (AKI) is a life-threatening disease with no known curative or preventive therapies. Data from multiple animal models and human studies have linked dysregulation of bone morphogenetic protein (BMP) signaling to AKI. Small molecules that potentiate endogenous BMP signaling should have a beneficial effect in AKI. We performed a high-throughput phenotypic screen and identified a series of FK506 analogs that act as potent BMP potentiators by sequestering FKBP12 from BMP type I receptors. We further showed that calcineurin inhibition was not required for this activity. We identified a calcineurin-sparing FK506 analog oxtFK through late-stage functionalization and structure-guided design. OxtFK demonstrated an improved safety profile in vivo relative to FK506. OxtFK stimulated BMP signaling in vitro and in vivo and protected the kidneys in an AKI mouse model, making it a promising candidate for future development as a first-in-class therapeutic for diseases with dysregulated BMP signaling.


  • Organizational Affiliation

    Novartis Institutes for Biomedical Research, Cambridge, MA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase FKBP1A109Homo sapiensMutation(s): 0 
Gene Names: FKBP1AFKBP1FKBP12
EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P62942 (Homo sapiens)
Explore P62942 
Go to UniProtKB:  P62942
PHAROS:  P62942
GTEx:  ENSG00000088832 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62942
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OP5 (Subject of Investigation/LOI)
Query on OP5

Download Ideal Coordinates CCD File 
B [auth A](1~{R},9~{S},12~{S},13~{R},14~{S},17~{R},18~{E},21~{S},23~{S},24~{R},25~{S},27~{R})-23,25-dimethoxy-12-[(~{E})-1-[(1~{R},3~{R},4~{R})-3-methoxy-4-oxidanyl-cyclohexyl]prop-1-en-2-yl]-13,19,21,27-tetramethyl-1,14-bis(oxidanyl)-17-(2-oxidanylidenepropyl)-11,28-dioxa-4-azatricyclo[22.3.1.0^{4,9}]octacos-18-ene-2,3,10,16-tetrone
C44 H69 N O13
DHEMNTLAGYUASY-BABZEESQSA-N
CD
Query on CD

Download Ideal Coordinates CCD File 
C [auth A]CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.03 Å
  • R-Value Free: 0.149 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.141 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.482α = 90
b = 57.482β = 90
c = 54.469γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2021-03-10 
  • Deposition Author(s): Kallen, J.

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-10
    Type: Initial release
  • Version 1.1: 2021-05-05
    Changes: Database references
  • Version 1.2: 2021-09-29
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Refinement description