6YF3 | pdb_00006yf3

FKBP12 in complex with the BMP potentiator compound 10 at 1.00A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 
    0.158 (Depositor), 0.158 (DCC) 
  • R-Value Work: 
    0.157 (Depositor), 0.156 (DCC) 
  • R-Value Observed: 
    0.157 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6YF3

Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 12.97 kDa 
  • Atom Count: 1,090 
  • Modeled Residue Count: 108 
  • Deposited Residue Count: 109 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OOZ
(Subject of Investigation/LOI)

Query on OOZ



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})-17-ethyl-25-methoxy-12-[(~{E})-1-[(1~{R},3~{R},4~{R})-3-methoxy-4-oxidanyl-cyclohexyl]prop-1-en-2-yl]-13,19,21,27-tetramethyl-1,14,23-tris(oxidanyl)-11,28-dioxa-4-azatricyclo[22.3.1.0^{4,9}]octacos-18-ene-2,3,10,16-tetrone
C42 H67 N O12
GORPFHTVXJBJQH-XJYRRQLNSA-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: 1.00 Å
  • R-Value Free:  0.158 (Depositor), 0.158 (DCC) 
  • R-Value Work:  0.157 (Depositor), 0.156 (DCC) 
  • R-Value Observed: 0.157 (Depositor) 
Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.279α = 90
b = 57.279β = 90
c = 54.296γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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