8RDX

PGGtase I in complex with probe BAY-6092


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.67 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.138 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of YAP1/TAZ pathway inhibitors through phenotypic screening with potent anti-tumor activity via blockade of Rho-GTPase signaling.

Graham, K.Lienau, P.Bader, B.Prechtl, S.Naujoks, J.Lesche, R.Weiske, J.Kuehnlenz, J.Brzezinka, K.Potze, L.Zanconato, F.Nicke, B.Montebaur, A.Bone, W.Golfier, S.Kaulfuss, S.Kopitz, C.Pilari, S.Steuber, H.Hayat, S.Kamburov, A.Steffen, A.Schlicker, A.Buchgraber, P.Braeuer, N.Font, N.A.Heinrich, T.Kuhnke, L.Nowak-Reppel, K.Stresemann, C.Steigemann, P.Walter, A.O.Blotta, S.Ocker, M.Lakner, A.von Nussbaum, F.Mumberg, D.Eis, K.Piccolo, S.Lange, M.

(2024) Cell Chem Biol 

  • DOI: https://doi.org/10.1016/j.chembiol.2024.02.013
  • Primary Citation of Related Structures:  
    8RDX

  • PubMed Abstract: 

    This study describes the identification and target deconvolution of small molecule inhibitors of oncogenic Yes-associated protein (YAP1)/TAZ activity with potent anti-tumor activity in vivo. A high-throughput screen (HTS) of 3.8 million compounds was conducted using a cellular YAP1/TAZ reporter assay. Target deconvolution studies identified the geranylgeranyltransferase-I (GGTase-I) complex as the direct target of YAP1/TAZ pathway inhibitors. The small molecule inhibitors block the activation of Rho-GTPases, leading to subsequent inactivation of YAP1/TAZ and inhibition of cancer cell proliferation in vitro. Multi-parameter optimization resulted in BAY-593, an in vivo probe with favorable PK properties, which demonstrated anti-tumor activity and blockade of YAP1/TAZ signaling in vivo.


  • Organizational Affiliation

    Bayer AG, Pharmaceuticals, Research & Development, Muellerstr. 178, 13353 Berlin, Germany; Nuvisan ICB GmbH, Muellerstr. 178, 13353 Berlin, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
A, C, E, G, I
A, C, E, G, I, K
314Rattus norvegicusMutation(s): 0 
Gene Names: Fnta
UniProt
Find proteins for Q04631 (Rattus norvegicus)
Explore Q04631 
Go to UniProtKB:  Q04631
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04631
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Geranylgeranyl transferase type-1 subunit beta
B, D, F, H, J
B, D, F, H, J, L
346Rattus norvegicusMutation(s): 0 
Gene Names: Pggt1b
UniProt
Find proteins for P53610 (Rattus norvegicus)
Explore P53610 
Go to UniProtKB:  P53610
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53610
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1HZ4 (Subject of Investigation/LOI)
Query on A1HZ4

Download Ideal Coordinates CCD File 
BA [auth H]
FA [auth J]
JA [auth L]
P [auth B]
T [auth D]
BA [auth H],
FA [auth J],
JA [auth L],
P [auth B],
T [auth D],
X [auth F]
(5~{R})-5-(2-methoxyphenyl)-9-[(2~{R})-3,3,3-tris(fluoranyl)-2-methoxy-2-phenyl-propanoyl]-3,9-diazaspiro[5.5]undecan-2-one
C26 H29 F3 N2 O4
RLJMERPAJNBSDE-NBGIEHNGSA-N
DPO
Query on DPO

Download Ideal Coordinates CCD File 
AA [auth H]
EA [auth J]
IA [auth L]
O [auth B]
S [auth D]
AA [auth H],
EA [auth J],
IA [auth L],
O [auth B],
S [auth D],
W [auth F]
DIPHOSPHATE
O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-J
ZN
Query on ZN

Download Ideal Coordinates CCD File 
CA [auth J]
GA [auth L]
M [auth B]
Q [auth D]
U [auth F]
CA [auth J],
GA [auth L],
M [auth B],
Q [auth D],
U [auth F],
Y [auth H]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
DA [auth J]
HA [auth L]
N [auth B]
R [auth D]
V [auth F]
DA [auth J],
HA [auth L],
N [auth B],
R [auth D],
V [auth F],
Z [auth H]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.67 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.138 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 270.891α = 90
b = 269.263β = 131.77
c = 185.248γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2024-02-14 
  • Deposition Author(s): Steuber, H.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-14
    Type: Initial release
  • Version 1.1: 2024-04-10
    Changes: Database references