3HDM

Crystal structure of serum and glucocorticoid-regulated kinase 1 in complex with compound 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Design and synthesis of orally bioavailable serum and glucocorticoid-regulated kinase 1 (SGK1) inhibitors.

Hammond, M.Washburn, D.G.Hoang, H.T.Manns, S.Frazee, J.S.Nakamura, H.Patterson, J.R.Trizna, W.Wu, C.Azzarano, L.M.Nagilla, R.Nord, M.Trejo, R.Head, M.S.Zhao, B.Smallwood, A.M.Hightower, K.Laping, N.J.Schnackenberg, C.G.Thompson, S.K.

(2009) Bioorg Med Chem Lett 19: 4441-4445

  • DOI: 10.1016/j.bmcl.2009.05.051
  • Primary Citation of Related Structures:  
    3HDM, 3HDN

  • PubMed Abstract: 
  • The lead serum and glucocorticoid-related kinase 1 (SGK1) inhibitors 4-(5-phenyl-1H-pyrrolo[2,3-b]pyridin-3-yl)benzoic acid (1) and {4-[5-(2-naphthalenyl)-1H-pyrrolo[2,3-b]pyridin-3-yl]phenyl}acetic acid (2) suffer from low DNAUC values in rat, due in part to formation and excretion of glucuronic acid conjugates ...

    The lead serum and glucocorticoid-related kinase 1 (SGK1) inhibitors 4-(5-phenyl-1H-pyrrolo[2,3-b]pyridin-3-yl)benzoic acid (1) and {4-[5-(2-naphthalenyl)-1H-pyrrolo[2,3-b]pyridin-3-yl]phenyl}acetic acid (2) suffer from low DNAUC values in rat, due in part to formation and excretion of glucuronic acid conjugates. These PK/glucuronidation issues were addressed either by incorporating a substituent on the 3-phenyl ring ortho to the key carboxylate functionality of 1 or by substituting on the group in between the carboxylate and phenyl ring of 2. Three of these analogs have been identified as having good SGK1 inhibition potency and have DNAUC values suitable for in vivo testing.


    Organizational Affiliation

    Department of Chemistry, Metabolic Pathways Centre for Excellence in Drug Discovery, GlaxoSmithKline Pharmaceuticals, 709 Swedeland Road, King of Prussia, PA 19406, USA. marlys.2.hammond@gsk.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase Sgk1 A373Homo sapiensMutation(s): 4 
Gene Names: SGKSGK1
EC: 2.7.11.1
Find proteins for O00141 (Homo sapiens)
Explore O00141 
Go to UniProtKB:  O00141
NIH Common Fund Data Resources
PHAROS:  O00141
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MMG
Query on MMG

Download Ideal Coordinates CCD File 
A
4-(5-phenyl-1H-pyrrolo[2,3-b]pyridin-3-yl)benzoic acid
C20 H14 N2 O2
KSFDVNIKNYXUIP-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MMGIC50 :  40   nM  PDBBind
MMGIC50:  40   nM  BindingDB
MMGIC50:  1300   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.978α = 90
b = 96.978β = 90
c = 150.769γ = 120
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2009-05-07 
  • Released Date: 2009-06-30 
  • Deposition Author(s): Zhao, B., Hammond, M.

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance