3HDN | pdb_00003hdn

Crystal structure of serum and glucocorticoid-regulated kinase 1 in complex with compound 2

• PDB DOI: https://doi.org/10.2210/pdb3HDN/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: unidentified baculovirus
• Mutation(s): Yes 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.278 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.250 (Depositor), 0.242 (DCC) 
• R-Value Observed: 
  0.251 (Depositor) 

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

• PubMed: 19497745 
• DOI: https://doi.org/10.1016/j.bmcl.2009.05.051
• Primary Citation 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. 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.

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Organizational Affiliation: 
• Department of Chemistry, Metabolic Pathways Centre for Excellence in Drug Discovery, GlaxoSmithKline Pharmaceuticals, 709 Swedeland Road, King of Prussia, PA 19406, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 42.68 kDa 
• Atom Count: 2,271 
• Modeled Residue Count: 280 
• Deposited Residue Count: 373 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase Sgk1	A	373	Homo sapiens	Mutation(s): 4  Gene Names: SGK, SGK1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O00141 (Homo sapiens) Explore O00141  Go to UniProtKB:  O00141
PHAROS:  O00141 GTEx:  ENSG00000118515

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GMG	B [auth A]	[4-(5-naphthalen-2-yl-1H-pyrrolo[2,3-b]pyridin-3-yl)phenyl]acetic acid C25 H18 N2 O2 SWXKLXXVFMYMDP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.278 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.250 (Depositor), 0.242 (DCC) 
• R-Value Observed: 0.251 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.812	α = 90
b = 96.812	β = 90
c = 150.779	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2009-06-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.3: 2024-02-21
  Changes: Data collection