5K0I | pdb_00005k0i

mpges1 bound to an inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5K0I/pdb

• Classification: Isomerase/Isomerase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2016-05-17 Released: 2016-09-14 
• Deposition Author(s): Luz, J.G., Kuklish, S.L.
• Funding Organization(s): Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.159 (Depositor), 0.161 (DCC) 
• R-Value Work: 
  0.145 (Depositor), 0.148 (DCC) 
• R-Value Observed: 
  0.146 (Depositor) 

Literature

Characterization of 3,3-dimethyl substituted N-aryl piperidines as potent microsomal prostaglandin E synthase-1 inhibitors.

Kuklish, S.L., Antonysamy, S., Bhattachar, S.N., Chandrasekhar, S., Fisher, M.J., Fretland, A.J., Gooding, K., Harvey, A., Hughes, N.E., Luz, J.G., Manninen, P.R., McGee, J.E., Navarro, A., Norman, B.H., Partridge, K.M., Quimby, S.J., Schiffler, M.A., Sloan, A.V., Warshawsky, A.M., York, J.S., Yu, X.P.

(2016) Bioorg Med Chem Lett 26: 4824-4828

• PubMed: 27554445 
• DOI: https://doi.org/10.1016/j.bmcl.2016.08.023
• Primary Citation Related Structures: 
  5K0I


• PubMed Abstract: 
  

  Here we report on novel, potent 3,3-dimethyl substituted N-aryl piperidine inhibitors of microsomal prostaglandin E synthases-1(mPGES-1). Example 14 potently inhibited PGE2 synthesis in an ex vivo human whole blood (HWB) assay with an IC50 of 7nM. In addition, 14 had no activity in human COX-1 or COX-2 assays at 30μM, and failed to inhibit human mPGES-2 at 62.5μM in a microsomal prep assay. These data are consistent with selective mPGES-1-mediated reduction of PGE2. In dog, 14 had oral bioavailability (74%), clearance (3.62mL/(min*kg)) and volume of distribution (Vd,ss=1.6L/kg) values within our target ranges. For these reasons, 14 was selected for further study.

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Organizational Affiliation: 
• Lilly Research Laboratories, A Division of Eli Lilly and Company, Indianapolis, IN 46285, USA. Electronic address: [e-mail].
Eli Lilly Biotechnology Center, San Diego, CA 92121, USA.
Lilly Research Laboratories, A Division of Eli Lilly and Company, Indianapolis, IN 46285, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 19.02 kDa 
• Atom Count: 1,489 
• Modeled Residue Count: 148 
• Deposited Residue Count: 154 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prostaglandin E synthase	A	154	Homo sapiens	Mutation(s): 0  Gene Names: PTGES, MGST1L1, MPGES1, PGES, PIG12 EC: 5.3.99.3 (PDB Primary Data), 1.11.1 (UniProt), 2.5.1.18 (UniProt) Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for O14684 (Homo sapiens) Explore O14684  Go to UniProtKB:  O14684
PHAROS:  O14684 GTEx:  ENSG00000148344

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6PW	B [auth A]	1,5-anhydro-2,3,4-trideoxy-3-{[(4S)-3,3-dimethyl-1-(8-methylquinolin-2-yl)piperidine-4-carbonyl]amino}-D-erythro-hexitol C24 H33 N3 O3 OLJFTJILJDDJGV-SLFFLAALSA-N
GSH	C [auth A]	Glutathione C10 H17 N3 O6 S RWSXRVCMGQZWBV-WDSKDSINSA-N
BOG	D [auth A], E [auth A]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N
PG4	F [auth A], G [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Binding Affinity Annotations
ID	Source	Binding Affinity
6PW	BindingDB:  5K0I	IC50: min: 2, max: 23 (nM) from 5 assay(s)

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002593 (GSH)	C [auth A]	Glutathione	Peptide-like / Oxidation-reduction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.159 (Depositor), 0.161 (DCC) 
• R-Value Work:  0.145 (Depositor), 0.148 (DCC) 
• R-Value Observed: 0.146 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.444	α = 90
b = 77.444	β = 90
c = 123.565	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-09-14 
Deposition Author(s): Luz, J.G., Kuklish, S.L.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-AC02-06CH11357

Revision History  

• Version 1.0: 2016-09-14
  Type: Initial release
  
• Version 1.1: 2016-09-21
  Changes: Database references
• Version 1.2: 2017-09-06
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.3: 2019-12-04
  Changes: Author supporting evidence
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.5: 2025-04-02
  Changes: Data collection, Database references, Structure summary