4YL3

Crystal Structures of mPGES-1 Inhibitor Complexes

• PDB DOI: https://doi.org/10.2210/pdb4YL3/pdb

• Classification: ISOMERASE/ISOMERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2015-03-04 Released: 2015-07-08 
• Deposition Author(s): Luz, J.G., Antonysamy, S., Kuklish, S.L., Fisher, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free: 0.183 
• R-Value Work: 0.166 
• R-Value Observed: 0.167 

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: 18.29 kDa 
• Atom Count: 1,454 
• Modelled Residue Count: 146 
• Deposited Residue Count: 148 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prostaglandin E synthase	A	148	Homo sapiens	Mutation(s): 0  Gene Names: PTGES, MGST1L1, MPGES1, PGES, PIG12 EC: 5.3.99.3 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
4U9	B [auth A]	5-[4-bromo-2-(2-chloro-6-fluorophenyl)-1H-imidazol-5-yl]-2-{[4-(trifluoromethyl)phenyl]ethynyl}pyridine C23 H11 Br Cl F4 N3 KPXLXMUZOLULFL-UHFFFAOYSA-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]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
4U9	Binding MOAD:  4YL3	IC50: 3940 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free: 0.183 
• R-Value Work: 0.166 
• R-Value Observed: 0.167 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.434	α = 90
b = 76.434	β = 90
c = 123.264	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
Coot	model building
SCALA	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-08 
Deposition Author(s): Luz, J.G., Antonysamy, S., Kuklish, S.L., Fisher, M.J.

Revision History  

• Version 1.0: 2015-07-08
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Structure summary