6VL4

Crystal Structure of mPGES-1 bound to DG-031

• PDB DOI: https://doi.org/10.2210/pdb6VL4/pdb

• Classification: ISOMERASE, MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2020-01-22 Released: 2020-12-02 
• Deposition Author(s): Ho, J.D., Lee, M.R., Rauch, C.T., Aznavour, K., Park, J.S., Luz, J.G., Antonysamy, S., Condon, B., Maletic, M., Zhang, A., Hickey, M.J., Hughes, N.E., Chandrasekhar, S., Sloan, A.V., Gooding, K., Harvey, A., Yu, X.P., Kahl, S.D., Norman, B.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.145 
• R-Value Work: 0.140 
• R-Value Observed: 0.140 

Literature

Structure-based, multi-targeted drug discovery approach to eicosanoid inhibition: Dual inhibitors of mPGES-1 and 5-lipoxygenase activating protein (FLAP).

Ho, J.D., Lee, M.R., Rauch, C.T., Aznavour, K., Park, J.S., Luz, J.G., Antonysamy, S., Condon, B., Maletic, M., Zhang, A., Hickey, M.J., Hughes, N.E., Chandrasekhar, S., Sloan, A.V., Gooding, K., Harvey, A., Yu, X.P., Kahl, S.D., Norman, B.H.

(2020) Biochim Biophys Acta Gen Subj 1865: 129800-129800

• PubMed: 33246032 
• DOI: https://doi.org/10.1016/j.bbagen.2020.129800
• Primary Citation of Related Structures:  
  6VGC, 6VGI, 6VL4


• PubMed Abstract: 
  

  Due to the importance of both prostaglandins (PGs) and leukotrienes (LTs) as pro-inflammatory mediators, and the potential for eicosanoid shunting in the presence of pathway target inhibitors, we have investigated an approach to inhibiting the formation of both PGs and LTs as part of a multi-targeted drug discovery effort.

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Organizational Affiliation: 

Lilly Biotechnology Center, San Diego, CA 92121, USA. Electronic address: [e-mail].

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 18.37 kDa 
• Atom Count: 1,298 
• Modelled Residue Count: 143 
• 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 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QY1 (Subject of Investigation/LOI)	B [auth A]	(2R)-cyclopentyl{4-[(quinolin-2-yl)methoxy]phenyl}acetic acid C23 H23 N O3 ZEYYDOLCHFETHQ-JOCHJYFZSA-N
BOG	C [auth A]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N
PG4	D [auth A], E [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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.145 
• R-Value Work: 0.140 
• R-Value Observed: 0.140 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.417	α = 90
b = 76.417	β = 90
c = 123.784	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-12-02 
Deposition Author(s): Ho, J.D., Lee, M.R., Rauch, C.T., Aznavour, K., Park, J.S., Luz, J.G., Antonysamy, S., Condon, B., Maletic, M., Zhang, A., Hickey, M.J., Hughes, N.E., Chandrasekhar, S., Sloan, A.V., Gooding, K., Harvey, A., Yu, X.P., Kahl, S.D., Norman, B.H.

Revision History  

• Version 1.0: 2020-12-02
  Type: Initial release
  
• Version 1.1: 2020-12-09
  Changes: Database references
• Version 1.2: 2020-12-16
  Changes: Database references