5LP1 | pdb_00005lp1

CRYSTAL STRUCTURE OF HUMAN LIPOPROTEIN-ASSOCIATED PHOSPHOLIPASE A2 IN COMPLEX WITH A [1.1.1]BICYCLOPENTANE-CONTAINING INHIBITOR AT 1.91A RESOLUTION.

• PDB DOI: https://doi.org/10.2210/pdb5LP1/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-08-11 Released: 2017-02-01 
• Deposition Author(s): Somers, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 
  0.192 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: other

Literature

Investigation of a Bicyclo[1.1.1]pentane as a Phenyl Replacement within an LpPLA2 Inhibitor.

Measom, N.D., Down, K.D., Hirst, D.J., Jamieson, C., Manas, E.S., Patel, V.K., Somers, D.O.

(2017) ACS Med Chem Lett 8: 43-48

• PubMed: 28105273 
• DOI: https://doi.org/10.1021/acsmedchemlett.6b00281
• Primary Citation Related Structures: 
  5LP1


• PubMed Abstract: 
  

  We describe the incorporation of a bicyclo[1.1.1]pentane moiety within two known LpPLA ₂ inhibitors to act as bioisosteric phenyl replacements. An efficient synthesis to the target compounds was enabled with a dichlorocarbene insertion into a bicyclo[1.1.0]butane system being the key transformation. Potency, physicochemical, and X-ray crystallographic data were obtained to compare the known inhibitors to their bioisosteric counterparts, which showed the isostere was well tolerated and positively impacted on the physicochemical profile.

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Organizational Affiliation: 
• GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K.; Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow, G1 1XL, U.K.
GlaxoSmithKline , Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K.
Department of Pure and Applied Chemistry, University of Strathclyde , Thomas Graham Building, 295 Cathedral Street, Glasgow, G1 1XL, U.K.
GlaxoSmithKline , 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 44.93 kDa 
• Atom Count: 3,420 
• Modeled Residue Count: 370 
• Deposited Residue Count: 388 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Platelet-activating factor acetylhydrolase	A	388	Homo sapiens	Mutation(s): 0  Gene Names: PLA2G7, PAFAH EC: 3.1.1.47
UniProt & NIH Common Fund Data Resources
Find proteins for Q13093 (Homo sapiens) Explore Q13093  Go to UniProtKB:  Q13093
PHAROS:  Q13093 GTEx:  ENSG00000146070

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
71H	D [auth A]	~{N}-[2-(diethylamino)ethyl]-2-[2-[(4-fluorophenyl)methylsulfanyl]-4-oxidanylidene-5~{H}-cyclopenta[d]pyrimidin-1-yl]-~{N}-[[3-[4-(trifluoromethyl)phenyl]-1-bicyclo[1.1.1]pentanyl]methyl]ethanamide C35 H38 F4 N4 O2 S SHVFOCPBEIJQSO-AQOUDTPCSA-N
CL	B [auth A], C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free:  0.192 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.28	α = 90
b = 91.56	β = 111.88
c = 51.65	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
REFMAC	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-02-01 
Deposition Author(s): Somers, D.

Revision History  

• Version 1.0: 2017-02-01
  Type: Initial release
  
• Version 1.1: 2019-06-12
  Changes: Data collection, Structure summary
• Version 1.2: 2024-05-01
  Changes: Data collection, Database references, Refinement description