6VGC | pdb_00006vgc

Crystal Structures of FLAP bound to DG-031


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 
    0.285 (Depositor), 0.289 (DCC) 
  • R-Value Work: 
    0.254 (Depositor), 0.256 (DCC) 
  • R-Value Observed: 
    0.255 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

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

  • DOI: https://doi.org/10.1016/j.bbagen.2020.129800
  • Primary Citation 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. We generated ligand-protein X-ray crystal structures of known inhibitors of microsomal prostaglandin E2 synthase-1 (mPGES-1) and the 5-Lipoxygenase Activating Protein (FLAP), with their respective proteins, to understand the overlapping pharmacophores. We subsequently used molecular modeling and structure-based drug design (SBDD) to identify hybrid structures intended to inhibit both targets. This work enabled the preparation of compounds 4 and 5, which showed potent in vitro inhibition of both targets. Our findings enhance the structural understanding of mPGES-1 and FLAP's unique ligand binding pockets and should accelerate the discovery of additional dual inhibitors for these two important integral membrane protein drug targets.


  • Organizational Affiliation
    • Lilly Biotechnology Center, San Diego, CA 92121, USA. Electronic address: ho_joseph_d@lilly.com.

Macromolecule Content 

  • Total Structure Weight: 118.5 kDa 
  • Atom Count: 7,340 
  • Modeled Residue Count: 901 
  • Deposited Residue Count: 1,026 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
5-lipoxygenase-activating protein
A, B, C, D, E
A, B, C, D, E, F
171Homo sapiensMutation(s): 0 
Gene Names: ALOX5APFLAP
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P20292 (Homo sapiens)
Explore P20292 
Go to UniProtKB:  P20292
PHAROS:  P20292
GTEx:  ENSG00000132965 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20292
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QY1
(Subject of Investigation/LOI)

Query on QY1



Download:Ideal Coordinates CCD File
G [auth A]
H [auth B]
J [auth C]
K [auth D]
M [auth E]
G [auth A],
H [auth B],
J [auth C],
K [auth D],
M [auth E],
N [auth F]
(2R)-cyclopentyl{4-[(quinolin-2-yl)methoxy]phenyl}acetic acid
C23 H23 N O3
ZEYYDOLCHFETHQ-JOCHJYFZSA-N
BOG

Query on BOG



Download:Ideal Coordinates CCD File
O [auth F]octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
I [auth B],
L [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free:  0.285 (Depositor), 0.289 (DCC) 
  • R-Value Work:  0.254 (Depositor), 0.256 (DCC) 
  • R-Value Observed: 0.255 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.911α = 90
b = 101.488β = 99.83
c = 111.864γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description