6NNA

Human Fatty Acid Synthase Psi/KR Tri-Domain with NADPH and Compound 22

• PDB DOI: https://doi.org/10.2210/pdb6NNA/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2019-01-14 Released: 2019-02-20 
• Deposition Author(s): Toms, A.V., Martin, M.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 0.251 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 

Literature

Discovery and optimization of novel piperazines as potent inhibitors of fatty acid synthase (FASN).

Martin, M.W., Lancia Jr., D.R., Li, H., Schiller, S.E.R., Toms, A.V., Wang, Z., Bair, K.W., Castro, J., Fessler, S., Gotur, D., Hubbs, S.E., Kauffman, G.S., Kershaw, M., Luke, G.P., McKinnon, C., Yao, L., Lu, W., Millan, D.S.

(2019) Bioorg Med Chem Lett 29: 1001-1006

• PubMed: 30803804 
• DOI: https://doi.org/10.1016/j.bmcl.2019.02.012
• Primary Citation of Related Structures:  
  6NNA


• PubMed Abstract: 
  

  The discovery, structure-activity relationships, and optimization of a novel class of fatty acid synthase (FASN) inhibitors is reported. High throughput screening identified a series of substituted piperazines with structural features that enable interactions with many of the potency-driving regions of the FASN KR domain binding site. Derived from this series was FT113, a compound with potent biochemical and cellular activity, which translated into excellent activity in in vivo models.

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Organizational Affiliation: 

FORMA Therapeutics, 500 Arsenal Street, Suite 100, Watertown, MA 02472, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 147.01 kDa 
• Atom Count: 10,100 
• Modelled Residue Count: 1,216 
• Deposited Residue Count: 1,320 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fatty acid synthase,Fatty acid synthase	A, B	660	Homo sapiens	Mutation(s): 2  Gene Names: FASN, FAS EC: 2.3.1.85 (PDB Primary Data), 2.3.1.38 (PDB Primary Data), 2.3.1.39 (PDB Primary Data), 2.3.1.41 (PDB Primary Data), 1.1.1.100 (PDB Primary Data), 4.2.1.59 (PDB Primary Data), 1.3.1.39 (PDB Primary Data), 3.1.2.14 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P49327 (Homo sapiens) Explore P49327  Go to UniProtKB:  P49327
PHAROS:  P49327 GTEx:  ENSG00000169710

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	C [auth A], L [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
KUA (Subject of Investigation/LOI)	D [auth A], M [auth B]	{4-[4-(1,3-benzoxazol-2-yl)benzene-1-carbonyl]piperazin-1-yl}(1-hydroxycyclopropyl)methanone C22 H21 N3 O4 FGXGECPNCZCUAJ-UHFFFAOYSA-N
EDO	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CAF	A, B	L-PEPTIDE LINKING	C5 H12 As N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 0.251 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.11	α = 65.57
b = 85.74	β = 90
c = 86.47	γ = 87

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-02-20 
Deposition Author(s): Toms, A.V., Martin, M.W.

Revision History  

• Version 1.0: 2019-02-20
  Type: Initial release
  
• Version 1.1: 2019-03-13
  Changes: Data collection, Database references
• Version 1.2: 2019-03-20
  Changes: Data collection, Database references
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Refinement description