3QK5

Crystal structure of fatty acid amide hydrolase with small molecule inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3QK5/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-01-31 Released: 2011-04-06 
• Deposition Author(s): Min, X., Walker, N.P.C., Wang, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.224 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 

Starting Model: experimental

Literature

Identification of potent, noncovalent fatty acid amide hydrolase (FAAH) inhibitors.

Gustin, D.J., Ma, Z., Min, X., Li, Y., Hedberg, C., Guimaraes, C., Porter, A.C., Lindstrom, M., Lester-Zeiner, D., Xu, G., Carlson, T.J., Xiao, S., Meleza, C., Connors, R., Wang, Z., Kayser, F.

(2011) Bioorg Med Chem Lett 21: 2492-2496

• PubMed: 21392988 
• DOI: https://doi.org/10.1016/j.bmcl.2011.02.052
• Primary Citation of Related Structures:  
  3QK5


• PubMed Abstract: 
  

  Starting from a series of ureas that were determined to be mechanism-based inhibitors of FAAH, several spirocyclic ureas and lactams were designed and synthesized. These efforts identified a series of novel, noncovalent FAAH inhibitors with in vitro potency comparable to known covalent FAAH inhibitors. The mechanism of action for these compounds was determined through a combination of SAR and co-crystallography with rat FAAH.

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Organizational Affiliation: 

Department of Chemistry, Amgen Inc., South San Francisco, 1120 Veterans Blvd., South San Francisco, CA 94080, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 131.14 kDa 
• Atom Count: 9,545 
• Modelled Residue Count: 1,095 
• Deposited Residue Count: 1,174 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fatty-acid amide hydrolase 1	A, B	587	Rattus norvegicus	Mutation(s): 0  Gene Names: Faah, Faah1 EC: 3.5.1.99 (PDB Primary Data), 3.1.1 (UniProt)
UniProt
Find proteins for P97612 (Rattus norvegicus) Explore P97612  Go to UniProtKB:  P97612

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QK5	C [auth A], K [auth B]	(3-{(3R)-1-[4-(1-benzothiophen-2-yl)pyrimidin-2-yl]piperidin-3-yl}-2-methyl-1H-pyrrolo[2,3-b]pyridin-1-yl)acetonitrile C27 H24 N6 S OZRJTNXVIRAQAD-FQEVSTJZSA-N
GOL	G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], F [auth A], H [auth A], I [auth A], J [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
QK5	PDBBind:  3QK5	IC50: 18 (nM) from 1 assay(s)
	BindingDB:  3QK5	IC50: 18 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.224 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.431	α = 90
b = 104.701	β = 90
c = 148.596	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-06 
Deposition Author(s): Min, X., Walker, N.P.C., Wang, Z.

Revision History  

• Version 1.0: 2011-04-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description