3KXO

An orally active inhibitor bound at the active site of HPGDS

• PDB DOI: https://doi.org/10.2210/pdb3KXO/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-12-03 Released: 2010-09-01 
• Deposition Author(s): Kiefer, J.R., Day, J.E., Thorarensen, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.222 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 

Literature

Discovery of an oral potent selective inhibitor of hematopoietic prostaglandin D synthase

Carron, C.P., Trujillo, J.I., Olson, K.L., Huang, W., Hamper, B.C., Dice, T., Neal, B.E., Pelc, M.J., Day, J., Rohrer, D.C., Kiefer, J.R., Moon, J.B., Schweitzer, B.A., Blake, T.D., Turner, S.R., Woerndle, R., Case, B.L., Bono, C.P., Dilworth, V.M., Funckes-Shippy, C.L., Hood, B.L., Jerome, G.M., Kornmeier, C.M., Radabaugh, M.R., Williams, M.L., Davies, M.S., Wegner, C.D., Welsch, D.J., Abraham, W.M., Warren, C.J., Dowty, M.E., Hua, F., Zutshi, A., Yang, J.Z., Thorarensen, A.

To be published.

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: 48.71 kDa 
• Atom Count: 3,764 
• Modelled Residue Count: 396 
• Deposited Residue Count: 404 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione-requiring prostaglandin D synthase	A, B	202	Homo sapiens	Mutation(s): 0  Gene Names: PTGDS2, PGDS EC: 5.3.99.2 (PDB Primary Data), 2.5.1.18 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O60760 (Homo sapiens) Explore O60760  Go to UniProtKB:  O60760
PHAROS:  O60760 GTEx:  ENSG00000163106

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KXO	D [auth A], G [auth B]	6-(3-fluorophenyl)-N-[1-(2,2,2-trifluoroethyl)piperidin-4-yl]pyridine-3-carboxamide C19 H19 F4 N3 O LPUCBGGXXIUBAZ-UHFFFAOYSA-N
GSH	C [auth A], F [auth B]	GLUTATHIONE C10 H17 N3 O6 S RWSXRVCMGQZWBV-WDSKDSINSA-N
MG	E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
KXO	BindingDB:  3KXO	Kd: min: 9.5, max: 20 (nM) from 2 assay(s)
		IC50: 200 (nM) from 1 assay(s)
		EC50: 35 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.222 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.799	α = 90
b = 78.364	β = 91.61
c = 52.455	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-01 
Deposition Author(s): Kiefer, J.R., Day, J.E., Thorarensen, A.

Revision History  

• Version 1.0: 2010-09-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-03-21
  Changes: Non-polymer description
• Version 1.3: 2017-11-01
  Changes: Refinement description
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references, Derived calculations