7G56 | pdb_00007g56

Crystal Structure of rat Autotaxin in complex with a dimer of [(2R,4S,5S)-5-ethynyl-1-azabicyclo[2.2.2]octan-2-yl]methyl N-cyclohexylcarbamate, i.e. SMILES O=C(NC1CCCCC1)OC[C@H]2C[C@@H]3CCN2C[C@@H]3C#CC#C[C@H]4CN5CC[C@H]4C[C@@H]5COC(=O)NC6CCCCC6 with IC50=4.47875 microM

• PDB DOI: https://doi.org/10.2210/pdb7G56/pdb
• Deposition Group: G_1002267 ExploreG_1002267

• Classification: HYDROLASE
• Organism(s): Rattus norvegicus
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2023-06-05 Released: 2024-12-18 
• Deposition Author(s): Stihle, M., Benz, J., Hunziker, D., Rudolph, M.G.
• Funding Organization(s): F. Hoffmann-La Roche LTD

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.233 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of a rat Autotaxin complex

Hunziker, D., Joachim, S.C., Ullmer, C., Rudolph, M.G.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 99.37 kDa 
• Atom Count: 7,099 
• Modeled Residue Count: 804 
• Deposited Residue Count: 846 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of Ectonucleotide pyrophosphatase/phosphodiesterase family member 2	A	846	Rattus norvegicus	Mutation(s): 3  Gene Names: Enpp2, Atx, Npps2 EC: 3.1.4.39 (PDB Primary Data), 3.1.4.4 (UniProt)
UniProt
Find proteins for Q64610 (Rattus norvegicus) Explore Q64610  Go to UniProtKB:  Q64610
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: Q64610-1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	7		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G16404YH GlyCosmos:  G16404YH GlyGen:  G16404YH

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YGT (Subject of Investigation/LOI)	C [auth A]	(R)-(cyclohexylamino){3-[(3R,4R)-3-{4-[(1R,3R,4R,6R)-6-{[(R)-(cyclohexylamino)(hydroxy)methoxy]methyl}-1-azabicyclo[2.2.2]octan-3-yl]butyl}piperidin-4-yl]propoxy}methanol C34 H50 N4 O4 AMBLGDNBWGSPMN-PWUUJYBQSA-N
ZN	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	F [auth A], H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.233 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.493	α = 90
b = 92.418	β = 90
c = 118.751	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-18 
Deposition Author(s): Stihle, M., Benz, J., Hunziker, D., Rudolph, M.G.

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Funding Organization	Location	Grant Number
F. Hoffmann-La Roche LTD	Switzerland	--

Revision History  

• Version 1.0: 2024-12-18
  Type: Initial release