7G44 | pdb_00007g44

Crystal Structure of rat Autotaxin in complex with (3,5-dichlorophenyl)methyl rac-(3aR,6aS)-2-(4-sulfamoylbenzoyl)-1,3,3a,4,6,6a-hexahydropyrrolo[3,4-c]pyrrole-5-carboxylate, i.e. SMILES C1N(C[C@H]2[C@@H]1CN(C2)C(=O)c1ccc(cc1)S(=O)(=O)N)C(=O)OCc1cc(cc(c1)Cl)Cl with IC50=0.0573624 microM

• PDB DOI: https://doi.org/10.2210/pdb7G44/pdb
• Deposition Group: G_1002267 | Explore  G_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., Mattei, P., Rudolph, M.G.
• Funding Organization(s): F. Hoffmann-La Roche LTD

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.226 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.191 (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: 99.65 kDa 
• Atom Count: 7,600 
• Modeled Residue Count: 806 
• 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	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-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	9		N-Glycosylation
Glycosylation Resources
GlyTouCan: G63337SS GlyCosmos: G63337SS GlyGen: G63337SS

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YF0 (Subject of Investigation/LOI)	C [auth A]	(3,5-dichlorophenyl)methyl (3aS,6aS)-5-(4-sulfamoylbenzoyl)hexahydropyrrolo[3,4-c]pyrrole-2(1H)-carboxylate C21 H21 Cl2 N3 O5 S IQCOXMRXONRSKN-UHFFFAOYSA-N
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	E [auth A], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	G [auth A], H [auth A], I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.226 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.798	α = 90
b = 91.706	β = 90
c = 119.736	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	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., Mattei, P., 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