7G54 | pdb_00007g54

Crystal Structure of rat Autotaxin in complex with tert-butyl (4aR)-9-(4-chloro-2-fluorophenyl)-5,11-dioxo-2,4,4a,6-tetrahydro-1H-pyrazino[2,1-c][1,4]benzodiazepine-3-carboxylate, i.e. SMILES c1cc(cc(c1c1cc2c(cc1)NC(=O)[C@@H]1N(C2=O)CCN(C1)C(=O)OC(C)(C)C)F)Cl with IC50=0.506839 microM

• PDB DOI: https://doi.org/10.2210/pdb7G54/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., 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: 2.38 Å
• R-Value Free: 
  0.293 (Depositor), 0.289 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.234 (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: 99.41 kDa 
• Atom Count: 7,001 
• 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	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-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	8		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G33303XH GlyCosmos:  G33303XH GlyGen:  G33303XH

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Y8U (Subject of Investigation/LOI)	C [auth A]	tert-butyl (5S,8M,12aR)-8-(4-chloro-2-fluorophenyl)-6,12-dioxo-3,4,6,11,12,12a-hexahydropyrazino[2,1-c][1,4]benzodiazepine-2(1H)-carboxylate C23 H23 Cl F N3 O4 BUYGMXFBMPEQNR-LJQANCHMSA-N
ZN	D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free:  0.293 (Depositor), 0.289 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.077	α = 90
b = 93.061	β = 90
c = 121.586	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., 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