7G6A | pdb_00007g6a

Crystal Structure of rat Autotaxin in complex with 5-(1-acetyl-4-piperidyl)-4-[(E)-[3,5-bis(trifluoromethyl)phenyl]azo]-1,2-dihydropyrazol-3-one, i.e. SMILES CC(=O)N1CCC(CC1)C2=C(\N=N\c3cc(cc(c3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 microM

PDB DOI: https://doi.org/10.2210/pdb7G6A/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., Rudolph, M.G.
Funding Organization(s): F. Hoffmann-La Roche LTD

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free:
0.220 (Depositor), 0.219 (DCC)
R-Value Work:
0.192 (Depositor), 0.191 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal Structure of a rat Autotaxin complex

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

To be published.

Macromolecule Content

Total Structure Weight: 99.63 kDa
Atom Count: 7,317
Modeled Residue Count: 809
Deposited Residue Count: 846
Unique protein chains: 1

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q64610
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A	Go to GlyGen: Q64610-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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-(1-2)-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	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G33303XH GlyCosmos: G33303XH GlyGen: G33303XH

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XW2 (Subject of Investigation/LOI) Query on XW2 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	5-(1-acetylpiperidin-4-yl)-4-{(E)-[3,5-bis(trifluoromethyl)phenyl]diazenyl}-1,2-dihydro-3H-pyrazol-3-one C₁₈ H₁₇ F₆ N₅ O₂ FTZTXTWTLRLQHR-IMVLJIQESA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain C [auth A] MOL2 format, chain J [auth A] MOL2 format, chain C [auth A] mmCIF format, chain J [auth A] mmCIF format, chain C [auth A]	C [auth A], J [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain J [auth A] Interactions & Density Focus chain C [auth A] Focus chain J [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain I [auth A]	I [auth A], K [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth A] Interactions & Density Focus chain I [auth A] Focus chain K [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free: 0.220 (Depositor), 0.219 (DCC)
R-Value Work: 0.192 (Depositor), 0.191 (DCC)
R-Value Observed: 0.193 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.657	α = 90
b = 91.334	β = 90
c = 118.662	γ = 90

Software Package:

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

Structure Validation

Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-12-18

Deposition Author(s):

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

Revision History (Full details and data files)

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

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