7G59 | pdb_00007g59

Crystal Structure of rat Autotaxin in complex with [2-fluoro-4-(2,2,2-trifluoroethoxy)phenyl]methyl 2-(4,5,6,7-tetrahydro-1H-benzotriazole-5-carbonyl)-2,7-diazaspiro[3.5]nonane-7-carboxylate, i.e. SMILES C1N(CC21CCN(CC2)C(=O)OCc1c(cc(cc1)OCC(F)(F)F)F)C(=O)[C@H]1CCC2=C(C1)N=NN2 with IC50=0.211229 microM

PDB DOI: https://doi.org/10.2210/pdb7G59/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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free:
0.241 (Depositor), 0.239 (DCC)
R-Value Work:
0.192 (Depositor), 0.191 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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: 100.88 kDa
Atom Count: 7,146
Modeled Residue Count: 804
Deposited Residue Count: 846
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q64610
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A	Go to GlyGen: Q64610-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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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-(1-6)-[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	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G63337SS GlyCosmos: G63337SS GlyGen: G63337SS

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YFX (Subject of Investigation/LOI) Query on YFX Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain C [auth A]	C [auth A], E [auth A]	[2-fluoro-4-(2,2,2-trifluoroethoxy)phenyl]methyl 2-[(5S)-4,5,6,7-tetrahydro-1H-benzotriazole-5-carbonyl]-2,7-diazaspiro[3.5]nonane-7-carboxylate C₂₄ H₂₇ F₄ N₅ O₄ HFJGRHYPTCNSKW-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain E [auth A]
ZIS Query on ZIS 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]	[2-fluoro-4-(2,2,2-trifluoroethoxy)phenyl]methyl 2-[(5R)-4,5,6,7-tetrahydro-1H-benzotriazole-5-carbonyl]-2,7-diazaspiro[3.5]nonane-7-carboxylate C₂₄ H₂₇ F₄ N₅ O₄ HFJGRHYPTCNSKW-OAHLLOKOSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A]	L [auth A], M [auth A], N [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain H [auth A] MOL2 format, chain K [auth A] MOL2 format, chain H [auth A] mmCIF format, chain K [auth A] mmCIF format, chain H [auth A]	H [auth A], K [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth A] Interactions & Density Focus chain H [auth A] Focus chain K [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain G [auth A]	G [auth A], I [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth A] Interactions & Density Focus chain G [auth A] Focus chain I [auth A]