7G5L | pdb_00007g5l

Crystal Structure of rat Autotaxin in complex with rac-(3aR,8aS)-6-[rac-(E)-3-[4-(trifluoromethoxy)phenyl]prop-2-enoyl]-N-(1H-triazol-5-ylmethyl)-1,3,3a,4,5,7,8,8a-octahydropyrrolo[3,4-d]azepine-2-carboxamide, i.e. SMILES c1c(ccc(c1)/C=C/C(=O)N1CC[C@@H]2[C@H](CC1)CN(C2)C(=O)NCC1=CN=NN1)OC(F)(F)F with IC50=0.493964 microM

PDB DOI: https://doi.org/10.2210/pdb7G5L/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: 2.51 Å
R-Value Free:
0.263 (Depositor), 0.268 (DCC)
R-Value Work:
0.207 (Depositor), 0.212 (DCC)
R-Value Observed:
0.210 (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: 100.7 kDa
Atom Count: 6,798
Modeled Residue Count: 805
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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XV2 (Subject of Investigation/LOI) Query on XV2 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	C [auth A], E [auth A], F [auth A]	(3aR,8aS)-N-[(1H-1,2,3-triazol-5-yl)methyl]-6-{(2E)-3-[4-(trifluoromethoxy)phenyl]prop-2-enoyl}octahydropyrrolo[3,4-d]azepine-2(1H)-carboxamide C₂₂ H₂₅ F₃ N₆ O₃ CKLJWCVZPSDUAH-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain F [auth A]
MES Query on MES 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-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-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 G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	G [auth A], H [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]