7G4I

Crystal Structure of rat Autotaxin in complex with 1H-benzotriazol-5-yl-[rac-(3aR,6aS)-5-[2-(3,5-dichlorophenyl)ethylsulfonyl]-3,3a,4,5,6,6a-hexahydro-1H-cyclopenta[c]pyrrol-2-yl]methanone, i.e. SMILES c1(ccc2c(c1)N=NN2)C(=O)N1C[C@@H]2[C@H](C1)C[C@H](C2)S(=O)(=O)CCc1cc(cc(c1)Cl)Cl with IC50=0.129444 microM

PDB DOI: https://doi.org/10.2210/pdb7G4I/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., Tang, G., Rudolph, M.G.
Funding Organization(s): F. Hoffmann-La Roche LTD

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.62 Å
R-Value Free:
0.271 (Depositor), 0.271 (DCC)
R-Value Work:
0.206 (Depositor), 0.205 (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: 99.18 kDa
Atom Count: 6,780
Modelled Residue Count: 808
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 LOADING

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)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	6		N-Glycosylation	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G47410OF GlyCosmos: G47410OF GlyGen: G47410OF

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Y2Q (Subject of Investigation/LOI) Query on Y2Q 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]	(1H-benzotriazol-5-yl)[(3aR,5r,6aS)-5-[2-(3,5-dichlorophenyl)ethanesulfonyl]hexahydrocyclopenta[c]pyrrol-2(1H)-yl]methanone C₂₂ H₂₂ Cl₂ N₄ O₃ S WHPLZWPELMTYQP-UHFFFAOYSA-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 E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth A] MOL2 format, chain C [auth A] MOL2 format, chain F [auth A] mmCIF format, chain C [auth A] mmCIF format, chain F [auth A]	C [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth A] Interactions & Density Focus chain C [auth A] Focus chain F [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]