7G4L | pdb_00007g4l

Crystal Structure of rat Autotaxin in complex with N-[2-amino-4-[3-[4-(trifluoromethyl)phenyl]propanoyl]phenyl]acetamide, i.e. SMILES c1c(ccc(c1N)NC(=O)C)C(=O)CCc1ccc(cc1)C(F)(F)F with IC50=0.529423 microM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 
    0.225 (Depositor), 0.224 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Model: experimental
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Literature

Crystal Structure of a rat Autotaxin complex

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

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of Ectonucleotide pyrophosphatase/phosphodiesterase family member 2846Rattus norvegicusMutation(s): 3 
Gene Names: Enpp2AtxNpps2
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ64610
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q64610-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D 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
8N-Glycosylation
Glycosylation Resources
GlyTouCan:  G33303XH
GlyCosmos:  G33303XH
GlyGen:  G33303XH
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YPO (Subject of Investigation/LOI)
Query on YPO

Download Ideal Coordinates CCD File 
C [auth A]N-(2-amino-4-{3-[4-(trifluoromethyl)phenyl]propanoyl}phenyl)acetamide
C18 H17 F3 N2 O2
NRSSDQYXMLRGOQ-UHFFFAOYSA-N
ZN
Query on ZN

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D [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

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F [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

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G [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

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E [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free:  0.225 (Depositor), 0.224 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.818α = 90
b = 91.749β = 90
c = 119.246γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
F. Hoffmann-La Roche LTDSwitzerland--

Revision History  (Full details and data files)

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