4ZGA

Structural basis for inhibition of human autotaxin by four novel compounds

• PDB DOI: https://doi.org/10.2210/pdb4ZGA/pdb

• Classification: Hydrolase/Hydrolase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2015-04-22 Released: 2015-10-14 
• Deposition Author(s): Stein, A.J., Bain, G., Hutchinson, J.H., Evans, J.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.274 
• R-Value Work: 0.208 
• R-Value Observed: 0.211 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 100.53 kDa 
• Atom Count: 5,870 
• Modelled Residue Count: 740 
• Deposited Residue Count: 863 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ectonucleotide pyrophosphatase/phosphodiesterase family member 2	A	863	Homo sapiens	Mutation(s): 0  Gene Names: ENPP2, ATX, PDNP2 EC: 3.1.4.39
UniProt & NIH Common Fund Data Resources
Find proteins for Q13822 (Homo sapiens) Explore Q13822  Go to UniProtKB:  Q13822
PHAROS:  Q13822 GTEx:  ENSG00000136960

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4O3	J [auth A]	(11aS)-6-(4-fluorobenzyl)-5,6,11,11a-tetrahydro-1H-imidazo[1',5':1,6]pyrido[3,4-b]indole-1,3(2H)-dione C20 H16 F N3 O2 LRGAZQBFSHLAGN-KRWDZBQOSA-N
ACD	I [auth A]	ARACHIDONIC ACID C20 H32 O2 YZXBAPSDXZZRGB-DOFZRALJSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
SCN	F [auth A], G [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M
CA	D [auth A], H [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
4O3	BindingDB:  4ZGA	IC50: 500 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.274 
• R-Value Work: 0.208 
• R-Value Observed: 0.211 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.672	α = 99.44
b = 64.001	β = 108.39
c = 70.505	γ = 98.61

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
SCALEPACK	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-14 
Deposition Author(s): Stein, A.J., Bain, G., Hutchinson, J.H., Evans, J.F.

Revision History  

• Version 1.0: 2015-10-14
  Type: Initial release
  
• Version 1.1: 2015-11-11
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary