5DLV

Crystal structure of Autotaxin (ENPP2) with tauroursodeoxycholic acid (TUDCA)

PDB DOI: https://doi.org/10.2210/pdb5DLV/pdb

Classification: HYDROLASE
Organism(s): Rattus norvegicus
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2015-09-07 Released: 2016-04-13
Deposition Author(s): Keune, W.J., Heidebrecht, T., von Castelmur, E., Joosten, R.P., Perrakis, A.
Funding Organization(s): NWO

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.227
R-Value Work: 0.193
R-Value Observed: 0.195

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 199.1 kDa
Atom Count: 13,814
Modelled Residue Count: 1,562
Deposited Residue Count: 1,654
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ectonucleotide pyrophosphatase/phosphodiesterase family member 2	A, B	827	Rattus norvegicus	Mutation(s): 2 Gene Names: c EC: 3.1.4.39
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
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-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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	C	9		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G37135JQ GlyCosmos: G37135JQ GlyGen: G37135JQ

Entity ID: 3
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-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	7		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G16404YH GlyCosmos: G16404YH GlyGen: G16404YH

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5D5 Query on 5D5 Download Ideal Coordinates CCD File SDF format, chain Y [auth A] SDF format, chain AB [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain AB [auth B]	AB [auth B], Y [auth A]	2-{[(3alpha,5beta,7alpha,8alpha,14beta,17alpha)-3,7-dihydroxy-24-oxocholan-24-yl]amino}ethanesulfonic acid C₂₆ H₄₅ N O₆ S BHTRKEVKTKCXOH-LBSADWJPSA-N		Interactions Focus chain AB [auth B] Focus chain Y [auth A] Interactions & Density Focus chain AB [auth B] Focus chain Y [auth A]
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain KA [auth B] SDF format, chain UA [auth B] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth B] SDF format, chain M [auth A] SDF format, chain MA [auth B] SDF format, chain N [auth A] SDF format, chain NA [auth B] SDF format, chain O [auth A] SDF format, chain OA [auth B] SDF format, chain P [auth A] SDF format, chain PA [auth B] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain R [auth A] SDF format, chain RA [auth B] SDF format, chain S [auth A] SDF format, chain SA [auth B] SDF format, chain T [auth A] SDF format, chain TA [auth B] SDF format, chain U [auth A] SDF format, chain VA [auth B] SDF format, chain WA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain UA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain WA [auth B]	H [auth A] I [auth A] J [auth A] K [auth A] KA [auth B] H [auth A], I [auth A], J [auth A], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], SA [auth B], T [auth A], TA [auth B], U [auth A], UA [auth B], VA [auth B], WA [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain V [auth A] SDF format, chain XA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain XA [auth B]	V [auth A], XA [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain V [auth A] Focus chain XA [auth B] Interactions & Density Focus chain V [auth A] Focus chain XA [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain DA [auth A] SDF format, chain BA [auth A] SDF format, chain CA [auth A] SDF format, chain DB [auth B] SDF format, chain EA [auth A] SDF format, chain EB [auth B] SDF format, chain FA [auth A] SDF format, chain FB [auth B] SDF format, chain GA [auth A] SDF format, chain GB [auth B] SDF format, chain HB [auth B] MOL2 format, chain DA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain DB [auth B] MOL2 format, chain EA [auth A] MOL2 format, chain EB [auth B] MOL2 format, chain FA [auth A] MOL2 format, chain FB [auth B] MOL2 format, chain GA [auth A] MOL2 format, chain GB [auth B] MOL2 format, chain HB [auth B]	BA [auth A] CA [auth A] DA [auth A] DB [auth B] EA [auth A] BA [auth A], CA [auth A], DA [auth A], DB [auth B], EA [auth A], EB [auth B], FA [auth A], FB [auth B], GA [auth A], GB [auth B], HB [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain EA [auth A] Focus chain EB [auth B] Focus chain FA [auth A] Focus chain FB [auth B] Focus chain GA [auth A] Focus chain GB [auth B] Focus chain HB [auth B] Interactions & Density Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain EA [auth A] Focus chain EB [auth B] Focus chain FA [auth A] Focus chain FB [auth B] Focus chain GA [auth A] Focus chain GB [auth B] Focus chain HB [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain HA [auth B] SDF format, chain IA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B]	E [auth A], F [auth A], HA [auth B], IA [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain HA [auth B] Focus chain IA [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain HA [auth B] Focus chain IA [auth B]
SCN Query on SCN Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BB [auth B] SDF format, chain CB [auth B] SDF format, chain Z [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain BB [auth B] MOL2 format, chain CB [auth B] MOL2 format, chain Z [auth A]	AA [auth A], BB [auth B], CB [auth B], Z [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain AA [auth A] Focus chain BB [auth B] Focus chain CB [auth B] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BB [auth B] Focus chain CB [auth B] Focus chain Z [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain JA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain JA [auth B]	G [auth A], JA [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain JA [auth B] Interactions & Density Focus chain G [auth A] Focus chain JA [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain YA [auth B] SDF format, chain ZA [auth B] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain YA [auth B] MOL2 format, chain ZA [auth B]	W [auth A], X [auth A], YA [auth B], ZA [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain W [auth A] Focus chain X [auth A] Focus chain YA [auth B] Focus chain ZA [auth B] Interactions & Density Focus chain W [auth A] Focus chain X [auth A] Focus chain YA [auth B] Focus chain ZA [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
5D5	Binding MOAD: 5DLV	IC50: 1.04e+4 (nM) from 1 assay(s)
5D5	BindingDB: 5DLV	IC50: 1.03e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.227
R-Value Work: 0.193
R-Value Observed: 0.195
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.88	α = 83.84
b = 77.832	β = 79.29
c = 92.437	γ = 77.08

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
Coot	model building
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-04-13

Deposition Author(s):

Funding Organization	Location	Grant Number
NWO	Netherlands	700.10.354
NWO	Netherlands	723.013.003

Revision History (Full details and data files)

Version 1.0: 2016-04-13
Type: Initial release
Version 1.1: 2016-04-27
Changes: Database references
Version 1.2: 2018-02-14
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary