5L0B | pdb_00005l0b

Crystal Structure of Autotaxin and Compound 1

PDB DOI: https://doi.org/10.2210/pdb5L0B/pdb

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

Deposited: 2016-07-27 Released: 2016-08-10
Deposition Author(s): Durbin, J.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free:
0.209 (Depositor), 0.223 (DCC)
R-Value Work:
0.176 (Depositor), 0.186 (DCC)
R-Value Observed:
0.176 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Novel Autotaxin Inhibitors for the Treatment of Osteoarthritis Pain: Lead Optimization via Structure-Based Drug Design.

Jones, S.B., Pfeifer, L.A., Bleisch, T.J., Beauchamp, T.J., Durbin, J.D., Klimkowski, V.J., Hughes, N.E., Rito, C.J., Dao, Y., Gruber, J.M., Bui, H., Chambers, M.G., Chandrasekhar, S., Lin, C., McCann, D.J., Mudra, D.R., Oskins, J.L., Swearingen, C.A., Thirunavukkarasu, K., Norman, B.H.

(2016) ACS Med Chem Lett 7: 857-861

PubMed: 27660691 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acsmedchemlett.6b00207
Primary Citation Related Structures:
5L0B, 5L0E, 5L0K

PubMed Abstract:
In an effort to develop a novel therapeutic agent aimed at addressing the unmet need of patients with osteoarthritis pain, we set out to develop an inhibitor for autotaxin with excellent potency and physical properties to allow for the clinical investigation of autotaxin-induced nociceptive and neuropathic pain. An initial hit identification campaign led to an aminopyrimidine series with an autotaxin IC50 of 500 nM. X-ray crystallography enabled the optimization to a lead compound that demonstrated favorable potency (IC50 = 2 nM), PK properties, and a robust PK/PD relationship.

Organizational Affiliation

Lilly Research Laboratories , A Division of Eli Lilly and Company, Indianapolis, Indiana 46285, United States.

Macromolecule Content

Total Structure Weight: 204.06 kDa
Atom Count: 13,448
Modeled Residue Count: 1,560
Deposited Residue Count: 1,742
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ectonucleotide pyrophosphatase/phosphodiesterase family member 2	A, B	871	Rattus norvegicus	Mutation(s): 2 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q64610
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain B	Go to GlyGen: Q64610-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	D 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	D	6		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G47410OF GlyCosmos: G47410OF GlyGen: G47410OF

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6ZM Query on 6ZM Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain F [auth A]	F [auth A], L [auth B]	1-{2-[(2,3-dihydro-1H-inden-2-yl)amino]-7,8-dihydropyrido[4,3-d]pyrimidin-6(5H)-yl}ethan-1-one C₁₈ H₂₀ N₄ O YZUQRESBRMOGBQ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain L [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B]	E [auth A], K [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain K [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] M [auth B] N [auth B] G [auth A], H [auth A], I [auth A], M [auth B], N [auth B], O [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain J [auth A] MOL2 format, chain P [auth B] MOL2 format, chain J [auth A] mmCIF format, chain P [auth B] mmCIF format, chain J [auth A]	J [auth A], P [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain P [auth B] Interactions & Density Focus chain J [auth A] Focus chain P [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
6ZM	BindingDB: 5L0B	IC50: min: 520, max: 1070 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free: 0.209 (Depositor), 0.223 (DCC)
R-Value Work: 0.176 (Depositor), 0.186 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 182.827	α = 90
b = 96.733	β = 112.86
c = 136.284	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Coot	model building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-08-10

Deposition Author(s):

Durbin, J.D.

Revision History (Full details and data files)

Version 1.0: 2016-08-10
Type: Initial release
Version 1.1: 2016-10-05
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: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary