Structure of PDB 5s9l Chain A Binding Site BS03

Receptor Information

>5s9l Chain A (length=805) Species: 10116 (Rattus norvegicus)

WTATSGSCKGRCFELQEVGPPDCRCDNLCKSYSSCCHDFDELCLKTARGW
ECTKDRCGEVRNEENACHCSEDCLSRGDCCTNYQVVCKGESHWVDDDCEE
IKVPECPAGFVRPPLIIFSVDGFRASYMKKGSKVMPNIEKLRSCGTHAPY
MRPVYPTKTFPNLYTLATGLYPESHGIVGNSMYDPVFDASFHLRGREKFN
HRWWGGQPLWITATKQGVRAGTFFWSVSIPHERRILTILQWLSLPDNERP
SVYAFYSEQPDFSGHKYGPFGPEMTNPLREIDKTVGQLMDGLKQLRLHRC
VNVIFVGDHGMEDVTCDRTEFLSNYLTNVDDITLVPGTLGRIRAKSINNS
KYDPKTIIAALTCKKPDQHFKPYMKQHLPKRLHYANNRRIEDIHLLVDRR
WHVARKPLDVYKKCFFQGDHGFDNKVNSMQTVFVGYGPTFKYRTKVPPFE
NIELYNVMCDLLGLKPAPNNGTHGSLNHLLRTNTFRPTMPDEVSRPNYPG
IMYLQSEFDLGCTCDDKVENKLEELNKRLHTKGSTKERHLLYGRPAVLYR
TSYDILYHTDFESGYSEIFLMPLWTSYTISKQAEVSSIPEHLTNCVRPDV
RVSPGFSQNCLAYKNDKQMSYGFLFPPYLSSSPEAKYDAFLVTNMVPMYP
AFKRVWAYFQRVLVKKYASERNGVNVISGPIFDYNYDGLRDTEDEIKQYV
EGSSIPVPTHYYSIITSCLDFTQPADKCDGPLSVSSFILPHRPDNDESCN
SSEDESKWVEELMKMHTARVRDIEHLTGLDFYRKTSRSYSEILTLKTYLH
TYESE

Ligand information

• Ligand ID: 6ZO
• InChI: InChI=1S/C22H21Cl2N3O5/c23-16-9-14(10-17(24)12-16)13-31-22(30)27-7-5-26(6-8-27)4-3-19(28)15-1-2-18-20(11-15)32-21(29)25-18/h1-2,9-12H,3-8,13H2,(H,25,29)
• InChIKey: JMSUDQYHPSNBSN-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.5: c1cc2c(cc1C(=O)CCN3CCN(CC3)C(=O)OCc4cc(cc(c4)Cl)Cl)OC(=O)N2
  CACTVS 3.385: Clc1cc(Cl)cc(COC(=O)N2CCN(CC2)CCC(=O)c3ccc4NC(=O)Oc4c3)c1
  ACDLabs 12.01: C(c1cc(cc(c1)Cl)Cl)OC(N4CCN(CCC(c3cc2OC(=O)Nc2cc3)=O)CC4)=O
• Formula: C22 H21 Cl2 N3 O5
• Name: (3,5-dichlorophenyl)methyl 4-[3-oxo-3-(2-oxo-2,3-dihydro-1,3-benzoxazol-6-yl)propyl]piperazine-1-carboxylate
• ChEMBL: CHEMBL3186509
• ZINC: ZINC000059263715
• PDB chain: 5s9l Chain A Residue 906

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5s9l Crystal Structure of a rat Autotaxin complex
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): D171 T209 F210 L213 L243 F273 F274 W275 Y306 D311 H315 H474
• Binding residue (residue number reindexed from 1): D121 T159 F160 L163 L193 F223 F224 W225 Y256 D261 H265 H420
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 3.1.4.39: alkylglycerophosphoethanolamine phosphodiesterase.

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0004528 phosphodiesterase I activity
• GO:0004622 lysophospholipase activity
• GO:0004630 phospholipase D activity
• GO:0005044 scavenger receptor activity
• GO:0005509 calcium ion binding
• GO:0008270 zinc ion binding
• GO:0016787 hydrolase activity
• GO:0016788 hydrolase activity, acting on ester bonds
• GO:0030247 polysaccharide binding
• GO:0046872 metal ion binding
• GO:0047391 alkylglycerophosphoethanolamine phosphodiesterase activity

Biological Process

• GO:0001953 negative regulation of cell-matrix adhesion
• GO:0006644 phospholipid metabolic process
• GO:0006935 chemotaxis
• GO:0006955 immune response
• GO:0008284 positive regulation of cell population proliferation
• GO:0009395 phospholipid catabolic process
• GO:0010634 positive regulation of epithelial cell migration
• GO:0016042 lipid catabolic process
• GO:0016192 vesicle-mediated transport
• GO:0030149 sphingolipid catabolic process
• GO:0030334 regulation of cell migration
• GO:0034638 phosphatidylcholine catabolic process
• GO:0044849 estrous cycle
• GO:0048714 positive regulation of oligodendrocyte differentiation
• GO:0050731 positive regulation of peptidyl-tyrosine phosphorylation
• GO:0051894 positive regulation of focal adhesion assembly
• GO:0060326 cell chemotaxis
• GO:0071276 cellular response to cadmium ion
• GO:0071392 cellular response to estradiol stimulus
• GO:1900026 positive regulation of substrate adhesion-dependent cell spreading
• GO:1903165 response to polycyclic arene
• GO:2000394 positive regulation of lamellipodium morphogenesis

Cellular Component

• GO:0005576 extracellular region
• GO:0005615 extracellular space

External links

• PDB: RCSB:5s9l, PDBe:5s9l, PDBj:5s9l
• PDBsum: 5s9l
• UniProt: Q64610|ENPP2_RAT Autotaxin (Gene Name=Enpp2)