Structure of PDB 3nkr Chain A Binding Site BS06

Receptor Information
>3nkr Chain A (length=779) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
WTNTSGSCKGRCFELQEVGPPDCRCDNLCKSYSSCCHDFDELCLKTARGW
ECTKDRCGEVRNEENACHCSEDCLSRGDCCTNYQVVCKGESHWVDDDCEE
IRVPECPAGFVRPPLIIFSVDGFRASYMKKGSKVMPNIEKLRSCGTHAPY
MRPVYPTKTFPNLYTLATGLYPESHGIVGNSMYDPVFDATFHLRGREKFN
HRWWGGQPLWITATKQGVRAGTFFWSVSIPHERRILTILQWLSLPDNERP
SVYAFYSEQPDFSGHKYGPFGPEMTNPLREIDKTVGQLMDGLKQLKLHRC
VNVIFVGDHGMEDVTCDRTEFLSNYLTNVDDITLVPGTLGRIRPKIPNNL
KYDPKAIIANLTCKKPDQHFKPYMKQHLPKRLHYANNRRIEDLHLLVERR
WHVARKPLCFFQGDHGFDNKVNSMQTVFVGYGPTFKYRTKVPPFENIELY
NVMCDLLGLKPAPNNGTHGSLNHLLRTNTFRPTLPEEVSRPNYPGIMYLQ
SDFDLGCTCDTEERHLLYGRPAVLYRTSYDILYHTDFESGYSEIFLMPLW
TSYTISKQAEVSSIPEHLTNCVRPDVRVSPGFSQNCLAYKNDKQMSYGFL
FPPYLSSSPEAKYDAFLVTNMVPMYPAFKRVWTYFQRVLVKKYASERNGV
NVISGPIFDYNYNGLRDIEDEIKQYVEGSSIPVPTHYYSIITSCLDFTQP
ADKCDGPLSVSSFILPHRPDNDESCNSSEDESKWVEELMKMHTARVRDIE
HLTGLDFYRKTSRSYSEILTLKTYLHTYE
Ligand information
Ligand IDNKR
InChIInChI=1S/C25H39O7P/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-25(27)31-22-24(26)23-32-33(28,29)30/h3-4,6-7,9-10,12-13,15-16,18-19,24,26H,2,5,8,11,14,17,20-23H2,1H3,(H2,28,29,30)/b4-3-,7-6-,10-9-,13-12+,16-15+,19-18-/t24-/m1/s1
InChIKeyUWHSPTWBPTXYMF-WTFJZYGXSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CCC=CCC=CCC=CCC=CCC=CCC=CCCC(=O)OC[CH](O)CO[P](O)(O)=O
ACDLabs 12.01O=P(OCC(O)COC(=O)CC\C=C/C/C=C/C/C=C/C\C=C/C\C=C/C\C=C/CC)(O)O
OpenEye OEToolkits 1.7.0CC/C=C\C/C=C\C/C=C\C/C=C/C/C=C/C/C=C\CCC(=O)OC[C@H](COP(=O)(O)O)O
CACTVS 3.370CC/C=C\C\C=C/C/C=C\C\C=C\C\C=C\C\C=C/CCC(=O)OC[C@@H](O)CO[P](O)(O)=O
OpenEye OEToolkits 1.7.0CCC=CCC=CCC=CCC=CCC=CCC=CCCC(=O)OCC(COP(=O)(O)O)O
FormulaC25 H39 O7 P
Name(2R)-2-hydroxy-3-(phosphonooxy)propyl (4Z,7E,10E,13Z,16Z,19Z)-docosa-4,7,10,13,16,19-hexaenoate;
22:6 LPA;
1-docosahexaenoyl-lysophosphatidic acid
ChEMBL
DrugBank
ZINCZINC000064744312
PDB chain3nkr Chain A Residue 1007 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3nkr Crystal structure of autotaxin and insight into GPCR activation by lipid mediators
Resolution1.704 Å
Binding residue
(original residue number in PDB)		F249 H251 W254 G255
Binding residue
(residue number reindexed from 1)		F199 H201 W204 G205
Annotation score3
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:0004551 dinucleotide phosphatase 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:0006644 phospholipid metabolic process
GO:0006935 chemotaxis
GO:0006955 immune response
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:0050731 positive regulation of peptidyl-tyrosine phosphorylation
GO:2000394 positive regulation of lamellipodium morphogenesis
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005886 plasma membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3nkr, PDBe:3nkr, PDBj:3nkr
PDBsum3nkr
PubMed21240269
UniProtQ9R1E6|ENPP2_MOUSE Autotaxin (Gene Name=Enpp2)

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