Structure of PDB 3nkr Chain A Binding Site BS05

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 1006 [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)		I167 S169 T209 F210 L213 N230 W260 F273 Y306 D311 H474
Binding residue
(residue number reindexed from 1)		I117 S119 T159 F160 L163 N180 W210 F223 Y256 D261 H415
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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