Structure of PDB 3wax Chain A Binding Site BS05

Receptor Information
>3wax Chain A (length=789) 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
WHVARKPCFFQGDHGFDNKVNSMQTVFVGYGPTFKYRTKVPPFENIELYN
VMCDLLGLKPAPNNGTHGSLNHLLRTNTFRPTLPEEVSRPNYPGIMYLQS
DFDLGCTCDDLEELNHTKGSTEERHLLYGRPAVLYRTSYDILYHTDFESG
YSEIFLMPLWTSYTISKQAEVSSIPEHLTNCVRPDVRVSPGFSQNCLAYK
NDKQMSYGFLFPPYLSSSPEAKYDAFLVTNMVPMYPAFKRVWTYFQRVLV
KKYASERNGVNVISGPIFDYNYNGLRDIEDEIKQYVEGSSIPVPTHYYSI
ITSCLDFTQPADKCDGPLSVSSFILPHRPDNDESCNSSEDESKWVEELMK
MHTARVRDIEHLTGLDFYRKTSRSYSEILTLKTYLHTYE
Ligand information
Ligand IDDWX
InChIInChI=1S/C21H20BCl2N3O3S/c23-17-5-4-14(11-18(17)24)12-19-20(28)25-21(31-19)27-8-6-26(7-9-27)13-15-2-1-3-16(10-15)22(29)30/h1-5,10-12,29-30H,6-9,13H2/b19-12-
InChIKeyZCKGWOBAJNWRNC-UNOMPAQXSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6B(c1cccc(c1)CN2CCN(CC2)C3=NC(=O)/C(=C/c4ccc(c(c4)Cl)Cl)/S3)(O)O
OpenEye OEToolkits 1.7.6B(c1cccc(c1)CN2CCN(CC2)C3=NC(=O)C(=Cc4ccc(c(c4)Cl)Cl)S3)(O)O
ACDLabs 12.01Clc1ccc(cc1Cl)\C=C2/SC(=NC2=O)N4CCN(Cc3cccc(B(O)O)c3)CC4
CACTVS 3.370OB(O)c1cccc(CN2CCN(CC2)C3=NC(=O)C(/S3)=C/c4ccc(Cl)c(Cl)c4)c1
CACTVS 3.370OB(O)c1cccc(CN2CCN(CC2)C3=NC(=O)C(S3)=Cc4ccc(Cl)c(Cl)c4)c1
FormulaC21 H20 B Cl2 N3 O3 S
Name[3-({4-[(5Z)-5-(3,4-dichlorobenzylidene)-4-oxo-4,5-dihydro-1,3-thiazol-2-yl]piperazin-1-yl}methyl)phenyl]boronic acid
ChEMBLCHEMBL4540122
DrugBank
ZINCZINC000169920296
PDB chain3wax Chain A Residue 936 [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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PDB3wax Screening and X-ray Crystal Structure-based Optimization of Autotaxin (ENPP2) Inhibitors, Using a Newly Developed Fluorescence Probe
Resolution1.899 Å
Binding residue
(original residue number in PDB)		D171 T209 L213 N230 L243 F273 F274 W275 Y306 D311 H474
Binding residue
(residue number reindexed from 1)		D121 T159 L163 N180 L193 F223 F224 W225 Y256 D261 H414
Annotation score1
Binding affinityMOAD: ic50=13nM
PDBbind-CN: -logKd/Ki=7.89,IC50=13nM
BindingDB: IC50=13nM
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3wax, PDBe:3wax, PDBj:3wax
PDBsum3wax
PubMed23688339
UniProtQ9R1E6|ENPP2_MOUSE Autotaxin (Gene Name=Enpp2)

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