Structure of PDB 5m0m Chain A Binding Site BS06

Receptor Information
>5m0m Chain A (length=774) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SGSCKGRCFELQEVGPPDCRCDNLCKSYSSCCHDFDELCLKTARGWECTK
DRCGEVRNEENACHCSEDCLSRGDCCTNYQVVCKGESHWVDDDCEEIKVP
ECPAGFVRPPLIIFSVDGFRASYMKKGSKVMPNIEKLRSCGTHAPYMRPV
YPTKTFPNLYTLATGLYPESHGIVGNSMYDPVFDASFHLRGREKFNHRWW
GGQPLWITATKQGVRAGTFFWSVSIPHERRILTILQWLSLPDNERPSVYA
FYSEQPDFSGHKYGPFGPEMTNPLREIDKTVGQLMDGLKQLRLHRCVNVI
FVGDHGMEDVTCDRTEFLSNYLTNVDDITLVPGTLGRIRAKSINNSKYDP
KTIIAALTCKKPDQHFKPYMKQHLPKRLHYANNRRIEDIHLLVDRRWHVA
RKPLFQGDHGFDNKVNSMQTVFVGYGPTFKYRTKVPPFENIELYNVMCDL
LGLKPAPNNGTHGSLNHLLRTNTFRPTMPDEVSRPNYPGIMYLQSEFDLG
CTCDSTKERHLLYGRPAVLYRTSYDILYHTDFESGYSEIFLMPLWTSYTI
SKQAEVSSIPEHLTNCVRPDVRVSPGFSQNCLAYKNDKQMSYGFLFPPYL
SSSPEAKYDAFLVTNMVPMYPAFKRVWAYFQRVLVKKYASERNGVNVISG
PIFDYNYDGLRDTEDEIKQYVEGSSIPVPTHYYSIITSCLDFTQPADKCD
GPLSVSSFILPHRPDNDESCASSEDESKWVEELMKMHTARVRDIEHLTGL
DFYRKTSRSYSEILTLKTYLHTYE
Ligand information
Ligand ID7CF
InChIInChI=1S/C36H52Cl2N2O5/c1-21(4-7-32(43)39-26-10-13-40(19-26)34(44)45-20-22-14-24(37)18-25(38)15-22)28-5-6-29-33-30(9-12-36(28,29)3)35(2)11-8-27(41)16-23(35)17-31(33)42/h14-15,18,21,23,26-31,33,41-42H,4-13,16-17,19-20H2,1-3H3,(H,39,43)/t21-,23+,26-,27-,28-,29+,30+,31+,33+,35+,36-/m1/s1
InChIKeyZEXNABOXYLWWLJ-WGEHOESMSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[C@H](CCC(=O)N[C@@H]1CCN(C1)C(=O)OCc2cc(Cl)cc(Cl)c2)[C@H]3CC[C@H]4[C@@H]5[C@@H](O)C[C@@H]6C[C@H](O)CC[C@]6(C)[C@H]5CC[C@]34C
OpenEye OEToolkits 2.0.6CC(CCC(=O)NC1CCN(C1)C(=O)OCc2cc(cc(c2)Cl)Cl)C3CCC4C3(CCC5C4C(CC6C5(CCC(C6)O)C)O)C
CACTVS 3.385C[CH](CCC(=O)N[CH]1CCN(C1)C(=O)OCc2cc(Cl)cc(Cl)c2)[CH]3CC[CH]4[CH]5[CH](O)C[CH]6C[CH](O)CC[C]6(C)[CH]5CC[C]34C
OpenEye OEToolkits 2.0.6C[C@H](CCC(=O)N[C@@H]1CCN(C1)C(=O)OCc2cc(cc(c2)Cl)Cl)[C@H]3CC[C@@H]4[C@@]3(CC[C@H]5[C@H]4[C@H](C[C@H]6[C@@]5(CC[C@H](C6)O)C)O)C
FormulaC36 H52 Cl2 N2 O5
Name[3,5-bis(chloranyl)phenyl]methyl (3~{R})-3-[[(4~{R})-4-[(3~{R},5~{S},7~{S},8~{R},9~{S},10~{S},13~{R},14~{S},17~{R})-10,13-dimethyl-3,7-bis(oxidanyl)-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1~{H}-cyclopenta[a]phenanthren-17-yl]pentanoyl]amino]pyrrolidine-1-carboxylate
ChEMBLCHEMBL4062929
DrugBank
ZINC
PDB chain5m0m Chain A Residue 925 [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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PDB5m0m Rational Design of Autotaxin Inhibitors by Structural Evolution of Endogenous Modulators.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		Y82 S169 F210 L213 K248 F249 W254 W260 F273 F274 W275 Y306
Binding residue
(residue number reindexed from 1)		Y28 S115 F156 L159 K194 F195 W200 W206 F219 F220 W221 Y252
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.22,Ki=6nM
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5m0m, PDBe:5m0m, PDBj:5m0m
PDBsum5m0m
PubMed28165241
UniProtQ64610|ENPP2_RAT Autotaxin (Gene Name=Enpp2)

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