Structure of PDB 5dlv Chain A Binding Site BS01

Receptor Information

>5dlv Chain A (length=781) Species: 10116 (Rattus norvegicus)

GSCKGRCFELQEVGPPDCRCDNLCKSYSSCCHDFDELCLKTARGWECTKD
RCGEVRNEENACHCSEDCLSRGDCCTNYQVVCKGESHWVDDDCEEIKVPE
CPAGFVRPPLIIFSVDGFRASYMKKGSKVMPNIEKLRSCGTHAPYMRPVY
PTKTFPNLYTLATGLYPESHGIVGNSMYDPVFDASFHLRGREKFNHRWWG
GQPLWITATKQGVRAGTFFWSVSIPHERRILTILQWLSLPDNERPSVYAF
YSEQPDFSGHKYGPFGPEMTNPLREIDKTVGQLMDGLKQLRLHRCVNVIF
VGDHGMEDVTCDRTEFLSNYLTNVDDITLVPGTLGRIRAKSINNSKYDPK
TIIAALTCKKPDQHFKPYMKQHLPKRLHYANNRRIEDIHLLVDRRWHVAR
KPLDVCFFQGDHGFDNKVNSMQTVFVGYGPTFKYRTKVPPFENIELYNVM
CDLLGLKPAPNNGTHGSLNHLLRTNTFRPTMPDEVSRPNYPGIMYLQSEF
DLGCTCDHTKGSTKERHLLYGRPAVLYRTSYDILYHTDFESGYSEIFLMP
LWTSYTISKQAEVSSIPEHLTNCVRPDVRVSPGFSQNCLAYKNDKQMSYG
FLFPPYLSSSPEAKYDAFLVTNMVPMYPAFKRVWAYFQRVLVKKYASERN
GVNVISGPIFDYNYDGLRDTEDEIKQYVEGSSIPVPTHYYSIITSCLDFT
QPADKCDGPLSVSSFILPHRPDNDESCASSEDESKWVEELMKMHTARVRD
IEHLTGLDFYRKTSRSYSEILTLKTYLHTYE

Ligand information

• Ligand ID: MAN
• InChI: InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5+,6+/m1/s1
• InChIKey: WQZGKKKJIJFFOK-PQMKYFCFSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C(C1C(C(C(C(O1)O)O)O)O)O
  CACTVS 3.341: OC[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
  CACTVS 3.341: OC[C@H]1O[C@H](O)[C@@H](O)[C@@H](O)[C@@H]1O
  OpenEye OEToolkits 1.5.0: C([C@@H]1[C@H]([C@@H]([C@@H]([C@H](O1)O)O)O)O)O
  ACDLabs 10.04: OC1C(O)C(OC(O)C1O)CO
• Formula: C6 H12 O6
• Name: alpha-D-mannopyranose;
  alpha-D-mannose;
  D-mannose;
  mannose
• ChEMBL: CHEMBL365590
• ZINC: ZINC000003860903
• PDB chain: 5dlv Chain C Residue 6

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5dlv Steroid binding to Autotaxin links bile salts and lysophosphatidic acid signalling.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): E223 S224 N436
• Binding residue (residue number reindexed from 1): E168 S169 N381
• 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:5dlv, PDBe:5dlv, PDBj:5dlv
• PDBsum: 5dlv
• PubMed: 27075612
• UniProt: Q64610|ENPP2_RAT Autotaxin (Gene Name=Enpp2)