Structure of PDB 3lvr Chain E Binding Site BS03

Receptor Information
>3lvr Chain E (length=419) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DLTKLLIAEVKSRPGNSQCCDCGAADPTWLSTNLGVLTCIQCSGVHRELG
VRFSRMQSLTLDLLGPSELLLALNMGNTSFNEVMEAQLPSHGGPKPSAES
DMGTRRDYIMAKYVEHRFARRCTEPQRLWTAICNRDLLSVLEAFANGQDF
GQPLPGPDAQAPEELVLHLAVKVANQASLPLVDFIIQNGGHLDAKADGNT
ALHYAALYNQPDCLKLLLKGRALVGTVNEAGETALDIARKKHHKECEELL
EQAQANKEMRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTYK
NVKFNVWDVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHR
IINDREMRDAIILIFANKQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSC
ATSGDGLYEGLTWLTSNYK
Ligand information
Ligand IDGDP
InChIInChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain3lvr Chain E Residue 737 [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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PDB3lvr The structure of an Arf-ArfGAP complex reveals a Ca2+ regulatory mechanism
Resolution3.38 Å
Binding residue
(original residue number in PDB)		R469 E470 A23 G25 K26 T27 T28 T41 N122 K123 D125 L126 C155 A156 T157
Binding residue
(residue number reindexed from 1)		R47 E48 A268 G270 K271 T272 T273 T286 N367 K368 D370 L371 C400 A401 T402
Annotation score4
Enzymatic activity
Enzyme Commision number ?
3.6.5.2: small monomeric GTPase.
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0003925 G protein activity
GO:0005096 GTPase activator activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0016787 hydrolase activity
GO:0019003 GDP binding
GO:0031996 thioesterase binding
GO:0035591 signaling adaptor activity
Biological Process
GO:0001889 liver development
GO:0006886 intracellular protein transport
GO:0007155 cell adhesion
GO:0007399 nervous system development
GO:0010975 regulation of neuron projection development
GO:0010976 positive regulation of neuron projection development
GO:0015031 protein transport
GO:0016192 vesicle-mediated transport
GO:0030154 cell differentiation
GO:0030838 positive regulation of actin filament polymerization
GO:0030866 cortical actin cytoskeleton organization
GO:0032456 endocytic recycling
GO:0034394 protein localization to cell surface
GO:0035020 regulation of Rac protein signal transduction
GO:0036010 protein localization to endosome
GO:0043547 positive regulation of GTPase activity
GO:0048261 negative regulation of receptor-mediated endocytosis
GO:0048488 synaptic vesicle endocytosis
GO:0050714 positive regulation of protein secretion
GO:0051301 cell division
GO:0051489 regulation of filopodium assembly
GO:0051549 positive regulation of keratinocyte migration
GO:0060998 regulation of dendritic spine development
GO:0072659 protein localization to plasma membrane
GO:0090162 establishment of epithelial cell polarity
GO:0097178 ruffle assembly
GO:0097284 hepatocyte apoptotic process
GO:0099562 maintenance of postsynaptic density structure
GO:0120183 positive regulation of focal adhesion disassembly
GO:1902217 erythrocyte apoptotic process
GO:1903078 positive regulation of protein localization to plasma membrane
GO:1903438 positive regulation of mitotic cytokinetic process
GO:1905345 protein localization to cleavage furrow
GO:1905606 regulation of presynapse assembly
GO:1990090 cellular response to nerve growth factor stimulus
GO:2000009 negative regulation of protein localization to cell surface
GO:2000171 negative regulation of dendrite development
Cellular Component
GO:0001726 ruffle
GO:0005737 cytoplasm
GO:0005768 endosome
GO:0005769 early endosome
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0005925 focal adhesion
GO:0005938 cell cortex
GO:0016020 membrane
GO:0030139 endocytic vesicle
GO:0030496 midbody
GO:0031527 filopodium membrane
GO:0031901 early endosome membrane
GO:0032154 cleavage furrow
GO:0042995 cell projection
GO:0055037 recycling endosome
GO:0055038 recycling endosome membrane
GO:0070062 extracellular exosome
GO:0090543 Flemming body
GO:0098793 presynapse
GO:0098794 postsynapse
GO:0098978 glutamatergic synapse

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3lvr, PDBe:3lvr, PDBj:3lvr
PDBsum3lvr
PubMed20510928
UniProtP62330|ARF6_HUMAN ADP-ribosylation factor 6 (Gene Name=ARF6);
Q8TDY4|ASAP3_HUMAN Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3 (Gene Name=ASAP3)

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