Structure of PDB 4m8n Chain E Binding Site BS02

Receptor Information
>4m8n Chain E (length=168) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MREYKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDAQQ
CMLEILDTAGTEQFTAMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQI
LRVKDTDDVPMILVGNKCDLEDERVVGKEQGQNLARQWNNCAFLESSAKS
KINVNEIFYDLVRQINSG
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 chain4m8n Chain E Residue 201 [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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PDB4m8n Structural basis for activation and non-canonical catalysis of the Rap GTPase activating protein domain of plexin.
Resolution3.294 Å
Binding residue
(original residue number in PDB)		G13 G15 K16 S17 A18 F28 K31 Y32 N116 K117 D119 L120 S147 A148 K149
Binding residue
(residue number reindexed from 1)		G13 G15 K16 S17 A18 F28 K31 Y32 N116 K117 D119 L120 S147 A148 K149
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:0005515 protein binding
GO:0005525 GTP binding
GO:0016787 hydrolase activity
GO:0019003 GDP binding
GO:0044877 protein-containing complex binding
Biological Process
GO:0007165 signal transduction
GO:0007264 small GTPase-mediated signal transduction
GO:0008283 cell population proliferation
GO:0017156 calcium-ion regulated exocytosis
GO:0030033 microvillus assembly
GO:0032486 Rap protein signal transduction
GO:0033625 positive regulation of integrin activation
GO:0045955 negative regulation of calcium ion-dependent exocytosis
GO:0051649 establishment of localization in cell
GO:0061028 establishment of endothelial barrier
GO:0070374 positive regulation of ERK1 and ERK2 cascade
GO:0071320 cellular response to cAMP
GO:0099010 modification of postsynaptic structure
GO:1901888 regulation of cell junction assembly
GO:2000114 regulation of establishment of cell polarity
GO:2000301 negative regulation of synaptic vesicle exocytosis
Cellular Component
GO:0005737 cytoplasm
GO:0005811 lipid droplet
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0005911 cell-cell junction
GO:0016020 membrane
GO:0035577 azurophil granule membrane
GO:0045121 membrane raft
GO:0070062 extracellular exosome
GO:0070161 anchoring junction
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:4m8n, PDBe:4m8n, PDBj:4m8n
PDBsum4m8n
PubMed24137545
UniProtP61224|RAP1B_HUMAN Ras-related protein Rap-1b (Gene Name=RAP1B)

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