Structure of PDB 1kao Chain A Binding Site BS01

Receptor Information
>1kao Chain A (length=167) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MREYKVVVLGSGGVGKSALTVQFVTGTFIEKYDPTIEDFYRKEIEVDSSP
SVLEILDTAGTEQFASMRDLYIKNGQGFILVYSLVNQQSFQDIKPMRDQI
IRVKRYEKVPVILVGNKVDLESEREVSSSEGRALAEEWGCPFMETSAKSK
TMVDELFAEIVRQMNYA
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 chain1kao Chain A Residue 170 [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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PDB1kao Crystal structures of the small G protein Rap2A in complex with its substrate GTP, with GDP and with GTPgammaS.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		G13 G15 K16 S17 A18 F28 E30 K31 N116 K117 D119 L120 S146 A147
Binding residue
(residue number reindexed from 1)		G13 G15 K16 S17 A18 F28 E30 K31 N116 K117 D119 L120 S146 A147
Annotation score4
Enzymatic activity
Enzyme Commision number 3.6.5.2: small monomeric GTPase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
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
Biological Process
GO:0001934 positive regulation of protein phosphorylation
GO:0007165 signal transduction
GO:0008104 protein localization
GO:0030033 microvillus assembly
GO:0030036 actin cytoskeleton organization
GO:0030336 negative regulation of cell migration
GO:0031954 positive regulation of protein autophosphorylation
GO:0032486 Rap protein signal transduction
GO:0045184 establishment of protein localization
GO:0045198 establishment of epithelial cell apical/basal polarity
GO:0046328 regulation of JNK cascade
GO:0048814 regulation of dendrite morphogenesis
GO:0051963 regulation of synapse assembly
GO:0071466 cellular response to xenobiotic stimulus
GO:0072659 protein localization to plasma membrane
GO:0099072 regulation of postsynaptic membrane neurotransmitter receptor levels
Cellular Component
GO:0005768 endosome
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0030496 midbody
GO:0030659 cytoplasmic vesicle membrane
GO:0045202 synapse
GO:0055037 recycling endosome
GO:0055038 recycling endosome membrane
GO:0097060 synaptic membrane
GO:0098588 bounding membrane of organelle
GO:0098685 Schaffer collateral - CA1 synapse

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1kao, PDBe:1kao, PDBj:1kao
PDBsum1kao
PubMed9312017
UniProtP10114|RAP2A_HUMAN Ras-related protein Rap-2a (Gene Name=RAP2A)

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