Structure of PDB 7y4a Chain A Binding Site BS02

Receptor Information
>7y4a Chain A (length=181) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MQSIKCVVVGDGAVGKTCLLICYTTNAFPKEYIPTVFDNYSAQSAVDGRT
VNLNLWDTAGQEEYDRLRTLSYPQTNVFVICFSIASPPSYENVRHKWHPE
VCHHCPDVPILLVGTKKDLRAQPDTLRRLKEQGQAPITPQQGQALAKQIH
AVRYLECSALQQDGVKEVFAEAVRAVLNPTP
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 chain7y4a Chain A Residue 203 [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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PDB7y4a Targeting Ras-binding domain of ELMO1 by computational nanobody design.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		A13 G15 K16 T17 C18 F28 Y32 K116 D118 L119 S158 L160
Binding residue
(residue number reindexed from 1)		A13 G15 K16 T17 C18 F28 Y32 K116 D118 L119 S158 L160
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0019901 protein kinase binding
Biological Process
GO:0007015 actin filament organization
GO:0007163 establishment or maintenance of cell polarity
GO:0007264 small GTPase-mediated signal transduction
GO:0007266 Rho protein signal transduction
GO:0008284 positive regulation of cell population proliferation
GO:0008360 regulation of cell shape
GO:0016601 Rac protein signal transduction
GO:0030036 actin cytoskeleton organization
GO:0030865 cortical cytoskeleton organization
GO:0032956 regulation of actin cytoskeleton organization
GO:0045893 positive regulation of DNA-templated transcription
GO:0060326 cell chemotaxis
GO:0090630 activation of GTPase activity
GO:0150052 regulation of postsynapse assembly
GO:1900027 regulation of ruffle assembly
GO:1903078 positive regulation of protein localization to plasma membrane
Cellular Component
GO:0005789 endoplasmic reticulum membrane
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005886 plasma membrane
GO:0005925 focal adhesion
GO:0030667 secretory granule membrane
GO:0031410 cytoplasmic vesicle
GO:0042995 cell projection
GO:0070062 extracellular exosome
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:7y4a, PDBe:7y4a, PDBj:7y4a
PDBsum7y4a
PubMed36932164
UniProtP84095|RHOG_HUMAN Rho-related GTP-binding protein RhoG (Gene Name=RHOG)

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