Structure of PDB 2ic5 Chain B Binding Site BS01

Receptor Information

>2ic5 Chain B (length=178) Species: 9606 (Homo sapiens)

MQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKP
VNLGLWDTAGQEDYDRLRPLSYPQTDVFLICFSLVSPASFENVRAKWYPE
VRHHCPHTPILLVGTKLDLRDDKDTIERLRDKKLAPITYPQGLAMAREIG
SVKYLECSALTQRGLKTVFDEAIRAVLG

Ligand information

• Ligand ID: GDP
• InChI: InChI=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
• InChIKey: QGWNDRXFNXRZMB-UUOKFMHZSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
  CACTVS 3.385: NC1=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 3.385: NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 12.01: O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
  OpenEye OEToolkits 1.7.6: c1nc2c(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
• Formula: C10 H15 N5 O11 P2
• Name: GUANOSINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL384759
• DrugBank: DB04315
• ZINC: ZINC000008215481
• PDB chain: 2ic5 Chain B Residue 502

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2ic5 Crystal structure of human RAC3 grown in the presence of Gpp(NH)p.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): A13 G15 K16 T17 C18 F28 I33 K116 D118 L119 S158 L160
• Binding residue (residue number reindexed from 1): A13 G15 K16 T17 C18 F28 I33 K116 D118 L119 S158 L160
• Annotation score: 4

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:0019901 protein kinase binding
• GO:0048306 calcium-dependent protein binding

Biological Process

• GO:0007015 actin filament organization
• GO:0007163 establishment or maintenance of cell polarity
• GO:0007264 small GTPase-mediated signal transduction
• GO:0008045 motor neuron axon guidance
• GO:0008360 regulation of cell shape
• GO:0014041 regulation of neuron maturation
• GO:0016055 Wnt signaling pathway
• GO:0016601 Rac protein signal transduction
• GO:0021894 cerebral cortex GABAergic interneuron development
• GO:0022604 regulation of cell morphogenesis
• GO:0030031 cell projection assembly
• GO:0030036 actin cytoskeleton organization
• GO:0030865 cortical cytoskeleton organization
• GO:0031175 neuron projection development
• GO:0032956 regulation of actin cytoskeleton organization
• GO:0033630 positive regulation of cell adhesion mediated by integrin
• GO:0035556 intracellular signal transduction
• GO:0043652 engulfment of apoptotic cell
• GO:0045730 respiratory burst
• GO:0048873 homeostasis of number of cells within a tissue
• GO:0050885 neuromuscular process controlling balance
• GO:0050905 neuromuscular process
• GO:0051932 synaptic transmission, GABAergic
• GO:0060326 cell chemotaxis
• GO:0098974 postsynaptic actin cytoskeleton organization
• GO:0150052 regulation of postsynapse assembly
• GO:1900026 positive regulation of substrate adhesion-dependent cell spreading
• GO:1902622 regulation of neutrophil migration

Cellular Component

• GO:0005737 cytoplasm
• GO:0005789 endoplasmic reticulum membrane
• GO:0005829 cytosol
• GO:0005856 cytoskeleton
• GO:0005886 plasma membrane
• GO:0012505 endomembrane system
• GO:0030027 lamellipodium
• GO:0030426 growth cone
• GO:0031410 cytoplasmic vesicle
• GO:0031941 filamentous actin
• GO:0042995 cell projection
• GO:0043005 neuron projection
• GO:0043020 NADPH oxidase complex
• GO:0043025 neuronal cell body
• GO:0048471 perinuclear region of cytoplasm
• GO:0070062 extracellular exosome
• GO:0071944 cell periphery
• GO:0098794 postsynapse
• GO:0098978 glutamatergic synapse

External links

• PDB: RCSB:2ic5, PDBe:2ic5, PDBj:2ic5
• PDBsum: 2ic5
• UniProt: P60763|RAC3_HUMAN Ras-related C3 botulinum toxin substrate 3 (Gene Name=RAC3)