Structure of PDB 1tu4 Chain A Binding Site BS01

Receptor Information
>1tu4 Chain A (length=169) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GNKICQFKLVLLGESAVGKSSLVLRFVKGQFHEFQESTIGAAFLTQTVCL
DDTTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNW
VKELQRQASPNIVIALSGNKADLANKRAVDFQEAQSYADDNSLLFMETSA
KTSMNVNEIFMAIAKKLPK
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 chain1tu4 Chain A Residue 1200 [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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PDB1tu4 Structural basis of Rab5-Rabaptin5 interaction in endocytosis
Resolution2.2 Å
Binding residue
(original residue number in PDB)		A30 G32 K33 S34 S35 N133 K134 D136 S163 A164 K165
Binding residue
(residue number reindexed from 1)		A16 G18 K19 S20 S21 N119 K120 D122 S149 A150 K151
Annotation score4
Enzymatic activity
Enzyme Commision number 3.6.5.2: small monomeric GTPase.
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005525 GTP binding

View graph for
Molecular Function
External links
PDB RCSB:1tu4, PDBe:1tu4, PDBj:1tu4
PDBsum1tu4
PubMed15378032
UniProtP20339|RAB5A_HUMAN Ras-related protein Rab-5A (Gene Name=RAB5A)

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