Structure of PDB 2o52 Chain B Binding Site BS01

Receptor Information
>2o52 Chain B (length=158) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SDFLFKFLVIGSAGTGKSCLLHQFIEVEFGSRVVNVGGKTVKLQIWDTAG
QERFRSVTRSYYRGAAGALLVYDITSRETYNSLAAWLTDARTLASPNIVV
ILCGNKKDLDPEREVTFLEASRFAQENELMFLETSALTGENVEEAFLKCA
RTILNKID
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 chain2o52 Chain B Residue 601 [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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PDB2o52 Crystal structure of human RAB4B in complex with GDP
Resolution2.2 Å
Binding residue
(original residue number in PDB)		G18 T19 G20 K21 S22 C23 N121 K122 D124 L125 S151 A152 L153
Binding residue
(residue number reindexed from 1)		G14 T15 G16 K17 S18 C19 N105 K106 D108 L109 S135 A136 L137
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
Biological Process
GO:0032482 Rab protein signal transduction

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2o52, PDBe:2o52, PDBj:2o52
PDBsum2o52
PubMed
UniProtP61018|RAB4B_HUMAN Ras-related protein Rab-4B (Gene Name=RAB4B)

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