Structure of PDB 2p5s Chain B Binding Site BS01

Receptor Information
>2p5s Chain B (length=161) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AYKIVLAGDAAVGKSSFLMRLCKNEFRGVDFQMKTLIVDGERTVLQLWDT
AGQERFRSIAKSYFRKADGVLLLYDVTCEKSFLNIREWVDMIEDAAVPIM
LVGNKADIRDTAATEGQKCVPGHFGEKLAMTYGALFCETSAKDGSNIVEA
VLHLAREVKKR
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 chain2p5s Chain B Residue 1001 [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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PDB2p5s RAB domain of human RASEF in complex with GDP
Resolution2.15 Å
Binding residue
(original residue number in PDB)		A551 G553 K554 S555 S556 F566 K655 D657 I658 S690 A691 K692
Binding residue
(residue number reindexed from 1)		A11 G13 K14 S15 S16 F26 K105 D107 I108 S140 A141 K142
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) L558
Catalytic site (residue number reindexed from 1) L18
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005525 GTP binding

View graph for
Molecular Function
External links
PDB RCSB:2p5s, PDBe:2p5s, PDBj:2p5s
PDBsum2p5s
PubMed
UniProtQ8IZ41|RASEF_HUMAN Ras and EF-hand domain-containing protein (Gene Name=RASEF)

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