Structure of PDB 5lpn Chain C Binding Site BS02

Receptor Information
>5lpn Chain C (length=167) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YDLLFKLLLIGDSGVGKTCVLFRFSDDAFNTTFISTIGIDFKIKTVELQG
KKIKLQIWDTAGQERFHTITTSYYRGAMGIMLVYDITNGKSFENISKWLR
NIDEHANEDVERMLLGNKCDMDDKRVVPKGKGEQIAREHGIETSAKANIN
IEKAFLTLAEDILRKTP
Ligand information
Ligand IDGNP
InChIInChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
InChIKeyUQABYHGXWYXDTK-UUOKFMHZSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
FormulaC10 H17 N6 O13 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
ChEMBLCHEMBL1233085
DrugBankDB02082
ZINCZINC000037868676
PDB chain5lpn Chain C Residue 202 [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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PDB5lpn bMERB domains are bivalent Rab8 family effectors evolved by gene duplication.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		S18 G19 V20 G21 K22 T23 C24 F34 T36 F38 T41 G67 N122 K123 D125 M126 A153 K154
Binding residue
(residue number reindexed from 1)		S13 G14 V15 G16 K17 T18 C19 F29 T31 F33 T36 G62 N117 K118 D120 M121 A145 K146
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) Q68
Catalytic site (residue number reindexed from 1) Q63
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:5lpn, PDBe:5lpn, PDBj:5lpn
PDBsum5lpn
PubMed27552051
UniProtP61026|RAB10_HUMAN Ras-related protein Rab-10 (Gene Name=RAB10)

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