Structure of PDB 5z2m Chain A Binding Site BS02

Receptor Information
>5z2m Chain A (length=172) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKVLLKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVMVDD
RLVTMQIWDTAGLERFQSLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRD
EFLIQASPRDPENFPFVVLGNKIDLENRQVATKRAQAWCYSKNNIPYFET
SAKEAINVEQAFQTIARNALKQ
Ligand information
Ligand IDGTP
InChIInChI=1S/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyXKMLYUALXHKNFT-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
FormulaC10 H16 N5 O14 P3
NameGUANOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL1233147
DrugBankDB04137
ZINCZINC000060094177
PDB chain5z2m Chain A 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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PDB5z2m A non-canonical GTPase interaction enables ORP1L-Rab7-RILP complex formation and late endosome positioning.
Resolution2.142 Å
Binding residue
(original residue number in PDB)		S17 G18 V19 G20 K21 T22 S23 F33 S34 N35 Y37 T40 G66 N125 K126 D128 L129 S155 A156 K157
Binding residue
(residue number reindexed from 1)		S13 G14 V15 G16 K17 T18 S19 F29 S30 N31 Y33 T36 G62 N121 K122 D124 L125 S151 A152 K153
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:5z2m, PDBe:5z2m, PDBj:5z2m
PDBsum5z2m
PubMed30012887
UniProtP51150|RAB7A_MOUSE Ras-related protein Rab-7a (Gene Name=Rab7a)

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