Structure of PDB 1y63 Chain A Binding Site BS06

Receptor Information
>1y63 Chain A (length=168) Species: 347515 (Leishmania major strain Friedlin) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EQPKGINILITGTPGTGKTSMAEMIAAELDGFQHLEVGKLVKENHFYTET
HIIEEKDEDRLLDFMEPIMVSRGNHVVDYHSSELFPERWFHMVVVLHTST
EVLFERLTKRQYSEAKRAENMEAEIQCICEEEARDAYEDDIVLVRENDTL
EQMAATVEEIRERVEVLK
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain1y63 Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB1y63 Crystal structural analysis of a probable kinase from Leishmania major Friedlin
Resolution1.7 Å
Binding residue
(original residue number in PDB)
G20 G22 K23 T24 S25 R117 N158 D159 T160 M164
Binding residue
(residue number reindexed from 1)
G15 G17 K18 T19 S20 R106 N147 D148 T149 M153
Annotation score5
Enzymatic activity
Enzyme Commision number 2.7.4.3: adenylate kinase.
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0004017 adenylate kinase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0016887 ATP hydrolysis activity
GO:0042134 rRNA primary transcript binding
GO:0046872 metal ion binding
Biological Process
GO:0006364 rRNA processing
GO:0006979 response to oxidative stress
GO:0009267 cellular response to starvation
GO:0016310 phosphorylation
GO:0030490 maturation of SSU-rRNA
GO:0042254 ribosome biogenesis
GO:0042274 ribosomal small subunit biogenesis
GO:0046940 nucleoside monophosphate phosphorylation
Cellular Component
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005929 cilium
GO:0010494 cytoplasmic stress granule
GO:0031981 nuclear lumen

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:1y63, PDBe:1y63, PDBj:1y63
PDBsum1y63
PubMed
UniProtQ4Q7A6

[Back to BioLiP]