Structure of PDB 3ngu Chain B Binding Site BS01

Receptor Information
>3ngu Chain B (length=151) Species: 5664 (Leishmania major) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MSSERTFIAVKPDGVQRGLVGEIIARFERKGYKLVALKILQPTTEQAQGH
YKDLCSKPFFPALVKYFSSGPIVCMVWEGKNVVKSGRVLLGATNPADSQP
GTIRGDFAVDVGRNVCHGSDSVESAEREIAFWFKADEIASWTSHSVSQIY
E
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 chain3ngu Chain B Residue 152 [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]
PDB3ngu Molecular adaptability of nucleoside diphosphate kinase b from trypanosomatid parasites: stability, oligomerization and structural determinants of nucleotide binding.
Resolution2.29 Å
Binding residue
(original residue number in PDB)		K11 F59 L63 R87 T93 V111 N114
Binding residue
(residue number reindexed from 1)		K11 F59 L63 R87 T93 V111 N114
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) K11 Y51 N114 H117 E128
Catalytic site (residue number reindexed from 1) K11 Y51 N114 H117 E128
Enzyme Commision number 2.7.4.6: nucleoside-diphosphate kinase.
Gene Ontology
Molecular Function
GO:0004550 nucleoside diphosphate kinase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
Biological Process
GO:0006183 GTP biosynthetic process
GO:0006228 UTP biosynthetic process
GO:0006241 CTP biosynthetic process
GO:0009142 nucleoside triphosphate biosynthetic process
GO:0016310 phosphorylation
Cellular Component
GO:0005737 cytoplasm
GO:0097014 ciliary plasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3ngu, PDBe:3ngu, PDBj:3ngu
PDBsum3ngu
PubMed21528129
UniProtQ9U1E1

[Back to BioLiP]