Structure of PDB 1zs6 Chain B Binding Site BS01

Receptor Information
>1zs6 Chain B (length=152) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TGAHERTFLAVKPDGVQRRLVGEIVRRFERKGFKLVALKLVQASEELLRE
HYAELRERPFYGRLVKYMASGPVVAMVWQGLDVVRTSRALIGATNPADAP
PGTIRGDFCIEVGKNLIHGSDSVESARREIALWFRADELLCWEDSAGHWL
YE
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 chain1zs6 Chain B Residue 202 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1zs6 Structure of human nucleoside-diphosphate kinase 3
Resolution2.3 Å
Binding residue
(original residue number in PDB)		K29 L72 F77 L81 R105 T111 V129 N132
Binding residue
(residue number reindexed from 1)		K12 L55 F60 L64 R88 T94 V112 N115
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) K29 Y69 N132 H135 E146
Catalytic site (residue number reindexed from 1) K12 Y52 N115 H118 E129
Enzyme Commision number 2.7.4.6: nucleoside-diphosphate kinase.
Gene Ontology
Molecular Function
GO:0004550 nucleoside diphosphate kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0046872 metal ion binding
Biological Process
GO:0006183 GTP biosynthetic process
GO:0006228 UTP biosynthetic process
GO:0006241 CTP biosynthetic process
GO:0006281 DNA repair
GO:0006915 apoptotic process
GO:0008053 mitochondrial fusion
GO:0009117 nucleotide metabolic process
GO:0009142 nucleoside triphosphate biosynthetic process
GO:0016310 phosphorylation
Cellular Component
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005741 mitochondrial outer membrane
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0036064 ciliary basal body
GO:0042995 cell projection

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1zs6, PDBe:1zs6, PDBj:1zs6
PDBsum1zs6
PubMed
UniProtQ13232|NDK3_HUMAN Nucleoside diphosphate kinase 3 (Gene Name=NME3)

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