Structure of PDB 1vc9 Chain B Binding Site BS01

Receptor Information
>1vc9 Chain B (length=126) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MELGAGGVVFNAKREVLLLRDRMGFWVFPKGHPEPGESLEEAAVREVWEQ
TGVRAEVLLPLYPTRYVNPKGVEREVHWFLMRGEGAPRLEEGMTGAGWFS
PEEARALLAFPEDLGLLEVALERLPL
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=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[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[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
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain1vc9 Chain B Residue 1002 [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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PDB1vc9 Crystal Structure of Nudix Protein Ndx1 from Thermus thermophilus HB8 in binary complex with diadenosine hexaphosphate
Resolution2.3 Å
Binding residue
(original residue number in PDB)		D21 M23 F25 K30 H32 Y66 N68 P69 R74 F110 E112
Binding residue
(residue number reindexed from 1)		D21 M23 F25 K30 H32 Y66 N68 P69 R74 F110 E112
Annotation score5
Binding affinityMOAD: Kd=13uM
Enzymatic activity
Enzyme Commision number 3.6.1.61: diadenosine hexaphosphate hydrolase (ATP-forming).
Gene Ontology
Molecular Function
GO:0004081 bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
GO:0046872 metal ion binding
Biological Process
GO:0006167 AMP biosynthetic process
GO:0006754 ATP biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1vc9, PDBe:1vc9, PDBj:1vc9
PDBsum1vc9
PubMed
UniProtQ75UV1|NDX1_THETH Diadenosine hexaphosphate hydrolase (Gene Name=ndx1)

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