Structure of PDB 8u0m Chain B Binding Site BS01

Receptor Information
>8u0m Chain B (length=247) Species: 582419 (Thermococcus paralvinellae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SHMIIIKLGGSVISDSFHRHIVEQIAEEIAQFYPDESFILVHGGGSFGHP
NAREYKITEGLVGDVDRKRIGFSKTHQAMLKLNDLIIQTFLEKGLPAYSV
SSSSIFLLENKEVVYGELEILRKLLELKFIPVLFGDTAIALDKGIDILSG
DQIVSYLAKMLKPSKVIFLMDVDGIYDRNPKERDAKLIEELNVEEIRHLL
ESIGNKLREALKIAKHSEVYFINGKVKENLGKAIRGEKVGTRLRKLE
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 chain8u0m Chain B Residue 301 [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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PDB8u0m Ternary complexes of isopentenyl phosphate kinase from Thermococcus paralvinellae reveal molecular determinants of non-natural substrate specificity.
Resolution2.54 Å
Binding residue
(original residue number in PDB)		K5 Y179 R181 P183 I217 K220
Binding residue
(residue number reindexed from 1)		K7 Y176 R178 P180 I203 K206
Annotation score5
Enzymatic activity
Enzyme Commision number 2.7.4.26: isopentenyl phosphate kinase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0102043 isopentenyl phosphate kinase activity
Biological Process
GO:0008299 isoprenoid biosynthetic process
GO:0016310 phosphorylation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8u0m, PDBe:8u0m, PDBj:8u0m
PDBsum8u0m
PubMed38333996
UniProtW0I5G2

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