Structure of PDB 8u0m Chain A Binding Site BS01

Receptor Information
>8u0m Chain A (length=247) Species: 582419 (Thermococcus paralvinellae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMIIIKLGGSVISDSFHRHIVEQIAEEIAQFYPDESFILVHGGGSFGHPN
AREYKITEGLVGDVDRKRIGFSKTHQAMLKLNDLIIQTFLEKGLPAYSVS
SSSIFLLENKEVVYGELEILRKLLELKFIPVLFGDTAIALDKGIDILSGD
QIVSYLAKMLKPSKVIFLMDVDGIYDRNPKERDAKLIEELNVEEIRHLLE
SGIGNKLREALKIAKHSEVYFINGKVKENLGKAIRGEKVGTRLRKLE
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 chain8u0m Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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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)		G8 V175 Y179 R181 P183 G216 I217 K220
Binding residue
(residue number reindexed from 1)		G9 V171 Y175 R177 P179 G202 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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