Structure of PDB 6dbz Chain B Binding Site BS01

Receptor Information
>6dbz Chain B (length=138) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AIPRVAVVVFILNGNSILLGRRRSSIGNSTFALPGGHLEFGESFEECAAR
EVMEETGLKIEKMKLLTVTNNVFKEAPTPSHYVSVSIRAVLVDPSQEPKN
MEPEKCEGWDWYDWENLPKPLFWPLEKLFGSGFNPFTH
Ligand information
Ligand IDIPR
InChIInChI=1S/C5H14O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h5H,3-4H2,1-2H3,(H,9,10)(H2,6,7,8)
InChIKeyIPFXNYPSBSIFOB-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C)CCOP(=O)(O)OP(=O)(O)O
CACTVS 3.341CC(C)CCO[P@](O)(=O)O[P](O)(O)=O
CACTVS 3.341CC(C)CCO[P](O)(=O)O[P](O)(O)=O
ACDLabs 10.04O=P(OP(=O)(O)O)(OCCC(C)C)O
OpenEye OEToolkits 1.5.0CC(C)CCO[P@@](=O)(O)OP(=O)(O)O
FormulaC5 H14 O7 P2
NameISOPENTYL PYROPHOSPHATE
ChEMBL
DrugBankDB02508
ZINCZINC000002579357
PDB chain6dbz Chain B Residue 201 [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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PDB6dbz Contribution of isopentenyl phosphate to plant terpenoid metabolism.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		R27 G40 G41 H42 K110 F127
Binding residue
(residue number reindexed from 1)		R22 G35 G36 H37 K105 F122
Annotation score1
Enzymatic activity
Enzyme Commision number 3.6.1.22: NAD(+) diphosphatase.
3.6.1.55: 8-oxo-dGTP diphosphatase.
3.6.1.67: dihydroneopterin triphosphate diphosphatase.
Gene Ontology
Molecular Function
GO:0000210 NAD+ diphosphatase activity
GO:0008413 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity
GO:0016787 hydrolase activity
GO:0019177 dihydroneopterin triphosphate pyrophosphohydrolase activity
GO:0035529 NADH pyrophosphatase activity
GO:0035539 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity
GO:0046872 metal ion binding
Biological Process
GO:0006974 DNA damage response
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:6dbz, PDBe:6dbz, PDBj:6dbz
PDBsum6dbz
PubMed30127411
UniProtQ9CA40|NUDT1_ARATH Nudix hydrolase 1 (Gene Name=NUDT1)

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