Structure of PDB 6ypf Chain A Binding Site BS01

Receptor Information
>6ypf Chain A (length=129) Species: 128735 (Rosa hybrid cultivar) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSIKVAVVVCLLRGQNVLLGRRRLGDSTFSLPSGHLEFGESFEECAAREL
KEETDLDIGKIELLTVTNNLFSQYVAVFMRAVLADPRQEPQNIEPEFCDG
WGWYEWDNLPKPLFWPLDNVVQDGFNPFP
Ligand information
Ligand IDGPP
InChIInChI=1S/C10H20O7P2/c1-9(2)5-4-6-10(3)7-8-16-19(14,15)17-18(11,12)13/h5,7H,4,6,8H2,1-3H3,(H,14,15)(H2,11,12,13)/b10-7+
InChIKeyGVVPGTZRZFNKDS-JXMROGBWSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(=CCCC(=CCOP(=O)(O)OP(=O)(O)O)C)C
OpenEye OEToolkits 1.5.0CC(=CCC/C(=C/CO[P@@](=O)(O)OP(=O)(O)O)/C)C
CACTVS 3.341CC(C)=CCCC(/C)=C/CO[P@](O)(=O)O[P](O)(O)=O
CACTVS 3.341CC(C)=CCCC(C)=CCO[P](O)(=O)O[P](O)(O)=O
ACDLabs 10.04O=P(OP(=O)(OC/C=C(/CC\C=C(/C)C)C)O)(O)O
FormulaC10 H20 O7 P2
NameGERANYL DIPHOSPHATE
ChEMBLCHEMBL41342
DrugBankDB02552
ZINCZINC000008215849
PDB chain6ypf Chain A Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6ypf Functional diversification in the Nudix hydrolase gene family drives sesquiterpene biosynthesis in Rosa × wichurana.
Resolution1.45 Å
Binding residue
(original residue number in PDB)		V20 R34 H49 Y94 F98 F134 P136
Binding residue
(residue number reindexed from 1)		V8 R22 H35 Y74 F78 F114 P116
Annotation score5
Enzymatic activity
Enzyme Commision number 3.6.1.68: geranyl diphosphate phosphohydrolase.
Gene Ontology
Molecular Function
GO:0016787 hydrolase activity
GO:0035539 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity
GO:0046872 metal ion binding
Biological Process
GO:0006203 dGTP catabolic process
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:6ypf, PDBe:6ypf, PDBj:6ypf
PDBsum6ypf
PubMed32639596
UniProtM4I1C6|NUDT1_ROSHC Geranyl diphosphate phosphohydrolase (Gene Name=NUDIX1)

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