Structure of PDB 7e38 Chain A Binding Site BS02

Receptor Information
>7e38 Chain A (length=313) Species: 93608 (Sinopodophyllum hexandrum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PLRLPVIDLSMKNLKPGTTSWNSVRTQVREALEEYGCFEAVIDAVSPELQ
KAVCNKGHELLNLPLETKMLNGNKPEYDGFTSIPNLNEGMGVGRITDLEK
VERFTNLMWPEGNKDFCETVYSYGKRMAEVDHILKMMVFESFGMEKHFDS
FCESTNYLLHFMRYQQPGKDGRSPALSLHKDKSILTIVNQNDVKGLEFET
KDGEWILPTADNHIVLLGDCFMAWSNGRLHSPLHRVTLVANQARLSTSSF
SFPKDIIETPAELVDEEHPLLFNPFEITELLAYCFTKEGAKAVCDLKQYK
AYTGALEHHHHHH
Ligand information
Ligand IDYTC
InChIInChI=1S/C22H24O7/c1-24-19-9-14(10-20(25-2)21(19)26-3)7-16-15(11-27-22(16)23)6-13-4-5-17-18(8-13)29-12-28-17/h4-5,8-10,15-16H,6-7,11-12H2,1-3H3/t15-,16+/m1/s1
InChIKeyGMLDZDDTZKXJLU-CVEARBPZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7COc1cc(cc(c1OC)OC)CC2C(COC2=O)Cc3ccc4c(c3)OCO4
CACTVS 3.385COc1cc(C[CH]2[CH](COC2=O)Cc3ccc4OCOc4c3)cc(OC)c1OC
CACTVS 3.385COc1cc(C[C@H]2[C@@H](COC2=O)Cc3ccc4OCOc4c3)cc(OC)c1OC
OpenEye OEToolkits 2.0.7COc1cc(cc(c1OC)OC)C[C@H]2[C@@H](COC2=O)Cc3ccc4c(c3)OCO4
FormulaC22 H24 O7
Name(3~{S},4~{S})-4-(1,3-benzodioxol-5-ylmethyl)-3-[(3,4,5-trimethoxyphenyl)methyl]oxolan-2-one
ChEMBLCHEMBL2021357
DrugBank
ZINC
PDB chain7e38 Chain A Residue 403 [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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PDB7e38 Mechanistic analysis of carbon-carbon bond formation by deoxypodophyllotoxin synthase.
Resolution2.05 Å
Binding residue
(original residue number in PDB)		H165 M167 L181 H184 K187 F255 F257 F290 V298
Binding residue
(residue number reindexed from 1)		H160 M162 L176 H179 K182 F250 F252 F285 V293
Annotation score5
Enzymatic activity
Enzyme Commision number 1.14.20.8: (-)-deoxypodophyllotoxin synthase.
Gene Ontology
Molecular Function
GO:0016706 2-oxoglutarate-dependent dioxygenase activity
GO:0046872 metal ion binding
GO:0051213 dioxygenase activity
Biological Process
GO:0009611 response to wounding
GO:0009699 phenylpropanoid biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:7e38, PDBe:7e38, PDBj:7e38
PDBsum7e38
PubMed34969844
UniProtA0A0N9HQ36|2ODD_SINHE Deoxypodophyllotoxin synthase (Gene Name=2-ODD)

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