Structure of PDB 2bgm Chain A Binding Site BS01

Receptor Information
>2bgm Chain A (length=267) Species: 35933 (Podophyllum peltatum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TNRLQDKVAIITGGAGGIGETTAKLFVRYGAKVVIADIADDHGQKVCNNI
GSPDVISFVHCDVTKDEDVRNLVDTTIAKHGKLDIMFGNVGVLSTTPYSI
LEAGNEDFKRVMDINVYGAFLVAKHAARVMIPAKKGSIVFTASISSFTAG
EGVSHVYTATKHAVLGLTTSLCTELGEYGIRVNCVSPYIVASPLLTDVFG
VDSSRVEELAHQAANLKGTLLRAEDVADAVAYLAGDESKYVSGLNLVIDG
GYTRTNPAFPTALKHGL
Ligand information
Ligand IDNAJ
InChIInChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBAWFJGJZGIEFAR-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.5c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)([O-])OCC3C(C(C(O3)n4cnc5c4nc[nH+]c5N)O)O)O)O)C(=O)N
OpenEye OEToolkits 1.7.5c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)([O-])OP(=O)([O-])OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4nc[nH+]c5N)O)O)O)O)C(=O)N
CACTVS 3.385NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P]([O-])(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)[nH+]cnc45)[C@@H](O)[C@H]2O
CACTVS 3.385NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P]([O-])(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)[nH+]cnc45)[CH](O)[CH]2O
FormulaC21 H27 N7 O14 P2
NameNICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM)
ChEMBLCHEMBL1234613
DrugBankDB14128
ZINC
PDB chain2bgm Chain A Residue 1300 [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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PDB2bgm Crystal Structures of Apo-Form and Binary/Ternary Complexes of Podophyllum Secoisolariciresinol Dehydrogenase, an Enzyme Involved in Formation of Health-Protecting and Plant Defense Lignans
Resolution2.0 Å
Binding residue
(original residue number in PDB)		G23 G26 I28 D47 I48 C71 D72 V73 N99 V100 G101 T151 S153 Y167 K171 V200
Binding residue
(residue number reindexed from 1)		G13 G16 I18 D37 I38 C61 D62 V63 N89 V90 G91 T141 S143 Y157 K161 V190
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) S153 Y167 K171
Catalytic site (residue number reindexed from 1) S143 Y157 K161
Enzyme Commision number 1.1.1.331: secoisolariciresinol dehydrogenase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0016491 oxidoreductase activity
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0102911 (-)-secoisolariciresinol dehydrogenase activity
Biological Process
GO:0009807 lignan biosynthetic process
GO:0051289 protein homotetramerization

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2bgm, PDBe:2bgm, PDBj:2bgm
PDBsum2bgm
PubMed15653677
UniProtQ94KL8|SILD_PODPE Secoisolariciresinol dehydrogenase (Fragment)

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