Structure of PDB 3ndr Chain B Binding Site BS01

Receptor Information
>3ndr Chain B (length=247) Species: 381 (Mesorhizobium loti) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TERLAGKTALVTGAAQGIGKAIAARLAADGATVIVSDINAEGAKAAAASI
GKKARAIAADISDPGSVKALFAEIQALTGGIDILVNNASIVPFVAWDDVD
LDHWRKIIDVNLTGTFIVTRAGTDQMRAAGKAGRVISIASNTFFAGTPNM
AAYVAAKGGVIGFTRALATELGKYNITANAVTPGLIESDGVKASPHNEAF
GFVEMLQAMKGKGQPEHIADVVSFLASDDARWITGQTLNVDAGMVRH
Ligand information
Ligand IDNAD
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
CACTVS 3.341NC(=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)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
CACTVS 3.341NC(=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)ncnc45)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
FormulaC21 H27 N7 O14 P2
NameNICOTINAMIDE-ADENINE-DINUCLEOTIDE
ChEMBLCHEMBL1234613
DrugBankDB14128
ZINC
PDB chain3ndr Chain B Residue 251 [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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PDB3ndr Crystallization and preliminary X-ray analysis of SDR-type pyridoxal dehydrogenase from Mesorhizobium loti
Resolution2.88 Å
Binding residue
(original residue number in PDB)		G14 Q17 G18 I19 D38 I39 D61 I62 N88 A89 S90 I139 S141 Y154 K158 P184 G185 L186 I187 S189 G191 V192
Binding residue
(residue number reindexed from 1)		G13 Q16 G17 I18 D37 I38 D60 I61 N87 A88 S89 I138 S140 Y153 K157 P183 G184 L185 I186 S188 G190 V191
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) G18 S141 Y154 K158
Catalytic site (residue number reindexed from 1) G17 S140 Y153 K157
Enzyme Commision number 1.1.1.107: pyridoxal 4-dehydrogenase.
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0050235 pyridoxal 4-dehydrogenase activity
Biological Process
GO:0042820 vitamin B6 catabolic process

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Molecular Function
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Biological Process
External links
PDB RCSB:3ndr, PDBe:3ndr, PDBj:3ndr
PDBsum3ndr
PubMed
UniProtQ988B7|PLDH_RHILO Pyridoxal 4-dehydrogenase (Gene Name=pldh-t)

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