Structure of PDB 5tpr Chain A Binding Site BS02

Receptor Information
>5tpr Chain A (length=400) Species: 240292 (Trichormus variabilis ATCC 29413) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVQAKFEAKETSFHVEGYEKIEYDLVYVDGIFEIQNSALADVYQGFGRCL
AIVDANVSRLYGNQIQAYFQYYGIELRLFPITITEPDKTIQTFERVIDVF
ADFKLVRKEPVLVVGGGLITDVVGFACSTYRRSSNYIRIPTTLIGLIDAS
VAIKVAVNHRKLKNRLGAYHASRKVFLDFSLLRTLPTDQVRNGMAELVKI
AVVAHQEVFELLEKYGEELLRTHFGNIDATPEIKEIAHRLTYKAIHKMLE
LEVPNLHELDLDRVIAYGHTWSPTLELAPRLPMFHGHAVNVDMAFSATIA
ARRGYITIAERDRILGLMSRVGLSLDHPMLDIDILWRGTESITLTRDGLL
RAAMPKPIGDCVFVNDLTREELAAALADHKELCTSYPRGGEGVDVYPVYQ
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 chain5tpr Chain A Residue 503 [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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PDB5tpr Evolution and Distribution of C7-Cyclitol Synthases in Prokaryotes and Eukaryotes.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		D56 N58 V59 E87 K90 G118 G119 L120 D123 T143 T144 I146 D150 A151 K165 T186 L187 Q191
Binding residue
(residue number reindexed from 1)		D54 N56 V57 E85 K88 G116 G117 L118 D121 T141 T142 I144 D148 A149 K163 T184 L185 Q189
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) R134 K156 E198 M250 E260 D264 A268 H271 P275 H287
Catalytic site (residue number reindexed from 1) R132 K154 E196 M248 E258 D262 A266 H269 P273 H285
Enzyme Commision number 4.2.3.154: demethyl-4-deoxygadusol synthase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003856 3-dehydroquinate synthase activity
GO:0016829 lyase activity
GO:0046872 metal ion binding
Biological Process
GO:0017000 antibiotic biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5tpr, PDBe:5tpr, PDBj:5tpr
PDBsum5tpr
PubMed28182402
UniProtQ3M6C3|DDGS_TRIV2 Demethyl-4-deoxygadusol synthase (Gene Name=Ava_3858)

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