Structure of PDB 2ekp Chain A Binding Site BS01

Receptor Information
>2ekp Chain A (length=238) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ERKALVTGGSRGIGRAIAEALVARGYRVAIASRNPEEAAQSLGAVPLPTD
LEKDDPKGLVKRALEALGGLHVLVHAAAVNVRKPALELSYEEWRRVLYLH
LDVAFLLAQAAAPHMAEAGWGRVLFIGSVTTFTAGGPVPIPAYTTAKTAL
LGLTRALAKEWARLGIRVNLLCPGYVETEFTLPLRQNPELYEPITARIPM
GRWARPEEIARVAAVLCGDEAEYLTGQAVAVDGGFLAY
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 chain2ekp 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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PDB2ekp The first crystal structure of NAD-dependent 3-dehydro-2-deoxy-D-gluconate dehydrogenase from Thermus thermophilus HB8
Resolution1.15 Å
Binding residue
(original residue number in PDB)
G9 S11 G13 I14 S33 T50 D51 L52 A77 A79 I127 G128 Y144 K148 P174 G175 V177 T179 F181 T182
Binding residue
(residue number reindexed from 1)
G8 S10 G12 I13 S32 T49 D50 L51 A76 A78 I126 G127 Y143 K147 P173 G174 V176 T178 F180 T181
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) G13 S129 Y144 K148
Catalytic site (residue number reindexed from 1) G12 S128 Y143 K147
Enzyme Commision number 1.1.1.125: 2-deoxy-D-gluconate 3-dehydrogenase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor

View graph for
Molecular Function
External links
PDB RCSB:2ekp, PDBe:2ekp, PDBj:2ekp
PDBsum2ekp
PubMed24699644
UniProtQ53W82

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