Structure of PDB 2ekp Chain A Binding Site BS01
Receptor Information
>2ekp Chain A (length=238) Species:
300852
(Thermus thermophilus HB8) [
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ERKALVTGGSRGIGRAIAEALVARGYRVAIASRNPEEAAQSLGAVPLPTD
LEKDDPKGLVKRALEALGGLHVLVHAAAVNVRKPALELSYEEWRRVLYLH
LDVAFLLAQAAAPHMAEAGWGRVLFIGSVTTFTAGGPVPIPAYTTAKTAL
LGLTRALAKEWARLGIRVNLLCPGYVETEFTLPLRQNPELYEPITARIPM
GRWARPEEIARVAAVLCGDEAEYLTGQAVAVDGGFLAY
Ligand information
Ligand ID
NAD
InChI
InChI=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
InChIKey
BAWFJGJZGIEFAR-NNYOXOHSSA-N
SMILES
Software
SMILES
CACTVS 3.341
NC(=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 1.5.0
c1cc(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 3.341
NC(=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 1.5.0
c1cc(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
Formula
C21 H27 N7 O14 P2
Name
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
ChEMBL
CHEMBL1234613
DrugBank
DB14128
ZINC
PDB chain
2ekp Chain A Residue 1300 [
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Receptor-Ligand Complex Structure
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PDB
2ekp
The first crystal structure of NAD-dependent 3-dehydro-2-deoxy-D-gluconate dehydrogenase from Thermus thermophilus HB8
Resolution
1.15 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 score
4
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
PDBsum
2ekp
PubMed
24699644
UniProt
Q53W82
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