Structure of PDB 3kb6 Chain D Binding Site BS02

Receptor Information
>3kb6 Chain D (length=334) Species: 63363 (Aquifex aeolicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNVLFTSVPQEDVPFYQEALKDLSLKIYTTDVSKVPENELKKAELISVFV
YDKLTEELLSKMPRLKLIHTRSVGFDHIDLDYCKKKGILVTHIPAYSPES
VAEHTFAMILTLVKRLKRIEDRVKKLNFSQDSEILARELNRLTLGVIGTG
RIGSRVAMYGLAFGMKVLCYDVVKREDLKEKGCVYTSLDELLKESDVISL
HVPYTKETHHMINEERISLMKDGVYLINTARGKVVDTDALYRAYQRGKFS
GLGLDVFEDEEILILKKYTEGKATDKNLKILELACKDNVIITPHIAYYTD
KSLERIREETVKVVKAFVKGDLEQIKGNFVVGPS
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 chain3kb6 Chain D Residue 400 [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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PDB3kb6 Structure of D-lactate dehydrogenase from Aquifex aeolicus complexed with NAD(+) and lactic acid (or pyruvate).
Resolution2.12 Å
Binding residue
(original residue number in PDB)		V73 Y96 V101 G150 R151 I152 D171 V172 V202 P203 T208 T229 A230 R231 H294 A296 Y297
Binding residue
(residue number reindexed from 1)		V73 Y96 V101 G150 R151 I152 D171 V172 V202 P203 T208 T229 A230 R231 H294 A296 Y297
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) S97 R231 D255 E260 H294
Catalytic site (residue number reindexed from 1) S97 R231 D255 E260 H294
Enzyme Commision number 1.1.1.28: D-lactate dehydrogenase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0008720 D-lactate dehydrogenase activity
GO:0016491 oxidoreductase activity
GO:0016614 oxidoreductase activity, acting on CH-OH group of donors
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0051287 NAD binding

View graph for
Molecular Function
External links
PDB RCSB:3kb6, PDBe:3kb6, PDBj:3kb6
PDBsum3kb6
PubMed20054113
UniProtO66939

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