Structure of PDB 3vdr Chain D Binding Site BS02

Receptor Information
>3vdr Chain D (length=260) Species: 511 (Alcaligenes faecalis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLKGKKAVVTGSTSGIGLAMATELAKAGADVVINGFGQPEDIERERSTLE
SKFGVKAYYLNADLSDAQATRDFIAKAAEALGGLDILVNNAGIQHTAPIE
EFPVDKWNAIIALNLSAVFHGTAAALPIMQKQGWGRIINIASAHGLVASV
NKSAYVAAKHGVVGLTKVTALENAGKGITCNAICPGWVRTPLVEKQIEAI
SQQKGIDIEAAARELLAEKQPSLQFVTPEQLGGAAVFLSSAAADQMTGTT
LSLDGGWTAR
Ligand information
Ligand IDNAI
InChIInChI=1S/C21H29N7O14P2/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/h1,3-4,7-8,10-11,13-16,20-21,29-32H,2,5-6H2,(H2,23,33)(H,34,35)(H,36,37)(H2,22,24,25)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBOPGDPNILDQYTO-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[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 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[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
FormulaC21 H29 N7 O14 P2
Name1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE;
NADH
ChEMBLCHEMBL1234616
DrugBankDB00157
ZINCZINC000008215403
PDB chain3vdr Chain D Residue 303 [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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PDB3vdr Structure of D-3-hydroxybutyrate dehydrogenase prepared in the presence of the substrate D-3-hydroxybutyrate and NAD+.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		G11 T13 S14 I16 F36 D63 L64 N90 A91 G92 L113 A141 S142 Y155 K159 V188 T190 L192 V193
Binding residue
(residue number reindexed from 1)		G11 T13 S14 I16 F36 D63 L64 N90 A91 G92 L113 A141 S142 Y155 K159 V188 T190 L192 V193
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) G15 N114 S142 Y155 K159 I200
Catalytic site (residue number reindexed from 1) G15 N114 S142 Y155 K159 I200
Enzyme Commision number 1.1.1.30: 3-hydroxybutyrate dehydrogenase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003858 3-hydroxybutyrate dehydrogenase activity
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding

View graph for
Molecular Function
External links
PDB RCSB:3vdr, PDBe:3vdr, PDBj:3vdr
PDBsum3vdr
PubMed19342772
UniProtD0VWQ0

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