Structure of PDB 3wmx Chain A Binding Site BS01

Receptor Information
>3wmx Chain A (length=310) Species: 381666 (Cupriavidus necator H16) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GKPKILIVGANGQIGSELALALAERYGRTNVITSDVVPTGRHVHLTHEML
NATDRGELATVVERHGITQVYLLAAALSATGEKAPQWAWNLNMTSLLNVL
ELARQTGLERVFWPSSIAAFGPTTPAGQTPQKTVMEPTTVYGISKQAGEG
WCRWYHANHGVDVRSVRYPGLISHKTPPGGGTTDYAVDIFHAAVTGEPYT
CFLKEDEALPMMYMPDAIRATIELMEAPADKLSERGSYNIAGMSFTPAQI
AAAIREQVPGFQIRYEPDYRQAIAQGWPDSIDDSVARADWGWKAQYGLKE
MVADMLANLK
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 chain3wmx Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3wmx Binding of NAD+ and L-Threonine Induces Stepwise Structural and Flexibility Changes in Cupriavidus necator L-Threonine Dehydrogenase
Resolution2.5 Å
Binding residue
(original residue number in PDB)		G12 G15 Q16 I17 D38 V39 N54 A55 L76 A77 A78 P117 S119 Y144 K148 Y171 L174
Binding residue
(residue number reindexed from 1)		G9 G12 Q13 I14 D35 V36 N51 A52 L73 A74 A75 P114 S116 Y141 K145 Y168 L171
Annotation score4
Enzymatic activity
Enzyme Commision number 5.3.-.-
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0008743 L-threonine 3-dehydrogenase activity
GO:0016853 isomerase activity
GO:0046872 metal ion binding
Biological Process
GO:0006567 threonine catabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3wmx, PDBe:3wmx, PDBj:3wmx
PDBsum3wmx
PubMed24558034
UniProtQ0K312

[Back to BioLiP]