Structure of PDB 3wbf Chain C Binding Site BS02

Receptor Information
>3wbf Chain C (length=297) Species: 292459 (Symbiobacterium thermophilum IAM 14863) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLRVAVVGYGNVGRYALEAVQAAPDMELVGVVRRKVLAATPPELTGVRVV
TDISQLEGVQGALLCVPTRSVPEYAEAMLRRGIHTVDSYDIHGDLADLRR
RLDPVAREHGAAAVISAGWDPGTDSIIRALLEFMAPKGITYTNFGPGMSM
GHSVAVKAIPGVRDALSMTIPAGMGVHKRAVYVELEPGADFAEVERAIKT
DPYFVRDETRVTQVESVSALMDVGHGVVMERKGVSGATHNQLFRFEMRIN
NPALTAQVMVAALRAAARQKPGCYTMIEIPVIDYLPGDREAWIRKLV
Ligand information
Ligand IDNAP
InChIInChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyXJLXINKUBYWONI-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)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[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
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[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]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)OP(=O)(O)O)O)O)O)C(=O)N
FormulaC21 H28 N7 O17 P3
NameNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE;
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
ChEMBLCHEMBL295069
DrugBankDB03461
ZINC
PDB chain3wbf Chain C Residue 308 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3wbf Structural and mutational studies on the unusual substrate specificity of meso-diaminopimelate dehydrogenase from Symbiobacterium thermophilum.
Resolution2.12 Å
Binding residue
(original residue number in PDB)		G10 Y11 G12 N13 V14 R35 R36 C67 V68 P69 T70 Y76 S90 D92 G120 W121 D122 P123 M152 G153 V156 N253 T257
Binding residue
(residue number reindexed from 1)		G8 Y9 G10 N11 V12 R33 R34 C65 V66 P67 T68 Y74 S88 D90 G118 W119 D120 P121 M150 G151 V154 N251 T255
Annotation score4
Enzymatic activity
Enzyme Commision number 1.4.1.16: diaminopimelate dehydrogenase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0016491 oxidoreductase activity
GO:0047850 diaminopimelate dehydrogenase activity
Biological Process
GO:0009085 lysine biosynthetic process
GO:0009089 lysine biosynthetic process via diaminopimelate
GO:0019877 diaminopimelate biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3wbf, PDBe:3wbf, PDBj:3wbf
PDBsum3wbf
PubMed24339368
UniProtQ67PI3

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