Structure of PDB 1vm6 Chain B Binding Site BS01

Receptor Information
>1vm6 Chain B (length=218) Species: 2336 (Thermotoga maritima) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HHHHHMKYGIVGYSGRMGQEIQKVFSEKGHELVLKVDVNGVEELDSPDVV
IDFSSPEALPKTVDLCKKYRAGLVLGTTALKEEHLQMLRELSKEVPVVQA
YNFSIGINVLKRFLSELVKVLEDWDVEIVETHHRFKKDAPSGTAILLESA
LGKSVPIHSLRVGGVPGDHVVVFGNIGETIEIKHRAISRTVFAIGALKAA
EFLVGKDPGMYSFEEVIF
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 chain1vm6 Chain B Residue 300 [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]
PDB1vm6 Crystal structure of Dihydrodipicolinate reductase (TM1520) from Thermotoga maritima at 2.27 A resolution
Resolution2.27 Å
Binding residue
(original residue number in PDB)		G7 S9 G10 R11 M12 D32 V33 F48 S49 S50 E52 A53 G71 T73 Y96 N97 F98 F187
Binding residue
(residue number reindexed from 1)		G12 S14 G15 R16 M17 D37 V38 F53 S54 S55 E57 A58 G76 T78 Y101 N102 F103 F192
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) H127 K131
Catalytic site (residue number reindexed from 1) H132 K136
Enzyme Commision number 1.17.1.8: 4-hydroxy-tetrahydrodipicolinate reductase.
Gene Ontology
Molecular Function
GO:0008839 4-hydroxy-tetrahydrodipicolinate reductase
GO:0016491 oxidoreductase activity
GO:0016726 oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor
GO:0050661 NADP binding
GO:0051287 NAD binding
Biological Process
GO:0009085 lysine biosynthetic process
GO:0009089 lysine biosynthetic process via diaminopimelate
GO:0019877 diaminopimelate biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1vm6, PDBe:1vm6, PDBj:1vm6
PDBsum1vm6
PubMed
UniProtQ9X1K8|DAPB_THEMA 4-hydroxy-tetrahydrodipicolinate reductase (Gene Name=dapB)

[Back to BioLiP]