Structure of PDB 5us6 Chain J Binding Site BS01

Receptor Information
>5us6 Chain J (length=267) Species: 216895 (Vibrio vulnificus CMCP6) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GMVRIAVAGAAGRMGRNLVKAAHHNPVAKVAAGSERPESSLVGVDLGELC
GEGKFDVVVCDDLAKQIDQFDVIIDFTAPASTLNNLALCQQYGKSIVIGT
TGFTEEQREQIDLVAQQVPVVMAPNYSVGVNLVFKLLEKAAKVMGDYCDI
EIVEAHHRHKVDAPSGTAIGMGEAIAGAMGNKLSDVAVYAREGITGERTK
DEIGFATIRAGDIVGEHTAMFADIGERVEITHKATDRMTFANGAVKAAVW
LHEKPAGFYTMTDVLGL
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 chain5us6 Chain J Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5us6 Comparative structural and mechanistic studies of 4-hydroxy-tetrahydrodipicolinate reductases from Mycobacterium tuberculosis and Vibrio vulnificus.
Resolution2.61 Å
Binding residue
(original residue number in PDB)		G8 G11 R12 M13 E34 R35 F75 T76 S80 G98 T100 P123 N124 Y125
Binding residue
(residue number reindexed from 1)		G9 G12 R13 M14 E35 R36 F76 T77 S81 G99 T101 P124 N125 Y126
Annotation score4
Enzymatic activity
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5us6, PDBe:5us6, PDBj:5us6
PDBsum5us6
PubMed32980502
UniProtQ8DEM0|DAPB_VIBVU 4-hydroxy-tetrahydrodipicolinate reductase (Gene Name=dapB)

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