Structure of PDB 6vlo Chain A Binding Site BS02

Receptor Information
>6vlo Chain A (length=319) Species: 212035 (Acanthamoeba polyphaga mimivirus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GHMKNILVTGGLGFIGSNFVNHISSKYDNVNIYVYDIGDYCASVENVEWN
NRTKLIKGDIRNFDLIMHTLTEHEIDTIVHFAAHSHVDNSFKNSLAFTET
NVFGTHVLLECSRMYGKLKLFFHMSTDEVYGEIDTTDTSREVSLLCPTNP
YAATKAGAEHIVKSYFLSYKLPIIIARCNNVYGRNQYPEKLIPKFICSLL
DGKKLHIQGTGNSRRNFIHAIDVADAVDLVINNGVIGETYNIGVTNEHSV
LDVAQILCDIAGVNLENQLEYVPDRLFNDFRYNITNDKIKSLGWEQSRKD
FKKELVELFDWYKVNRHRY
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 chain6vlo Chain A Residue 402 [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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PDB6vlo Biochemical analysis of a sugar 4,6-dehydratase from Acanthamoeba polyphaga Mimivirus.
Resolution2.05 Å
Binding residue
(original residue number in PDB)		G8 G11 F12 I13 D34 I35 A40 D57 I58 F79 A80 A81 S83 M122 T124 K153
Binding residue
(residue number reindexed from 1)		G10 G13 F14 I15 D36 I37 A42 D59 I60 F81 A82 A83 S85 M124 T126 K155
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) T124 D125 E126 Y149 K153
Catalytic site (residue number reindexed from 1) T126 D127 E128 Y151 K155
Enzyme Commision number 4.2.1.46: dTDP-glucose 4,6-dehydratase.
Gene Ontology
Molecular Function
GO:0008460 dTDP-glucose 4,6-dehydratase activity
GO:0016829 lyase activity
Biological Process
GO:0009225 nucleotide-sugar metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6vlo, PDBe:6vlo, PDBj:6vlo
PDBsum6vlo
PubMed32083779
UniProtQ5UR12|TGDS_MIMIV Putative dTDP-D-glucose 4,6-dehydratase (Gene Name=MIMI_R141)

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