Structure of PDB 6vlo Chain A Binding Site BS01

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 IDTYD
InChIInChI=1S/C10H16N2O11P2/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(22-8)4-21-25(19,20)23-24(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
InChIKeyUJLXYODCHAELLY-XLPZGREQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(O)OP(=O)(O)O)O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)O)O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2O
CACTVS 3.341CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
CACTVS 3.341CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
FormulaC10 H16 N2 O11 P2
NameTHYMIDINE-5'-DIPHOSPHATE
ChEMBLCHEMBL259724
DrugBankDB03103
ZINCZINC000008215882
PDB chain6vlo Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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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)		N178 K188 L189 K192 H204 Q206 R213 V248 R273 R279
Binding residue
(residue number reindexed from 1)		N180 K190 L191 K194 H206 Q208 R215 V250 R275 R281
Annotation score2
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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