Structure of PDB 1tkc Chain B Binding Site BS01

Receptor Information
>1tkc Chain B (length=678) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QFTDIDKLAVSTIRILAVDTVSKANSGHPGAPLGMAPAAHVLWSQMRMNP
TNPDWINRDRFVLSNGHAVALLYSMLHLTGYDLSIEDLKQFRQLGSRTPG
HPEFELPGVEVTTGPLGQGISNAVGMAMAQANLAATYNKPGFTLSDNYTY
VFLGDGCLQEGISSEASSLAGHLKLGNLIAIYDDNKITIDGATSISFDED
VAKRYEAYGWEVLYVENGNEDLAGIAKAIAQAKLSKDKPTLIKMTTTIGY
GSLHAGSHSVHGAPLKADDVKQLKSKFGFNPDKSFVVPQEVYDHYQKTIL
KPGVEANNKWNKLFSEYQKKFPELGAELARRLSGQLPANWESKLPTYTAK
DSAVATRKLSETVLEDVYNQLPELIGGSADLTPSNLTRWKEALDFQPPSS
GSGNYSGRYIRYGIREHAMGAIMNGISAFGANYKPYGGTFLNFVSYAAGA
VRLSALSGHPVIWVATHDSIGVGEDGPTHQPIETLAHFRSLPNIQVWRPA
DGNEVSAAYKNSLESKHTPSIIALSRQNLPQLEGSSIESASKGGYVLQDV
ANPDIILVATGSEVSLSVEAAKTLAAKNIKARVVSLPDFFTFDKQPLEYR
LSVLPDNVPIMSVEVLATTCWGKYAHQSFGIDRFGASGKAPEVFKFFGFT
PEGVAERAQKTIAFYKGDKLISPLKKAF
Ligand information
Ligand IDM6T
InChIInChI=1S/C13H20N4O7P2S/c1-8-11(13(14)16-10(3)15-8)6-17-7-27-12(9(17)2)4-5-23-26(21,22)24-25(18,19)20/h7H,4-6H2,1-3H3,(H4-,14,15,16,18,19,20,21,22)
InChIKeyXTYXJYCWAJSHCY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0Cc1c(c(nc(n1)C)N)C[n+]2csc(c2C)CCO[P@](=O)(O)O[P@](=O)(O)[O-]
OpenEye OEToolkits 1.5.0Cc1c(c(nc(n1)C)N)C[n+]2csc(c2C)CCOP(=O)(O)OP(=O)(O)[O-]
CACTVS 3.341Cc1nc(C)c(C[n+]2csc(CCO[P](O)(=O)O[P](O)([O-])=O)c2C)c(N)n1
CACTVS 3.341Cc1nc(C)c(C[n+]2csc(CCO[P@@](O)(=O)O[P](O)([O-])=O)c2C)c(N)n1
FormulaC13 H20 N4 O7 P2 S
Name6'-METHYL-THIAMIN DIPHOSPHATE
ChEMBL
DrugBankDB01682
ZINC
PDB chain1tkc Chain A Residue 681 [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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PDB1tkc Specificity of coenzyme binding in thiamin diphosphate-dependent enzymes. Crystal structures of yeast transketolase in complex with analogs of thiamin diphosphate.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		I416 E418 F445 Y448
Binding residue
(residue number reindexed from 1)		I414 E416 F443 Y446
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.85,Kd=14uM
Enzymatic activity
Catalytic site (original residue number in PDB) H30 I250 H263 E418 H481
Catalytic site (residue number reindexed from 1) H28 I248 H261 E416 H479
Enzyme Commision number 2.2.1.1: transketolase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004802 transketolase activity
GO:0005515 protein binding
GO:0016740 transferase activity
GO:0046872 metal ion binding
Biological Process
GO:0006098 pentose-phosphate shunt
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:1tkc, PDBe:1tkc, PDBj:1tkc
PDBsum1tkc
PubMed8144674
UniProtP23254|TKT1_YEAST Transketolase 1 (Gene Name=TKL1)

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