Structure of PDB 1ker Chain A Binding Site BS01

Receptor Information
>1ker Chain A (length=346) Species: 1307 (Streptococcus suis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QFKNIIVTGGAGFIGSNFVHYVYNNHPDVHVTVLDKLTYAGNKANLEAIL
GDRVELVVGDIADAELVDKLAAKADAIVHYAAESHNDNSLNDPSPFIHTN
FIGTYTLLEAARKYDIRFHHVSTDEVYGDLPLREDLPGHGEGPGEKFTAE
TNYNPSSPYSSTKAASDLIVKAWVRSFGVKATISNCSNNYGPYQHIEKFI
PRQITNILAGIKPKLYGEGKNVRDWIHTNDHSTGVWAILTKGRMGETYLI
GADGEKNNKEVLELILEKMGQPKDAYDHVTDRAGHDLRYAIDASKLRDEL
GWTPQFTDFSEGLEETIQWYTDNQDWWKAEKEAVEANYAKTQEVIK
Ligand information
Ligand IDDAU
InChIInChI=1S/C16H26N2O16P2/c1-6-3-18(16(25)17-14(6)24)10-2-7(20)9(31-10)5-30-35(26,27)34-36(28,29)33-15-13(23)12(22)11(21)8(4-19)32-15/h3,7-13,15,19-23H,2,4-5H2,1H3,(H,26,27)(H,28,29)(H,17,24,25)/t7-,8+,9+,10+,11+,12-,13+,15+/m0/s1
InChIKeyYSYKRGRSMLTJNL-URARBOGNSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[CH]3O[CH](CO)[CH](O)[CH](O)[CH]3O)O2)C(=O)NC1=O
OpenEye OEToolkits 1.7.6CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OC3C(C(C(C(O3)CO)O)O)O)O
CACTVS 3.370CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)O2)C(=O)NC1=O
OpenEye OEToolkits 1.7.6CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(O)O[P@](=O)(O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O)O
ACDLabs 12.01O=C1C(=CN(C(=O)N1)C2OC(C(O)C2)COP(=O)(OP(=O)(OC3OC(C(O)C(O)C3O)CO)O)O)C
FormulaC16 H26 N2 O16 P2
Name2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALPHA-D-GLUCOSE
ChEMBLCHEMBL412989
DrugBankDB03751
ZINC
PDB chain1ker Chain A Residue 2573 [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]
PDB1ker Toward a structural understanding of the dehydratase mechanism.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		S86 N88 T125 D126 E127 Y161 N190 K200 F201 R204 Q205 K216 L217 Y218 R225 N260 R284 H287
Binding residue
(residue number reindexed from 1)		S84 N86 T123 D124 E125 Y159 N188 K198 F199 R202 Q203 K214 L215 Y216 R223 N258 R282 H285
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) T125 D126 E127 Y161 K165
Catalytic site (residue number reindexed from 1) T123 D124 E125 Y159 K163
Enzyme Commision number 4.2.1.46: dTDP-glucose 4,6-dehydratase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
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:1ker, PDBe:1ker, PDBj:1ker
PDBsum1ker
PubMed11796113
UniProtQ8GIP9

[Back to BioLiP]