Structure of PDB 1r6d Chain A Binding Site BS02

Receptor Information
>1r6d Chain A (length=322) Species: 54571 (Streptomyces venezuelae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRLLVTGGAGFIGSHFVRQLLAGAYPDVPADEVIVLDSLTYAGNRANLAP
VDADPRLRFVHGDIRDAGLLARELRGVDAIVHFAAESHVDRSIAGASVFT
ETNVQGTQTLLQCAVDAGVGRVVHVSTNQVYGSIDSGSWTESSPLEPNSP
YAASKAGSDLVARAYHRTYGLDVRITRCCNNYGPYQHPEKLIPLFVTNLL
DGGTLPLYGDGANVREWVHTDDHCRGIALVLAGGRAGEIYHIGGGLELTN
RELTGILLDSLGADWSSVRKVADRKGHDLRYSLDGGKIERELGYRPQVSF
ADGLARTVRWYRENRGWWEPLK
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 chain1r6d Chain A Residue 401 [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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PDB1r6d High Resolution X-ray Structure of dTDP-Glucose 4,6-Dehydratase from Streptomyces venezuelae
Resolution1.35 Å
Binding residue
(original residue number in PDB)		S87 H88 T127 N128 Q129 Y151 N180 K190 L191 P206 Y208 R215 N250 R274 H277 Y281
Binding residue
(residue number reindexed from 1)		S87 H88 T127 N128 Q129 Y151 N180 K190 L191 P206 Y208 R215 N250 R274 H277 Y281
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) T127 N128 Q129 Y151 K155
Catalytic site (residue number reindexed from 1) T127 N128 Q129 Y151 K155
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:0016491 oxidoreductase 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:1r6d, PDBe:1r6d, PDBj:1r6d
PDBsum1r6d
PubMed14570895
UniProtQ9ZGH3

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