Structure of PDB 4oqd Chain C Binding Site BS02

Receptor Information
>4oqd Chain C (length=241) Species: 1906 (Streptomyces fradiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GPQADYSGEIAELYDLVHQGKGKDYHREAADLAALVRRHSPKAASLLDVA
CGTGMHLRHLADSFGTVEGLELSADMLAIARRRNPDAVLHHGDMRDFSLG
RRFSAVTCMFSSIGHLAGQAELDAALERFAAHVLPDGVVVVEPWWFPENF
TPGYVAAGTVEAGGTTVTRVSHSSREGEATRIEVHYLVAGPDRGITHHEE
SHRITLFTREQYERAFTAAGLSVEFMPGGPSGRGLFTGLPG
Ligand information
Ligand IDQDM
InChIInChI=1S/C18H31N3O14P2/c1-8-6-21(18(26)19-16(8)25)12-5-10(22)11(33-12)7-31-36(27,28)35-37(29,30)34-17-15(24)13(20(3)4)14(23)9(2)32-17/h6,9-15,17,22-24H,5,7H2,1-4H3,(H,27,28)(H,29,30)(H,19,25,26)/t9-,10+,11-,12-,13+,14-,15-,17-/m1/s1
InChIKeyIJJNPDQFXCRKOA-WHRNYZGVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6C[C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H](C[C@@H](O2)N3C=C(C(=O)NC3=O)C)O)O)N(C)C)O
CACTVS 3.385C[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH](C[CH]2O)N3C=C(C)C(=O)NC3=O)[CH](O)[CH]([CH]1O)N(C)C
OpenEye OEToolkits 1.7.6CC1C(C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(CC(O2)N3C=C(C(=O)NC3=O)C)O)O)N(C)C)O
ACDLabs 12.01O=C1C(=CN(C(=O)N1)C2OC(C(O)C2)COP(=O)(OP(=O)(OC3OC(C(O)C(N(C)C)C3O)C)O)O)C
CACTVS 3.385C[C@H]1O[C@H](O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N3C=C(C)C(=O)NC3=O)[C@H](O)[C@H]([C@@H]1O)N(C)C
FormulaC18 H31 N3 O14 P2
NameTDP-3,6-dideoxy-3-N,N-dimethylglucose
ChEMBL
DrugBank
ZINCZINC000008436954
PDB chain4oqd Chain C Residue 301 [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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PDB4oqd Production of a novel N-monomethylated dideoxysugar.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		Y14 K29 F118 S119 W152 W153 F158 T159 Y162 R177 S179 S181 R241
Binding residue
(residue number reindexed from 1)		Y6 K21 F110 S111 W144 W145 F150 T151 Y154 R169 S171 S173 R233
Annotation score4
Enzymatic activity
Enzyme Commision number 2.1.1.235: dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase.
Gene Ontology
Molecular Function
GO:0008168 methyltransferase activity
GO:0008757 S-adenosylmethionine-dependent methyltransferase activity
GO:0042803 protein homodimerization activity
Biological Process
GO:0009058 biosynthetic process
GO:0017000 antibiotic biosynthetic process
GO:0032259 methylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4oqd, PDBe:4oqd, PDBj:4oqd
PDBsum4oqd
PubMed24512254
UniProtP95748|TYLM1_STRFR dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase (Gene Name=tylM1)

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