Structure of PDB 3px2 Chain A Binding Site BS02

Receptor Information
>3px2 Chain A (length=240) Species: 1906 (Streptomyces fradiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PQADYSGEIAELYDLVHQGKGKDYHREAADLAALVRRHSPKAASLLDVAC
GTGMHLRHLADSFGTVEGLELSADMLAIARRRNPDAVLHHGDMRDFSLGR
RFSAVTCMFSSIGNLAGQAELDAALERFAAHVLPDGVVVVEPWWFPENFT
PGYVAAGTVEAGGTTVTRVSHSSREGEATRIEVHYLVAGPDRGITHHEES
HRITLFTREQYERAFTAAGLSVEFMPGGPSGRGLFTGLPG
Ligand information
Ligand IDT3Q
InChIInChI=1S/C16H27N3O14P2/c1-6-4-19(16(24)18-14(6)23)10-3-8(20)9(31-10)5-29-34(25,26)33-35(27,28)32-15-13(22)11(17)12(21)7(2)30-15/h4,7-13,15,20-22H,3,5,17H2,1-2H3,(H,25,26)(H,27,28)(H,18,23,24)/t7-,8+,9-,10-,11+,12-,13-,15-/m1/s1
InChIKeyKVYJLJOGNUNRJK-HALQBZCBSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(OC1OC(C(O)C(N)C1O)C)(O)OP(=O)(O)OCC3OC(N2C=C(C(=O)NC2=O)C)CC3O
CACTVS 3.341C[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](N)[CH]1O
OpenEye OEToolkits 1.5.0CC1C(C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(CC(O2)N3C=C(C(=O)NC3=O)C)O)O)N)O
OpenEye OEToolkits 1.5.0C[C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]2[C@H](C[C@@H](O2)N3C=C(C(=O)NC3=O)C)O)O)N)O
CACTVS 3.341C[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](N)[C@@H]1O
FormulaC16 H27 N3 O14 P2
Name[(3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-methyloxan-2-yl][hydroxy-[[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate;
thymidine-5'-diphosphate-alpha-D-3,6-dideoxy-3-aminoglucose
ChEMBL
DrugBank
ZINCZINC000008436920
PDB chain3px2 Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3px2 Molecular Architecture of TylM1 from Streptomyces fradiae: An N,N-Dimethyltransferase Involved in the Production of dTDP-d-mycaminose .
Resolution1.65 Å
Binding residue
(original residue number in PDB)		Y14 H26 K29 F118 W152 W153 F158 T159 Y162 R177 S179 S181 I190 R241
Binding residue
(residue number reindexed from 1)		Y5 H17 K20 F109 W143 W144 F149 T150 Y153 R168 S170 S172 I181 R232
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:3px2, PDBe:3px2, PDBj:3px2
PDBsum3px2
PubMed21142177
UniProtP95748|TYLM1_STRFR dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase (Gene Name=tylM1)

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