Structure of PDB 6m81 Chain C Binding Site BS02

Receptor Information
>6m81 Chain C (length=237) Species: 1906 (Streptomyces fradiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DFSGEIAELYDLVHQGKGKDYHREAADLAALVRRHSPKAASLLDVACGTG
MHLRHLADSFGTVEGLELSADMLAIARRRNPDAVLHHGDMRDFSLGRRFS
AVTCMFSSIGHLAGQAELDAALERFAAHVLPDGVVVVEPWWFPENFTPGY
VAAGTVEAGGTTVTRVSHSSREGEATRIEVHYLVAGPDRGITHHEESHRI
TLFTREQYERAFTAAGLSVEFMPGGPSGRGLFTGLPG
Ligand information
Ligand IDSAH
InChIInChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
InChIKeyZJUKTBDSGOFHSH-WFMPWKQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341N[CH](CCSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
CACTVS 3.341N[C@@H](CCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O
ACDLabs 10.04O=C(O)C(N)CCSCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CSCC[C@@H](C(=O)O)N)O)O)N
FormulaC14 H20 N6 O5 S
NameS-ADENOSYL-L-HOMOCYSTEINE
ChEMBLCHEMBL418052
DrugBankDB01752
ZINCZINC000004228232
PDB chain6m81 Chain C Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6m81 Structural and Functional Characterization of Sulfonium Carbon-Oxygen Hydrogen Bonding in the Deoxyamino Sugar Methyltransferase TylM1.
Resolution1.782 Å
Binding residue
(original residue number in PDB)		F14 Y22 Y33 A58 E79 L80 D101 M102 S120
Binding residue
(residue number reindexed from 1)		F2 Y10 Y21 A46 E67 L68 D89 M90 S108
Annotation score5
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:6m81, PDBe:6m81, PDBj:6m81
PDBsum6m81
PubMed30810306
UniProtP95748|TYLM1_STRFR dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase (Gene Name=tylM1)

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