Structure of PDB 4oqd Chain C Binding Site BS01

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 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 chain4oqd Chain C Residue 300 [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]
PDB4oqd Production of a novel N-monomethylated dideoxysugar.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		Y14 Y22 Y33 A58 G60 E79 L80 M84 D101 M102 F118 S120 H123
Binding residue
(residue number reindexed from 1)		Y6 Y14 Y25 A50 G52 E71 L72 M76 D93 M94 F110 S112 H115
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: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)

[Back to BioLiP]