Structure of PDB 4ymg Chain B Binding Site BS01

Receptor Information
>4ymg Chain B (length=239) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LGSILPFNEETADRVSAYCEKNSHGIPDALVEHWEWTRTRFPDADKMSSR
LQGSWMIFTARDRKPKRILEIGCYSGYSALAWYEGTRDTKAEIVTLEYSP
KMIAASREAFKKYGVGDRVKLIEGPAENTLKTLEGEFDLIFVDANKDGYA
GYVKTILDQGLLSANGIILCDNVFARGLTIGPDCAPWLNDHVRPYWNGCG
QALDKFSAGLMEDPRIDVLLLPVFDGVTQIRWKDGAQRA
Ligand information
Ligand IDSAM
InChIInChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
InChIKeyMEFKEPWMEQBLKI-FCKMPRQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341C[S@@+](CC[C@H](N)C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
CACTVS 3.341C[S+](CC[CH](N)C([O-])=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0C[S@@+](CC[C@@H](C(=O)[O-])N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
ACDLabs 10.04[O-]C(=O)C(N)CC[S+](C)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC15 H22 N6 O5 S
NameS-ADENOSYLMETHIONINE
ChEMBLCHEMBL1235831
DrugBank
ZINC
PDB chain4ymg Chain B Residue 1001 [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]
PDB4ymg Structure and Biophysical Characterization of the S-Adenosylmethionine-dependent O-Methyltransferase PaMTH1, a Putative Enzyme Accumulating during Senescence of Podospora anserina.
Resolution1.899 Å
Binding residue
(original residue number in PDB)		S49 G73 Y75 S79 E98 Y99 P126 A127 E128 D144 A145 N146 Y153
Binding residue
(residue number reindexed from 1)		S48 G72 Y74 S78 E97 Y98 P125 A126 E127 D143 A144 N145 Y152
Annotation score4
Binding affinityMOAD: Kd=21uM
Enzymatic activity
Catalytic site (original residue number in PDB) D144 K147 D172 N173
Catalytic site (residue number reindexed from 1) D143 K146 D171 N172
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0008168 methyltransferase activity
GO:0008171 O-methyltransferase activity
GO:0008757 S-adenosylmethionine-dependent methyltransferase activity
Biological Process
GO:0032259 methylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4ymg, PDBe:4ymg, PDBj:4ymg
PDBsum4ymg
PubMed25979334
UniProtQ9HGR1

[Back to BioLiP]