Structure of PDB 4ymh Chain A Binding Site BS01

Receptor Information
>4ymh Chain A (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 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 chain4ymh Chain A 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]
PDB4ymh Structure and Biophysical Characterization of the S-Adenosylmethionine-dependent O-Methyltransferase PaMTH1, a Putative Enzyme Accumulating during Senescence of Podospora anserina.
Resolution1.876 Å
Binding residue
(original residue number in PDB)		K47 M48 S49 G73 Y75 S79 E98 Y99 A127 D144 N146
Binding residue
(residue number reindexed from 1)		K46 M47 S48 G72 Y74 S78 E97 Y98 A126 D143 N145
Annotation score4
Binding affinityMOAD: Kd=3.2uM
PDBbind-CN: -logKd/Ki=6.46,Kd=0.35uM
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:4ymh, PDBe:4ymh, PDBj:4ymh
PDBsum4ymh
PubMed25979334
UniProtQ9HGR1

[Back to BioLiP]