Structure of PDB 5wp5 Chain A Binding Site BS01

Receptor Information
>5wp5 Chain A (length=463) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EERDIQKSYWMEHRPEVLSLIPPYEGKSVLELGAGIGRFTGELAQKAGEV
IALDFIESAIQKNESVNGHYKNIKFMCADVTSPDLKIKDGSIDLIFSNWL
LMYLSDKEVELMAERMIGWVKPGGYIFFRESCFHQSGDSKRKSNPTHYRE
PRFYTKVFQECQTRDASGNSFELSMVGCKCIGAYVKNKKNQNQICWIWQK
VSVENDKDFQRFLDNVQYKSSGILRYERVFGEGYVSTGGFETTKEFVAKM
DLKPGQKVLDVGCGIGGGDFYMAENFDVHVVGIDLSVNMISFALERAIGL
KCSVEFEVADCTTKTYPDNSFDVIYSRDTILHIQDKPALFRTFFKWLKPG
GKVLITDYCRSAETPSPEFAEYIKQRGYDLHDVQAYGQMLKDAGFDDVIA
EDRTDQFVQVLRRELEKVEKEKEEFISDFSEEDYNDIVGGWSAKLERTAS
GEQKWGLFIADKK
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 chain5wp5 Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5wp5 Conformational changes in the di-domain structure of Arabidopsis phosphoethanolamine methyltransferase leads to active-site formation.
Resolution1.5 Å
Binding residue
(original residue number in PDB)		V263 S264 G290 G292 D312 L313 M317 D338 C339 R355 T357 H360
Binding residue
(residue number reindexed from 1)		V235 S236 G262 G264 D284 L285 M289 D310 C311 R327 T329 H332
Annotation score5
Binding affinityMOAD: Kd=4.6uM
PDBbind-CN: -logKd/Ki=5.34,Kd=4.6uM
Enzymatic activity
Enzyme Commision number 2.1.1.103: phosphoethanolamine N-methyltransferase.
Gene Ontology
Molecular Function
GO:0000234 phosphoethanolamine N-methyltransferase activity
GO:0003729 mRNA binding
GO:0008168 methyltransferase activity
Biological Process
GO:0006656 phosphatidylcholine biosynthetic process
GO:0008654 phospholipid biosynthetic process
GO:0009058 biosynthetic process
GO:0032259 methylation
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5wp5, PDBe:5wp5, PDBj:5wp5
PDBsum5wp5
PubMed29084845
UniProtQ944H0|PEAM2_ARATH Phosphoethanolamine N-methyltransferase 2 (Gene Name=NMT2)

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