Structure of PDB 5wp5 Chain B Binding Site BS02

Receptor Information
>5wp5 Chain B (length=462) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EERDIQKSYWMEHSEVLSLIPPYEGKSVLELGAGIGRFTGELAQKAGEVI
ALDFIESAIQKNESVNGHYKNIKFMCADVTSPDLKIKDGSIDLIFSNWLL
MYLSDKEVELMAERMIGWVKPGGYIFFRESCFHQSGDSKRKSNPTHYREP
RFYTKVFQECQTRDASGNSFELSMVGCKCIGAYVKNKKNQNQICWIWQKV
SVENDKDFQRFLDNVQYKSSGILRYERVFGEGYVSTGGFETTKEFVAKMD
LKPGQKVLDVGCGIGGGDFYMAENFDVHVVGIDLSVNMISFALERAIGLK
CSVEFEVADCTTKTYPDNSFDVIYSRDTILHIQDKPALFRTFFKWLKPGG
KVLITDYCRSAETPSPEFAEYIKQRGYDLHDVQAYGQMLKDAGFDDVIAE
DRTDQFVQVLRRELEKVEKEKEEFISDFSEEDYNDIVGGWSAKLERTASG
EQKWGLFIADKK
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 B Residue 702 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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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)		V234 S235 G261 G263 D283 L284 M288 D309 C310 R326 T328 H331
Annotation score5
Binding affinityMOAD: 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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