Structure of PDB 5wp4 Chain A Binding Site BS03

Receptor Information
>5wp4 Chain A (length=485) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EERDIQKNYWIEHSADLTVEAMMLDSRASDLDKEERPEVLSLLPPYEGKS
VLELGAGIGRFTGELAQKAGELIALDFIDNVIKKNESINGHYKNVKFMCA
DVTSPDLKITDGSLDLIFSNWLLMYLSDKEVELLAERMVGWIKVGGYIFF
RESCFHQSGDSKRKSNPTHYREPRFYSKVFQECQTRDAAGNSFELSMIGC
KCIGAYVKNKKNQNQICWIWQKVSSENDRGFQRFLDNVQYKSSGILRYER
VFGQGFVSTGGLETTKEFVEKMNLKPGQKVLDVGCGIGGGDFYMAEKFDV
HVVGIDLSVNMISFALERAIGLSCSVEFEVADCTTKHYPDNSFDVIYSRD
TILHIQDKPALFRTFFKWLKPGGKVLISDYCRSPKTPSAEFSEYIKQRGY
DLHDVQAYGQMLKDAGFTDVIAEDRTDQFMQVLKRELDRVEKEKEKFISD
FSKEDYDDIVGGWKSKLERCASDEQKWGLFIANKN
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 chain5wp4 Chain A Residue 703 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5wp4 Conformational changes in the di-domain structure of Arabidopsis phosphoethanolamine methyltransferase leads to active-site formation.
Resolution1.341 Å
Binding residue
(original residue number in PDB)		L241 Y246 V263 S264 G290 D312 L313 M317 D338 C339 R355 T357 H360 I361
Binding residue
(residue number reindexed from 1)		L235 Y240 V257 S258 G284 D306 L307 M311 D332 C333 R349 T351 H354 I355
Annotation score5
Enzymatic activity
Enzyme Commision number 2.1.1.103: phosphoethanolamine N-methyltransferase.
Gene Ontology
Molecular Function
GO:0000234 phosphoethanolamine N-methyltransferase activity
GO:0008168 methyltransferase activity
Biological Process
GO:0006656 phosphatidylcholine biosynthetic process
GO:0008654 phospholipid biosynthetic process
GO:0009058 biosynthetic process
GO:0009555 pollen development
GO:0009826 unidimensional cell growth
GO:0009860 pollen tube growth
GO:0010183 pollen tube guidance
GO:0032259 methylation
GO:0042425 choline biosynthetic process
GO:0048528 post-embryonic root development
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:5wp4, PDBe:5wp4, PDBj:5wp4
PDBsum5wp4
PubMed29084845
UniProtQ9FR44|PEAM1_ARATH Phosphoethanolamine N-methyltransferase 1 (Gene Name=NMT1)

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