Structure of PDB 5wp4 Chain A Binding Site BS01

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 701 [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)		W16 M28 G61 R66 F67 D82 F83 D107 V108 N126 W127 L128
Binding residue
(residue number reindexed from 1)		W10 M22 G55 R60 F61 D76 F77 D101 V102 N120 W121 L122
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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