Structure of PDB 8fsd Chain D Binding Site BS03

Receptor Information
>8fsd Chain D (length=469) Species: 3847 (Glycine max) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMDPVSVWGNTPLATVDPEIHDLIEKEKRRQCRGIELIASENFTSFAVIE
ALGSALTNKYSEGMPGNRYYGGNEYIDQIENLCRSRALQAFHLDAQSWGV
NVQPYSGSPANFAAYTAVLNPHDRIMGLDLRSGGHLTHGYYTSGGKKISA
TSIYFESLPYKVNSTTGYIDYDRLEEKALDFRPKLIICGGSAYPRDWDYK
RFREVADKCGALLLCDMAHTSGLVAAQEVNSPFEYCDIVTTTTHKSLRGP
RAGMIFYRKGPKPPKKGQPENAVYDFEDKINFAVFPSLQGGPHNHQIGAL
AVALKQAASPGFKAYAKQVKANAVALGKYLMGKGYSLVTGGTENHLVLWD
LRPLGLTGNKVEKLCDLCNITVNKNAVFGDLAPGGVRIGAPAMTSRGLVE
KDFEQIGEFLHRAVTLTLEIQKEHGKLLKDFNKGLVNNKAIEDLKADVEK
FSALFDMPGFLVSEMKYKD
Ligand information
Ligand IDPLG
InChIInChI=1S/C10H15N2O7P/c1-6-10(15)8(3-11-4-9(13)14)7(2-12-6)5-19-20(16,17)18/h2,11,15H,3-5H2,1H3,(H,13,14)(H2,16,17,18)
InChIKeyFEVQWBMNLWUBTF-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(CNCC(O)=O)c1O
ACDLabs 10.04O=P(O)(O)OCc1cnc(c(O)c1CNCC(=O)O)C
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)CNCC(=O)O)O
FormulaC10 H15 N2 O7 P
NameN-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE];
N-PYRIDOXYL-GLYCINE-5-MONOPHOSPHATE
ChEMBL
DrugBankDB02824
ZINCZINC000002046831
PDB chain8fsd Chain D Residue 703 [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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PDB8fsd Structural and functional analysis of two SHMT8 variants associated with soybean cyst nematode resistance.
Resolution1.49 Å
Binding residue
(original residue number in PDB)		S39 S105 G106 S107 H134 G189 S190 D215 A217 H218 H243 K244 R389
Binding residue
(residue number reindexed from 1)		S40 S106 G107 S108 H135 G190 S191 D216 A218 H219 H244 K245 R387
Annotation score1
Enzymatic activity
Enzyme Commision number 2.1.2.1: glycine hydroxymethyltransferase.
Gene Ontology
Molecular Function
GO:0004372 glycine hydroxymethyltransferase activity
GO:0030170 pyridoxal phosphate binding
Biological Process
GO:0019264 glycine biosynthetic process from serine
GO:0035999 tetrahydrofolate interconversion

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:8fsd, PDBe:8fsd, PDBj:8fsd
PDBsum8fsd
PubMed37811683
UniProtA0A0R0IK90

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