Structure of PDB 8dsk Chain A Binding Site BS02

Receptor Information
>8dsk Chain A (length=472) Species: 3847 (Glycine max) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMDPVSVWGNTPLATVDPEIHDLIEKEKRRQCRGIELIASENFTSFAVIE
ALGSALTNKYSEGMPGNRYYGGNEYIDQIENLCRSRALQAFHLDAQSWGV
NVQPYSGSPANFAAYTAVLNPHDRIMGLDLPSGGHLTHGYYTSGGKKISA
TSIYFESLPYKVNSTTGYIDYDRLEEKALDFRPKLIICGGSAYPRDWDYK
RFREVADKCGALLLCDMAHTSGLVAAQEVNSPFEYCDIVTTTTHKSLRGP
RAGMIFYRKGPKPPKKGQPENAVYDFEDKINFAVFPSLQGGPHNHQIGAL
AVALKQAASPGFKAYAKQVKANAVALGKYLMGKGYSLVTGGTENHLVLWD
LRPLGLTGYKVEKLCDLCNITVNKNAVFGDSSALAPGGVRIGAPAMTSRG
LVEKDFEQIGEFLHRAVTLTLEIQKEHGKLLKDFNKGLVNNKAIEDLKAD
VEKFSALFDMPGFLVSEMKYKD
Ligand information
Ligand IDFFO
InChIInChI=1S/C20H23N7O7/c21-20-25-16-15(18(32)26-20)27(9-28)12(8-23-16)7-22-11-3-1-10(2-4-11)17(31)24-13(19(33)34)5-6-14(29)30/h1-4,9,12-13,22H,5-8H2,(H,24,31)(H,29,30)(H,33,34)(H4,21,23,25,26,32)/t12-,13-/m0/s1
InChIKeyVVIAGPKUTFNRDU-STQMWFEESA-N
SMILES
SoftwareSMILES
CACTVS 3.370NC1=NC2=C(N(C=O)[CH](CNc3ccc(cc3)C(=O)N[CH](CCC(O)=O)C(O)=O)CN2)C(=O)N1
OpenEye OEToolkits 1.7.2c1cc(ccc1C(=O)NC(CCC(=O)O)C(=O)O)NCC2CNC3=C(N2C=O)C(=O)NC(=N3)N
ACDLabs 12.01O=C(O)C(NC(=O)c1ccc(cc1)NCC2N(C=O)C=3C(=O)NC(=NC=3NC2)N)CCC(=O)O
CACTVS 3.370NC1=NC2=C(N(C=O)[C@@H](CNc3ccc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O)CN2)C(=O)N1
FormulaC20 H23 N7 O7
NameN-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid;
[6S]-5-FORMYL-TETRAHYDROFOLATE;
6S-FOLINIC ACID
ChEMBLCHEMBL1908841
DrugBankDB11596
ZINCZINC000009212427
PDB chain8dsk Chain A Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8dsk Structural and functional analysis of two SHMT8 variants associated with soybean cyst nematode resistance.
Resolution1.63 Å
Binding residue
(original residue number in PDB)
L129 G132 G133 H134 L135 Y139 S190 N374 A382
Binding residue
(residue number reindexed from 1)
L130 G133 G134 H135 L136 Y140 S191 N375 A383
Annotation score3
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:8dsk, PDBe:8dsk, PDBj:8dsk
PDBsum8dsk
PubMed37811683
UniProtA0A0R0IK90

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