Structure of PDB 6uxj Chain A Binding Site BS04

Receptor Information
>6uxj Chain A (length=471) 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
LRPLGLTGNKVEKLCDLCNITVNKNAVFGDSSALAPGGVRIGAPAMTSRG
LVEKDFEQIGEFLHRAVTLTLEIQKEHGKLLKDFNKGLVNNKAIEDLKAD
VEKFSALFDMPGFLVSEMKYK
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 chain6uxj Chain B Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6uxj Impaired folate binding of serine hydroxymethyltransferase 8 from soybean underlies resistance to the soybean cyst nematode.
Resolution1.4 Å
Binding residue
(original residue number in PDB)		E61 Y68 Y69 F281
Binding residue
(residue number reindexed from 1)		E62 Y69 Y70 F282
Annotation score3
Binding affinityMOAD: Kd=17uM
Enzymatic activity
Catalytic site (original residue number in PDB) Y59 E61 D215 T241 K244 R250
Catalytic site (residue number reindexed from 1) Y60 E62 D216 T242 K245 R251
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:6uxj, PDBe:6uxj, PDBj:6uxj
PDBsum6uxj
PubMed32014996
UniProtA0A0R0IK90

[Back to BioLiP]