Structure of PDB 6smr Chain B Binding Site BS03

Receptor Information
>6smr Chain B (length=472) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AMEPVSSWGNTSLVSVDPEIHDLIEKEKRRQCRGIELIASENFTSFAVIE
ALGSALTNKYSEGIPGNRYYGGNEFIDEIENLCRSRALEAFHCDPAAWGV
NVQPYSGSPANFAAYTALLQPHDRIMGLDLPSGGHLTHGYYTSGGKKISA
TSIYFESLPYKVNFTTGYIDYDKLEEKALDFRPKLLICGGSAYPRDWDYA
RFRAIADKVGALLLCDMAHISGLVAAQEAANPFEYCDVVTTTTHKSLRGP
RAGMIFYRKGPKPPKKGQPEGAVYDFEDKINFAVFPALQGGPHNHQIGAL
AVALKQANTPGFKVYAKQVKANAVALGNYLMSKGYQIVTNGTENHLVLWD
LRPLGLTGNKVEKLCDLCSITLNKNAVFGDSSALAPGGVRIGAPAMTSRG
LVEKDFEQIGEFLSRAVTLTLDIQKTYGKLLKDFNKGLVNNKDLDQLKAD
VEKFSASYEMPGFLMSEMKYKD
Ligand information
Ligand IDMTX
InChIInChI=1S/C20H22N8O5/c1-28(9-11-8-23-17-15(24-11)16(21)26-20(22)27-17)12-4-2-10(3-5-12)18(31)25-13(19(32)33)6-7-14(29)30/h2-5,8,13H,6-7,9H2,1H3,(H,25,31)(H,29,30)(H,32,33)(H4,21,22,23,26,27)/t13-/m0/s1
InChIKeyFBOZXECLQNJBKD-ZDUSSCGKSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CN(Cc1cnc2nc(N)nc(N)c2n1)c3ccc(cc3)C(=O)N[CH](CCC(O)=O)C(O)=O
CACTVS 3.341CN(Cc1cnc2nc(N)nc(N)c2n1)c3ccc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O
OpenEye OEToolkits 1.5.0CN(Cc1cnc2c(n1)c(nc(n2)N)N)c3ccc(cc3)C(=O)NC(CCC(=O)O)C(=O)O
ACDLabs 10.04O=C(O)C(NC(=O)c1ccc(cc1)N(C)Cc2nc3c(nc2)nc(nc3N)N)CCC(=O)O
OpenEye OEToolkits 1.5.0CN(Cc1cnc2c(n1)c(nc(n2)N)N)c3ccc(cc3)C(=O)N[C@@H](CCC(=O)O)C(=O)O
FormulaC20 H22 N8 O5
NameMETHOTREXATE
ChEMBLCHEMBL34259
DrugBankDB00563
ZINCZINC000001529323
PDB chain6smr Chain B Residue 501 [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]
PDB6smr Structural basis of methotrexate and pemetrexed action on serine hydroxymethyltransferases revealed using plant models.
Resolution2.12 Å
Binding residue
(original residue number in PDB)		Y68 P285
Binding residue
(residue number reindexed from 1)		Y69 P286
Annotation score2
Binding affinityMOAD: Ki=179.3uM
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:0005515 protein binding
GO:0016740 transferase activity
GO:0030170 pyridoxal phosphate binding
GO:1901149 salicylic acid binding
Biological Process
GO:0006730 one-carbon metabolic process
GO:0007623 circadian rhythm
GO:0019264 glycine biosynthetic process from serine
GO:0035999 tetrahydrofolate interconversion
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0009506 plasmodesma

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6smr, PDBe:6smr, PDBj:6smr
PDBsum6smr
PubMed31873125
UniProtO23254|GLYC4_ARATH Serine hydroxymethyltransferase 4 (Gene Name=SHM4)

[Back to BioLiP]