Structure of PDB 6smw Chain C Binding Site BS04

Receptor Information
>6smw Chain C (length=475) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SRSSWIKQLNASLDEIDPEVADIIELEKARQWKGFELIPSENFTSLSVMQ
AVGSVMTNKYSEGYPGARYYGGNEYIDMAETLCQKRALEAFQLDPSKWGV
NVQSLSGSPANFQVYTALLKPHERIMALDLPHGGHLSHGYQTDTKKISAV
SIFFETMPYRLDENTGYIDYDQLEKSAVLFRPKLIVAGASAYARLYDYAR
IRKVCNKQKAVMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLRGPR
GAMIFFRKGLKEINKQGKEVMYDYEDRINQAVFPGLQGGPHNHTITGLAV
ALKQARTPEYKAYQDQVLRNCSKFAETLLAKGYDLVSGGTDNHLVLVNLK
NKGIDGSRVEKVLELVHIAANKNTVPGDVSAMVPGGIRMGTPALTSRGFI
EEDFAKVAEYFDLAVKIALKIKAESQGTKLKDFVATMQSNEKLQSEMSKL
REMVEEYAKQFPTIGFEKETMRYKE
Ligand information
Ligand IDLYA
InChIInChI=1S/C20H21N5O6/c21-20-24-16-15(18(29)25-20)12(9-22-16)6-3-10-1-4-11(5-2-10)17(28)23-13(19(30)31)7-8-14(26)27/h1-2,4-5,9,13H,3,6-8H2,(H,23,28)(H,26,27)(H,30,31)(H4,21,22,24,25,29)/t13-/m0/s1
InChIKeyWBXPDJSOTKVWSJ-ZDUSSCGKSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=NC(=O)c2c(CCc3ccc(cc3)C(=O)N[CH](CCC(O)=O)C(O)=O)c[nH]c2N1
CACTVS 3.341NC1=NC(=O)c2c(CCc3ccc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O)c[nH]c2N1
ACDLabs 10.04O=C(O)C(NC(=O)c1ccc(cc1)CCc2cnc3NC(=NC(=O)c23)N)CCC(=O)O
OpenEye OEToolkits 1.5.0c1cc(ccc1CCc2c[nH]c3c2C(=O)N=C(N3)N)C(=O)NC(CCC(=O)O)C(=O)O
OpenEye OEToolkits 1.5.0c1cc(ccc1CCc2c[nH]c3c2C(=O)N=C(N3)N)C(=O)N[C@@H](CCC(=O)O)C(=O)O
FormulaC20 H21 N5 O6
Name2-{4-[2-(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDIN-5-YL)-ETHYL]-BENZOYLAMINO}-PENTANEDIOIC ACID;
LY231514
ChEMBLCHEMBL225072
DrugBankDB00642
ZINCZINC000001540998
PDB chain6smw Chain D Residue 1305 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6smw Structural basis of methotrexate and pemetrexed action on serine hydroxymethyltransferases revealed using plant models.
Resolution1.54 Å
Binding residue
(original residue number in PDB)		E104 Y111
Binding residue
(residue number reindexed from 1)		E62 Y69
Annotation score2
Binding affinityMOAD: Ki=119.4uM
Enzymatic activity
Catalytic site (original residue number in PDB) Y102 E104 D257 T283 K286 R292
Catalytic site (residue number reindexed from 1) Y60 E62 D215 T241 K244 R250
Enzyme Commision number 2.1.2.1: glycine hydroxymethyltransferase.
Gene Ontology
Molecular Function
GO:0004372 glycine hydroxymethyltransferase activity
GO:0008270 zinc ion binding
GO:0016740 transferase activity
GO:0030170 pyridoxal phosphate binding
GO:0050897 cobalt ion binding
Biological Process
GO:0006544 glycine metabolic process
GO:0006563 L-serine metabolic process
GO:0006730 one-carbon metabolic process
GO:0019264 glycine biosynthetic process from serine
GO:0035999 tetrahydrofolate interconversion
Cellular Component
GO:0005739 mitochondrion
GO:0009536 plastid

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6smw, PDBe:6smw, PDBj:6smw
PDBsum6smw
PubMed31873125
UniProtQ94C74|GLYM2_ARATH Serine hydroxymethyltransferase 2, mitochondrial (Gene Name=SHM2)

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