Structure of PDB 9box Chain D Binding Site BS01

Receptor Information
>9box Chain D (length=453) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
WTGQESLSDSDPEMWELLQREKDRQCRGLELIASENFCSRAALEALGSCL
NNKYSEGYPGKRYYGGAEVVDEIELLCQRRALEAFDLDPAQWGVNVQPYS
GSPANLAVYTALLQPHDRIMGLDLPDGGHLTHGYMSDVKRISATSIFFES
MPYKLNPKTGLIDYNQLALTARLFRPRLIIAGTSAYARLIDYARMREVCD
EVKAHLLADMAHISGLVAAKVIPSPFKHADIVTTTTHKTLRGARSGLIFY
RKGVKAPYTFEDRINFAVFPSLQGGPHNHAIAAVAVALKQACTPMFREYS
LQVLKNARAMADALLERGYSLVSGGTDNHLVLVDLRPKGLDGARAERVLE
LVSITANKNTCPGDRSAITPGGLRLGAPALTSRQFREDDFRRVVDFIDEG
VNIGLEVKSKTAKLQDFKSFLLKDSETSQRLANLRQRVEQFARAFPMPGF
DEH
Ligand information
Ligand IDA1AQW
InChIInChI=1S/C10H13N2O7P/c1-6-10(15)8(3-11-4-9(13)14)7(2-12-6)5-19-20(16,17)18/h2-3,15H,4-5H2,1H3,(H,13,14)(H2,16,17,18)/b11-3+
InChIKeyHQEMYVORUPOKEX-QDEBKDIKSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1ncc(CO[P](O)(O)=O)c(C=NCC(O)=O)c1O
OpenEye OEToolkits 2.0.7Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/CC(=O)O)O
ACDLabs 12.01Oc1c(/C=N/CC(=O)O)c(cnc1C)COP(=O)(O)O
OpenEye OEToolkits 2.0.7Cc1c(c(c(cn1)COP(=O)(O)O)C=NCC(=O)O)O
FormulaC10 H13 N2 O7 P
Name(E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)glycine
ChEMBL
DrugBank
ZINC
PDB chain9box Chain B Residue 601 [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]
PDB9box Universality of critical active site glutamate as an acid-base catalyst in serine hydroxymethyltransferase function.
Resolution2.1 Å
Binding residue
(original residue number in PDB)
Y96 Y106 G325
Binding residue
(residue number reindexed from 1)
Y54 Y64 G274
Annotation score1
External links
PDB RCSB:9box, PDBe:9box, PDBj:9box
PDBsum9box
PubMed39148791
UniProtP34897|GLYM_HUMAN Serine hydroxymethyltransferase, mitochondrial (Gene Name=SHMT2)

[Back to BioLiP]