Structure of PDB 9box Chain D Binding Site BS03

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 D Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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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)
S76 S142 G143 S144 H171 S226 D251 H254 H279 K280 R425
Binding residue
(residue number reindexed from 1)
S34 S100 G101 S102 H129 S184 D209 H212 H237 K238 R374
Annotation score1
External links
PDB RCSB:9box, PDBe:9box, PDBj:9box
PDBsum9box
PubMed39148791
UniProtP34897|GLYM_HUMAN Serine hydroxymethyltransferase, mitochondrial (Gene Name=SHMT2)

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