Structure of PDB 8t4o Chain B Binding Site BS01

Receptor Information
>8t4o Chain B (length=459) 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
RKGVKAPKTGREIPYTFEDRINFAVFPSLQGGPHNHAIAAVAVALKQACT
PMFREYSLQVLKNARAMADALLERGYSLVSGGTDNHLVLVDLRPKGLDGA
RAERVLELVSITANKNTCPGDRSITPGGLRLGAPALTSRQFREDDFRRVV
DFIDEGVNIGLEVKSKTAKLQDFKSFLLKDSETSQRLANLRQRVEQFARA
FPMPGFDEH
Ligand information
Ligand IDY5C
InChIInChI=1S/C17H17FN4O3/c18-12-9-10(4-5-11(12)16(24)25)3-1-2-7-22-8-6-13-14(22)15(23)21-17(19)20-13/h4-6,8-9H,1-3,7H2,(H,24,25)(H3,19,20,21,23)
InChIKeyMKEZEFIAXUENAX-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385NC1=Nc2ccn(CCCCc3ccc(C(O)=O)c(F)c3)c2C(=O)N1
OpenEye OEToolkits 2.0.7c1cc(c(cc1CCCCn2ccc3c2C(=O)NC(=N3)N)F)C(=O)O
ACDLabs 12.01O=C(O)c1ccc(cc1F)CCCCn1ccc2N=C(N)NC(=O)c21
FormulaC17 H17 F N4 O3
Name4-[4-(2-amino-4-oxo-3,4-dihydro-5H-pyrrolo[3,2-d]pyrimidin-5-yl)butyl]-2-fluorobenzoic acid
ChEMBL
DrugBank
ZINC
PDB chain8t4o Chain A 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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PDB8t4o Structural Characterization of 5-Substituted Pyrrolo[3,2- d ]pyrimidine Antifolate Inhibitors in Complex with Human Serine Hydroxymethyl Transferase 2.
Resolution2.68 Å
Binding residue
(original residue number in PDB)		E98 Y105 Y106 F320
Binding residue
(residue number reindexed from 1)		E56 Y63 Y64 F276
Annotation score1
Enzymatic activity
Enzyme Commision number 2.1.2.1: glycine hydroxymethyltransferase.
Gene Ontology
Molecular Function
GO:0003682 chromatin binding
GO:0004372 glycine hydroxymethyltransferase activity
GO:0005515 protein binding
GO:0008732 L-allo-threonine aldolase activity
GO:0016597 amino acid binding
GO:0016740 transferase activity
GO:0030170 pyridoxal phosphate binding
GO:0042802 identical protein binding
Biological Process
GO:0002082 regulation of oxidative phosphorylation
GO:0006544 glycine metabolic process
GO:0006545 glycine biosynthetic process
GO:0006563 L-serine metabolic process
GO:0006564 L-serine biosynthetic process
GO:0006730 one-carbon metabolic process
GO:0008284 positive regulation of cell population proliferation
GO:0019264 glycine biosynthetic process from serine
GO:0034340 response to type I interferon
GO:0035999 tetrahydrofolate interconversion
GO:0046653 tetrahydrofolate metabolic process
GO:0051262 protein tetramerization
GO:0051289 protein homotetramerization
GO:0070129 regulation of mitochondrial translation
GO:0070536 protein K63-linked deubiquitination
GO:1903715 regulation of aerobic respiration
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0005759 mitochondrial matrix
GO:0015630 microtubule cytoskeleton
GO:0042645 mitochondrial nucleoid
GO:0070062 extracellular exosome
GO:0070552 BRISC complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8t4o, PDBe:8t4o, PDBj:8t4o
PDBsum8t4o
PubMed38324671
UniProtP34897|GLYM_HUMAN Serine hydroxymethyltransferase, mitochondrial (Gene Name=SHMT2)

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