Structure of PDB 8gkt Chain B Binding Site BS02

Receptor Information
>8gkt Chain B (length=456) 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
RKGVKGREIPYTFEDRINFAVFPSLQGGPHNHAIAAVAVALKQACTPMFR
EYSLQVLKNARAMADALLERGYSLVSGGTDNHLVLVDLRPKGLDGARAER
VLELVSITANKNTCPGDRSAITPGGLRLGAPALTSRQFREDDFRRVVDFI
DEGVNIGLEVKSKTAKLQDFKSFLLKDSETSQRLANLRQRVEQFARAFPM
PGFDEH
Ligand information
Ligand IDY7L
InChIInChI=1S/C21H25N5O6S/c22-21-24-13-9-11-26(17(13)19(30)25-21)10-3-1-2-4-12-5-7-15(33-12)18(29)23-14(20(31)32)6-8-16(27)28/h5,7,9,11,14H,1-4,6,8,10H2,(H,23,29)(H,27,28)(H,31,32)(H3,22,24,25,30)/t14-/m0/s1
InChIKeyRQAHNHUMMCUWMX-AWEZNQCLSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(O)C(CCC(=O)O)NC(=O)c1ccc(CCCCCn2ccc3N=C(N)NC(=O)c32)s1
OpenEye OEToolkits 2.0.7c1cc(sc1CCCCCn2ccc3c2C(=O)NC(=N3)N)C(=O)N[C@@H](CCC(=O)O)C(=O)O
CACTVS 3.385NC1=Nc2ccn(CCCCCc3sc(cc3)C(=O)N[CH](CCC(O)=O)C(O)=O)c2C(=O)N1
CACTVS 3.385NC1=Nc2ccn(CCCCCc3sc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O)c2C(=O)N1
OpenEye OEToolkits 2.0.7c1cc(sc1CCCCCn2ccc3c2C(=O)NC(=N3)N)C(=O)NC(CCC(=O)O)C(=O)O
FormulaC21 H25 N5 O6 S
NameN-{5-[5-(2-amino-4-oxo-3,4-dihydro-5H-pyrrolo[3,2-d]pyrimidin-5-yl)pentyl]thiophene-2-carbonyl}-L-glutamic acid
ChEMBL
DrugBank
ZINC
PDB chain8gkt Chain A Residue 602 [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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PDB8gkt Structural Characterization of 5-Substituted Pyrrolo[3,2- d ]pyrimidine Antifolate Inhibitors in Complex with Human Serine Hydroxymethyl Transferase 2.
Resolution2.64 Å
Binding residue
(original residue number in PDB)		E98 Y105
Binding residue
(residue number reindexed from 1)		E56 Y63
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:8gkt, PDBe:8gkt, PDBj:8gkt
PDBsum8gkt
PubMed38324671
UniProtP34897|GLYM_HUMAN Serine hydroxymethyltransferase, mitochondrial (Gene Name=SHMT2)

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