Structure of PDB 8gkt Chain B Binding Site BS04

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 B 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)		L166 G169 G170 H171 L172 Y176 K181 S226
Binding residue
(residue number reindexed from 1)		L124 G127 G128 H129 L130 Y134 K139 S184
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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