Structure of PDB 8t4p Chain B Binding Site BS02

Receptor Information
>8t4p Chain B (length=454) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
WTGQESLSDSDPEMWELLQREKDRQCRGLELIASENFCSRAALEALGSCL
NNKYSEGYPGKRYYGGAEVVDEIELLCQRRALEAFDLDPAQWGVNVQPYS
GSPANLAVYTALLQPHDRIMGLDLPDGGHLTHGYMSDVKRISATSIFFES
MPYKNPKTGLIDYNQLALTARLFRPRLIIAGTSAYARLIDYARMREVCDE
VKAHLLADMAHISGLVAAKVIPSPFKHADIVTTTTHKTLRGARSGLIFYR
KGVVDPKTEIPYTFEDRINFAVFPSLQGGPHNHAIAAVAVALKQACTPMF
REYSLQVLKNARAMADALLERGYSLVSGGTDNHLVLVDLKGDGARAERVL
ELVSITANKNTCPGDRSTITPGGLRLGAPALTSRQFREDDFRRVVDFIDE
GVNIGLEVKSKTAKLQDFKSFLLKDSETSQRLANLRQRVEQFARAFPMPG
FDEH
Ligand information
Ligand IDY5Z
InChIInChI=1S/C27H31FN6O9/c28-16-13-14(3-1-2-11-34-12-10-17-22(34)24(39)33-27(29)32-17)4-5-15(16)23(38)31-19(26(42)43)6-8-20(35)30-18(25(40)41)7-9-21(36)37/h4-5,10,12-13,18-19H,1-3,6-9,11H2,(H,30,35)(H,31,38)(H,36,37)(H,40,41)(H,42,43)(H3,29,32,33,39)/t18-,19-/m0/s1
InChIKeyHMMICCIWWRSKPK-OALUTQOASA-N
SMILES
SoftwareSMILES
CACTVS 3.385NC1=Nc2ccn(CCCCc3ccc(c(F)c3)C(=O)N[CH](CCC(=O)N[CH](CCC(O)=O)C(O)=O)C(O)=O)c2C(=O)N1
ACDLabs 12.01O=C(O)C(CCC(=O)O)NC(=O)CCC(NC(=O)c1ccc(cc1F)CCCCn1ccc2N=C(N)NC(=O)c21)C(=O)O
OpenEye OEToolkits 2.0.7c1cc(c(cc1CCCCn2ccc3c2C(=O)NC(=N3)N)F)C(=O)NC(CCC(=O)NC(CCC(=O)O)C(=O)O)C(=O)O
OpenEye OEToolkits 2.0.7c1cc(c(cc1CCCCn2ccc3c2C(=O)NC(=N3)N)F)C(=O)N[C@@H](CCC(=O)N[C@@H](CCC(=O)O)C(=O)O)C(=O)O
CACTVS 3.385NC1=Nc2ccn(CCCCc3ccc(c(F)c3)C(=O)N[C@@H](CCC(=O)N[C@@H](CCC(O)=O)C(O)=O)C(O)=O)c2C(=O)N1
FormulaC27 H31 F N6 O9
NameN-{4-[4-(2-amino-4-oxo-3,4-dihydro-5H-pyrrolo[3,2-d]pyrimidin-5-yl)butyl]-2-fluorobenzoyl}-L-gamma-glutamyl-L-glutamic acid
ChEMBL
DrugBank
ZINC
PDB chain8t4p 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

[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]
PDB8t4p Structural Characterization of 5-Substituted Pyrrolo[3,2- d ]pyrimidine Antifolate Inhibitors in Complex with Human Serine Hydroxymethyl Transferase 2.
Resolution2.801 Å
Binding residue
(original residue number in PDB)		E98 Y105 Y106
Binding residue
(residue number reindexed from 1)		E56 Y63 Y64
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8t4p, PDBe:8t4p, PDBj:8t4p
PDBsum8t4p
PubMed38324671
UniProtP34897|GLYM_HUMAN Serine hydroxymethyltransferase, mitochondrial (Gene Name=SHMT2)

[Back to BioLiP]