Structure of PDB 8gks Chain A Binding Site BS03

Receptor Information
>8gks Chain A (length=462) 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
RKGVKAVDPKTGREIPYTFEDRINFAVFPSLQGGPHNHAIAAVAVALKQA
CTPMFREYSLQVLKNARAMADALLERGYSLVSGGTDNHLVLVDLRPKGLD
GARAERVLELVSITANKNTCPGDRSAITPGGLRLGAPALTSRQFREDDFR
RVVDFIDEGVNIGLEVKSKTAKLQDFKSFLLKDSETSQRLANLRQRVEQF
ARAFPMPGFDEH
Ligand information
Ligand IDY6U
InChIInChI=1S/C21H23N5O6/c22-21-24-14-9-11-26(17(14)19(30)25-21)10-1-2-12-3-5-13(6-4-12)18(29)23-15(20(31)32)7-8-16(27)28/h3-6,9,11,15H,1-2,7-8,10H2,(H,23,29)(H,27,28)(H,31,32)(H3,22,24,25,30)/t15-/m0/s1
InChIKeyIBENGLXKAUDADJ-HNNXBMFYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1cc(ccc1CCCn2ccc3c2C(=O)NC(=N3)N)C(=O)NC(CCC(=O)O)C(=O)O
CACTVS 3.385NC1=Nc2ccn(CCCc3ccc(cc3)C(=O)N[CH](CCC(O)=O)C(O)=O)c2C(=O)N1
OpenEye OEToolkits 2.0.7c1cc(ccc1CCCn2ccc3c2C(=O)NC(=N3)N)C(=O)N[C@@H](CCC(=O)O)C(=O)O
CACTVS 3.385NC1=Nc2ccn(CCCc3ccc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O)c2C(=O)N1
ACDLabs 12.01O=C(O)C(CCC(=O)O)NC(=O)c1ccc(cc1)CCCn1ccc2N=C(N)NC(=O)c21
FormulaC21 H23 N5 O6
NameN-{4-[3-(2-amino-4-oxo-3,4-dihydro-5H-pyrrolo[3,2-d]pyrimidin-5-yl)propyl]benzoyl}-L-glutamic acid
ChEMBL
DrugBank
ZINC
PDB chain8gks Chain A Residue 702 [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]
PDB8gks Structural Characterization of 5-Substituted Pyrrolo[3,2- d ]pyrimidine Antifolate Inhibitors in Complex with Human Serine Hydroxymethyl Transferase 2.
Resolution2.99 Å
Binding residue
(original residue number in PDB)		E98 Y105 Y106 F320
Binding residue
(residue number reindexed from 1)		E56 Y63 Y64 F278
Annotation score2
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:8gks, PDBe:8gks, PDBj:8gks
PDBsum8gks
PubMed38324671
UniProtP34897|GLYM_HUMAN Serine hydroxymethyltransferase, mitochondrial (Gene Name=SHMT2)

[Back to BioLiP]