Structure of PDB 8gku Chain B Binding Site BS01

Receptor Information
>8gku Chain B (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 IDZV1
InChIInChI=1S/C23H26FN5O6/c24-15-12-13(5-6-14(15)20(32)26-17(22(34)35)7-8-18(30)31)4-2-1-3-10-29-11-9-16-19(29)21(33)28-23(25)27-16/h5-6,9,11-12,17H,1-4,7-8,10H2,(H,26,32)(H,30,31)(H,34,35)(H3,25,27,28,33)/t17-/m1/s1
InChIKeySPSKTOLBULFCQW-QGZVFWFLSA-N
SMILES
SoftwareSMILES
CACTVS 3.385NC1=Nc2ccn(CCCCCc3ccc(c(F)c3)C(=O)N[C@H](CCC(O)=O)C(O)=O)c2C(=O)N1
OpenEye OEToolkits 2.0.7c1cc(c(cc1CCCCCn2ccc3c2C(=O)NC(=N3)N)F)C(=O)NC(CCC(=O)O)C(=O)O
CACTVS 3.385NC1=Nc2ccn(CCCCCc3ccc(c(F)c3)C(=O)N[CH](CCC(O)=O)C(O)=O)c2C(=O)N1
ACDLabs 12.01O=C(O)C(CCC(=O)O)NC(=O)c1ccc(cc1F)CCCCCn1ccc2N=C(N)NC(=O)c21
OpenEye OEToolkits 2.0.7c1cc(c(cc1CCCCCn2ccc3c2C(=O)NC(=N3)N)F)C(=O)N[C@H](CCC(=O)O)C(=O)O
FormulaC23 H26 F N5 O6
NameN-{4-[5-(2-amino-4-oxo-3,4-dihydro-5H-pyrrolo[3,2-d]pyrimidin-5-yl)pentyl]-2-fluorobenzoyl}-D-glutamic acid
ChEMBL
DrugBank
ZINC
PDB chain8gku 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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PDB8gku Structural Characterization of 5-Substituted Pyrrolo[3,2- d ]pyrimidine Antifolate Inhibitors in Complex with Human Serine Hydroxymethyl Transferase 2.
Resolution3.06 Å
Binding residue
(original residue number in PDB)		E98 Y105 Y106 P321
Binding residue
(residue number reindexed from 1)		E56 Y63 Y64 P279
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:8gku, PDBe:8gku, PDBj:8gku
PDBsum8gku
PubMed38324671
UniProtP34897|GLYM_HUMAN Serine hydroxymethyltransferase, mitochondrial (Gene Name=SHMT2)

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