Structure of PDB 8gky Chain B Binding Site BS01

Receptor Information
>8gky Chain B (length=461) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
WTGQESLSDSDPEMWELLQREKDRQCRGLELIASENFCSRAALEALGSCL
NNKYSEGYPGKRFYGGAEVVDEIELLCQRRALEAFDLDPAQWGVNVQPYS
GSPANLAVYTALLQPHDRIMGLDLPDGGHLTHGYMSDVKRISATSIFFES
MPYKLNPKTGLIDYNQLALTARLFRPRLIIAGTSAYARLIDYARMREVCD
EVKAHLLADMAHISGLVAAKVIPSPFKHADIVTTTTHKTLRGARSGLIFY
RKGVKADPKTGREIPYTFEDRINFAVFPSLQGGPHNHAIAAVAVALKQAC
TPMFREYSLQVLKNARAMADALLERGYSLVSGGTDNHLVLVDLRPKGLDG
ARAERVLELVSITANKNTCPGDRSAITPGGLRLGAPALTSRQFREDDFRR
VVDFIDEGVNIGLEVKSKTAKLQDFKSFLLKDSETSQRLANLRQRVEQFA
RAFPMPGFDEH
Ligand information
Ligand IDZVR
InChIInChI=1S/C21H22FN5O6/c22-13-10-11(2-1-8-27-9-7-14-17(27)19(31)26-21(23)25-14)3-4-12(13)18(30)24-15(20(32)33)5-6-16(28)29/h3-4,7,9-10,15H,1-2,5-6,8H2,(H,24,30)(H,28,29)(H,32,33)(H3,23,25,26,31)/t15-/m0/s1
InChIKeyVOXSIQHYUGLGIP-HNNXBMFYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385NC1=Nc2ccn(CCCc3ccc(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)CCCn1ccc2N=C(N)NC(=O)c21
OpenEye OEToolkits 2.0.7c1cc(c(cc1CCCn2ccc3c2C(=O)NC(=N3)N)F)C(=O)NC(CCC(=O)O)C(=O)O
OpenEye OEToolkits 2.0.7c1cc(c(cc1CCCn2ccc3c2C(=O)NC(=N3)N)F)C(=O)N[C@@H](CCC(=O)O)C(=O)O
CACTVS 3.385NC1=Nc2ccn(CCCc3ccc(c(F)c3)C(=O)N[C@@H](CCC(O)=O)C(O)=O)c2C(=O)N1
FormulaC21 H22 F N5 O6
NameN-{4-[3-(2-amino-4-oxo-3,4-dihydro-5H-pyrrolo[3,2-d]pyrimidin-5-yl)propyl]-2-fluorobenzoyl}-L-glutamic acid
ChEMBL
DrugBank
ZINC
PDB chain8gky 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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PDB8gky Structural Characterization of 5-Substituted Pyrrolo[3,2- d ]pyrimidine Antifolate Inhibitors in Complex with Human Serine Hydroxymethyl Transferase 2.
Resolution2.77 Å
Binding residue
(original residue number in PDB)		E98 F105 Y106 F320
Binding residue
(residue number reindexed from 1)		E56 F63 Y64 F277
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:8gky, PDBe:8gky, PDBj:8gky
PDBsum8gky
PubMed38324671
UniProtP34897|GLYM_HUMAN Serine hydroxymethyltransferase, mitochondrial (Gene Name=SHMT2)

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