Structure of PDB 6c98 Chain B Binding Site BS01

Receptor Information
>6c98 Chain B (length=99) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVE
HSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM
Ligand information
Ligand IDER7
InChIInChI=1S/C14H11FN4O/c1-8-12(9(2)20)13(10-4-3-5-11(15)6-10)19-14(18-8)16-7-17-19/h3-7H,1-2H3
InChIKeyVMZVIJOZARWDNG-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6Cc1c(c(n2c(n1)ncn2)c3cccc(c3)F)C(=O)C
ACDLabs 12.01n1c3n(nc1)c(c2cc(ccc2)F)c(c(C)n3)C(C)=O
CACTVS 3.385CC(=O)c1c(C)nc2ncnn2c1c3cccc(F)c3
FormulaC14 H11 F N4 O
Name1-[7-(3-fluorophenyl)-5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-6-yl]ethan-1-one
ChEMBL
DrugBank
ZINC
PDB chain6c98 Chain B Residue 101 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6c98 Insight into small molecule binding to the neonatal Fc receptor by X-ray crystallography and 100 kHz magic-angle-spinning NMR.
Resolution1.85 Å
Binding residue
(original residue number in PDB)		S52 Y63 L64 L65
Binding residue
(residue number reindexed from 1)		S52 Y63 L64 L65
Annotation score1
Binding affinityMOAD: Kd~80uM
PDBbind-CN: -logKd/Ki=4.10,Kd~80uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005198 structural molecule activity
GO:0005515 protein binding
GO:0023026 MHC class II protein complex binding
GO:0042605 peptide antigen binding
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
Biological Process
GO:0001913 T cell mediated cytotoxicity
GO:0001916 positive regulation of T cell mediated cytotoxicity
GO:0002237 response to molecule of bacterial origin
GO:0002474 antigen processing and presentation of peptide antigen via MHC class I
GO:0002481 antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent
GO:0002502 peptide antigen assembly with MHC class I protein complex
GO:0002503 peptide antigen assembly with MHC class II protein complex
GO:0002726 positive regulation of T cell cytokine production
GO:0006826 iron ion transport
GO:0006879 intracellular iron ion homeostasis
GO:0006955 immune response
GO:0007608 sensory perception of smell
GO:0007611 learning or memory
GO:0010977 negative regulation of neuron projection development
GO:0019885 antigen processing and presentation of endogenous peptide antigen via MHC class I
GO:0019886 antigen processing and presentation of exogenous peptide antigen via MHC class II
GO:0032092 positive regulation of protein binding
GO:0033077 T cell differentiation in thymus
GO:0034756 regulation of iron ion transport
GO:0042026 protein refolding
GO:0045646 regulation of erythrocyte differentiation
GO:0048260 positive regulation of receptor-mediated endocytosis
GO:0050680 negative regulation of epithelial cell proliferation
GO:0050768 negative regulation of neurogenesis
GO:0050778 positive regulation of immune response
GO:0050870 positive regulation of T cell activation
GO:0051289 protein homotetramerization
GO:0060586 multicellular organismal-level iron ion homeostasis
GO:0071281 cellular response to iron ion
GO:0071283 cellular response to iron(III) ion
GO:0071316 cellular response to nicotine
GO:1900121 negative regulation of receptor binding
GO:1900122 positive regulation of receptor binding
GO:1904434 positive regulation of ferrous iron binding
GO:1904437 positive regulation of transferrin receptor binding
GO:1990000 amyloid fibril formation
GO:2000774 positive regulation of cellular senescence
GO:2000978 negative regulation of forebrain neuron differentiation
Cellular Component
GO:0000139 Golgi membrane
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005765 lysosomal membrane
GO:0005783 endoplasmic reticulum
GO:0005788 endoplasmic reticulum lumen
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0005925 focal adhesion
GO:0009897 external side of plasma membrane
GO:0009986 cell surface
GO:0012507 ER to Golgi transport vesicle membrane
GO:0016020 membrane
GO:0030670 phagocytic vesicle membrane
GO:0031901 early endosome membrane
GO:0031902 late endosome membrane
GO:0031905 early endosome lumen
GO:0035580 specific granule lumen
GO:0042612 MHC class I protein complex
GO:0042613 MHC class II protein complex
GO:0042824 MHC class I peptide loading complex
GO:0055038 recycling endosome membrane
GO:0070062 extracellular exosome
GO:1904724 tertiary granule lumen
GO:1990712 HFE-transferrin receptor complex

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6c98, PDBe:6c98, PDBj:6c98
PDBsum6c98
PubMed29782488
UniProtP61769|B2MG_HUMAN Beta-2-microglobulin (Gene Name=B2M)

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