Structure of PDB 8dgt Chain A Binding Site BS01

Receptor Information
>8dgt Chain A (length=431) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SPQKPIVRVFLPNKQRTVVPARCGVTVRDSLKKALMMRGLIPECCAVYRI
QEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRKTFFTLAFCDFCR
KLLFQGFRCQTCGYKFHQRCSTEVPLMCVNRDRSSSAPNVHDWEIPDGQI
TVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQAFKNEVGVLRK
TRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHIIETKFEMIKLIDIA
RQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATVKSRWSGS
HQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYS
NINNRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLF
PQILASIELLARSLPKIHRSASEPSLNRAGF
Ligand information
Ligand IDAGS
InChIInChI=1S/C10H16N5O12P3S/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(25-10)1-24-28(18,19)26-29(20,21)27-30(22,23)31/h2-4,6-7,10,16-17H,1H2,(H,18,19)(H,20,21)(H2,11,12,13)(H2,22,23,31)/t4-,6-,7-,10-/m1/s1
InChIKeyNLTUCYMLOPLUHL-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[C@@H](O)[C@H]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
ACDLabs 12.01O=P(O)(OP(=S)(O)O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC10 H16 N5 O12 P3 S
NamePHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER;
ATP-GAMMA-S;
ADENOSINE 5'-(3-THIOTRIPHOSPHATE);
ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE);
ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE
ChEMBLCHEMBL131890
DrugBankDB02930
ZINCZINC000008295128
PDB chain8dgt Chain A Residue 801 [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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PDB8dgt Cryo-EM structure of a RAS/RAF recruitment complex.
Resolution3.9 Å
Binding residue
(original residue number in PDB)		I463 G466 S467 F468 V471 W531 C532 K578 N581 F583 D594
Binding residue
(residue number reindexed from 1)		I156 G159 S160 F161 V164 W224 C225 K271 N274 F276 D287
Annotation score4
Enzymatic activity
Enzyme Commision number 2.7.11.1: non-specific serine/threonine protein kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0004708 MAP kinase kinase activity
GO:0004709 MAP kinase kinase kinase activity
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0031267 small GTPase binding
GO:0031434 mitogen-activated protein kinase kinase binding
GO:0042802 identical protein binding
GO:0044024 histone H2AS1 kinase activity
GO:0044877 protein-containing complex binding
GO:0046872 metal ion binding
GO:0097110 scaffold protein binding
GO:0106310 protein serine kinase activity
Biological Process
GO:0000165 MAPK cascade
GO:0001934 positive regulation of protein phosphorylation
GO:0002318 myeloid progenitor cell differentiation
GO:0006338 chromatin remodeling
GO:0006468 protein phosphorylation
GO:0007165 signal transduction
GO:0007173 epidermal growth factor receptor signaling pathway
GO:0008542 visual learning
GO:0009887 animal organ morphogenesis
GO:0010628 positive regulation of gene expression
GO:0010764 negative regulation of fibroblast migration
GO:0010828 positive regulation of D-glucose transmembrane transport
GO:0016079 synaptic vesicle exocytosis
GO:0016310 phosphorylation
GO:0030154 cell differentiation
GO:0030878 thyroid gland development
GO:0033077 T cell differentiation in thymus
GO:0033138 positive regulation of peptidyl-serine phosphorylation
GO:0034446 substrate adhesion-dependent cell spreading
GO:0035019 somatic stem cell population maintenance
GO:0036211 protein modification process
GO:0042127 regulation of cell population proliferation
GO:0043066 negative regulation of apoptotic process
GO:0043149 stress fiber assembly
GO:0043367 CD4-positive, alpha-beta T cell differentiation
GO:0043368 positive T cell selection
GO:0043369 CD4-positive or CD8-positive, alpha-beta T cell lineage commitment
GO:0043434 response to peptide hormone
GO:0043524 negative regulation of neuron apoptotic process
GO:0045580 regulation of T cell differentiation
GO:0046632 alpha-beta T cell differentiation
GO:0048538 thymus development
GO:0048679 regulation of axon regeneration
GO:0048680 positive regulation of axon regeneration
GO:0050772 positive regulation of axonogenesis
GO:0050852 T cell receptor signaling pathway
GO:0051496 positive regulation of stress fiber assembly
GO:0051591 response to cAMP
GO:0060291 long-term synaptic potentiation
GO:0060323 head morphogenesis
GO:0060324 face development
GO:0070371 ERK1 and ERK2 cascade
GO:0070374 positive regulation of ERK1 and ERK2 cascade
GO:0071277 cellular response to calcium ion
GO:0071466 cellular response to xenobiotic stimulus
GO:0072577 endothelial cell apoptotic process
GO:0090150 establishment of protein localization to membrane
GO:0099170 postsynaptic modulation of chemical synaptic transmission
GO:1900026 positive regulation of substrate adhesion-dependent cell spreading
GO:1902531 regulation of intracellular signal transduction
GO:1990090 cellular response to nerve growth factor stimulus
GO:2000301 negative regulation of synaptic vesicle exocytosis
GO:2000352 negative regulation of endothelial cell apoptotic process
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0043005 neuron projection
GO:0043231 intracellular membrane-bounded organelle
GO:0044297 cell body
GO:0098793 presynapse
GO:0098794 postsynapse
GO:0098978 glutamatergic synapse

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8dgt, PDBe:8dgt, PDBj:8dgt
PDBsum8dgt
PubMed37516774
UniProtP15056|BRAF_HUMAN Serine/threonine-protein kinase B-raf (Gene Name=BRAF)

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