Structure of PDB 4fl3 Chain A Binding Site BS01

Receptor Information
>4fl3 Chain A (length=538) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRNYLGGFALSVAHG
RKAHHYTIERELNGTYAIAGGRTHASPADLCHYHSQESDGLVCLLKKPFN
RPQGVQPKTGPFEDLKENLIREYVKQTWNLQGQALEQAIISQKPQLEKLI
ATTAHEKMPWFHGKISREESEQIVLIGSKTNGKFLIRARDNNGSYALCLL
HEGKVLHYRIDKDKTGKLSIPEGKKFDTLWQLVEHYSYKADGLLRVLTVP
CQKREALPMDTEVFESPFADPEEIRPKEVYLDRKLLTLEDKELGSGNFGT
VKKGYYQMKKVVKTVAVKILKNEANDPALKDELLAEANVMQQLDNPYIVR
MIGICEAESWMLVMEMAELGPLNKYLQQNRHVKDKNIIELVHQVSMGMKY
LEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRAPVKWYAPECINYY
KFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGC
PREMYDLMNLCWTYDVENRPGFAAVELRLRNYYYDVVN
Ligand information
Ligand IDANP
InChIInChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
InChIKeyPVKSNHVPLWYQGJ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
ACDLabs 12.01O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N
FormulaC10 H17 N6 O12 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
ChEMBLCHEMBL1230989
DrugBank
ZINCZINC000008660410
PDB chain4fl3 Chain A Residue 701 [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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PDB4fl3 Structural and biophysical characterization of the syk activation switch.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		S379 G380 N381 V385 A400 K402 A451 P455 R498 L501
Binding residue
(residue number reindexed from 1)		S295 G296 N297 V301 A316 K318 A367 P371 R414 L417
Annotation score3
Binding affinityMOAD: Kd=150uM
PDBbind-CN: -logKd/Ki=3.82,Kd=150uM
Enzymatic activity
Catalytic site (original residue number in PDB) D494 A496 R498 N499 D512
Catalytic site (residue number reindexed from 1) D410 A412 R414 N415 D428
Enzyme Commision number 2.7.10.2: non-specific protein-tyrosine kinase.
Gene Ontology
Molecular Function
GO:0001784 phosphotyrosine residue binding
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0004713 protein tyrosine kinase activity
GO:0004715 non-membrane spanning protein tyrosine kinase activity
GO:0005102 signaling receptor binding
GO:0005178 integrin binding
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016170 interleukin-15 receptor binding
GO:0016301 kinase activity
GO:0019901 protein kinase binding
GO:0019902 phosphatase binding
GO:0035325 Toll-like receptor binding
GO:0042169 SH2 domain binding
GO:0043274 phospholipase binding
GO:0097110 scaffold protein binding
Biological Process
GO:0001525 angiogenesis
GO:0001775 cell activation
GO:0001819 positive regulation of cytokine production
GO:0001820 serotonin secretion
GO:0001945 lymph vessel development
GO:0002092 positive regulation of receptor internalization
GO:0002223 stimulatory C-type lectin receptor signaling pathway
GO:0002250 adaptive immune response
GO:0002281 macrophage activation involved in immune response
GO:0002283 neutrophil activation involved in immune response
GO:0002366 leukocyte activation involved in immune response
GO:0002554 serotonin secretion by platelet
GO:0002684 positive regulation of immune system process
GO:0002862 negative regulation of inflammatory response to antigenic stimulus
GO:0006468 protein phosphorylation
GO:0006606 protein import into nucleus
GO:0007159 leukocyte cell-cell adhesion
GO:0007166 cell surface receptor signaling pathway
GO:0007167 enzyme-linked receptor protein signaling pathway
GO:0007169 cell surface receptor protein tyrosine kinase signaling pathway
GO:0007229 integrin-mediated signaling pathway
GO:0009887 animal organ morphogenesis
GO:0010543 regulation of platelet activation
GO:0010803 regulation of tumor necrosis factor-mediated signaling pathway
GO:0016310 phosphorylation
GO:0018108 peptidyl-tyrosine phosphorylation
GO:0019370 leukotriene biosynthetic process
GO:0019722 calcium-mediated signaling
GO:0030154 cell differentiation
GO:0030168 platelet activation
GO:0030183 B cell differentiation
GO:0030593 neutrophil chemotaxis
GO:0031334 positive regulation of protein-containing complex assembly
GO:0031623 receptor internalization
GO:0032481 positive regulation of type I interferon production
GO:0032725 positive regulation of granulocyte macrophage colony-stimulating factor production
GO:0032733 positive regulation of interleukin-10 production
GO:0032735 positive regulation of interleukin-12 production
GO:0032752 positive regulation of interleukin-3 production
GO:0032753 positive regulation of interleukin-4 production
GO:0032755 positive regulation of interleukin-6 production
GO:0032757 positive regulation of interleukin-8 production
GO:0032760 positive regulation of tumor necrosis factor production
GO:0032765 positive regulation of mast cell cytokine production
GO:0032928 regulation of superoxide anion generation
GO:0032930 positive regulation of superoxide anion generation
GO:0033630 positive regulation of cell adhesion mediated by integrin
GO:0035556 intracellular signal transduction
GO:0038063 collagen-activated tyrosine kinase receptor signaling pathway
GO:0038095 Fc-epsilon receptor signaling pathway
GO:0038096 Fc-gamma receptor signaling pathway involved in phagocytosis
GO:0038156 interleukin-3-mediated signaling pathway
GO:0042492 gamma-delta T cell differentiation
GO:0042742 defense response to bacterium
GO:0043280 positive regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0043303 mast cell degranulation
GO:0043306 positive regulation of mast cell degranulation
GO:0043313 regulation of neutrophil degranulation
GO:0043366 beta selection
GO:0043410 positive regulation of MAPK cascade
GO:0045087 innate immune response
GO:0045579 positive regulation of B cell differentiation
GO:0045588 positive regulation of gamma-delta T cell differentiation
GO:0045780 positive regulation of bone resorption
GO:0046638 positive regulation of alpha-beta T cell differentiation
GO:0046641 positive regulation of alpha-beta T cell proliferation
GO:0048514 blood vessel morphogenesis
GO:0050731 positive regulation of peptidyl-tyrosine phosphorylation
GO:0050764 regulation of phagocytosis
GO:0050776 regulation of immune response
GO:0050850 positive regulation of calcium-mediated signaling
GO:0050853 B cell receptor signaling pathway
GO:0051090 regulation of DNA-binding transcription factor activity
GO:0051649 establishment of localization in cell
GO:0051712 positive regulation of killing of cells of another organism
GO:0070372 regulation of ERK1 and ERK2 cascade
GO:0071226 cellular response to molecule of fungal origin
GO:0071396 cellular response to lipid
GO:0071404 cellular response to low-density lipoprotein particle stimulus
GO:0071639 positive regulation of monocyte chemotactic protein-1 production
GO:0090237 regulation of arachidonate secretion
GO:0090330 regulation of platelet aggregation
GO:0097242 amyloid-beta clearance
GO:0120162 positive regulation of cold-induced thermogenesis
GO:1904263 positive regulation of TORC1 signaling
GO:1904646 cellular response to amyloid-beta
GO:1990858 cellular response to lectin
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0019815 B cell receptor complex
GO:0032009 early phagosome
GO:0032991 protein-containing complex
GO:0042101 T cell receptor complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4fl3, PDBe:4fl3, PDBj:4fl3
PDBsum4fl3
PubMed23154170
UniProtP43405|KSYK_HUMAN Tyrosine-protein kinase SYK (Gene Name=SYK)

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