Structure of PDB 5cxz Chain A Binding Site BS01

Receptor Information
>5cxz Chain A (length=269) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VYLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVAVKILKNALKDEL
LAEANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHVT
DKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSK
ALRADENYYKAQTHKWPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSY
GQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPG
FAAVELRLRNYYYDVVNHH
Ligand information
Ligand ID55U
InChIInChI=1S/C19H23N5/c1-24(2)15-8-6-14(7-9-15)17-13-18-16(5-3-11-21-18)19(23-17)22-12-4-10-20/h3,5-9,11,13H,4,10,12,20H2,1-2H3,(H,22,23)
InChIKeyRIWJHDIYQSQOAT-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2CN(C)c1ccc(cc1)c2cc3c(cccn3)c(n2)NCCCN
CACTVS 3.385CN(C)c1ccc(cc1)c2cc3ncccc3c(NCCCN)n2
ACDLabs 12.01c3(c1ccc(N(C)C)cc1)cc2c(cccn2)c(n3)NCCCN
FormulaC19 H23 N5
NameN-{7-[4-(dimethylamino)phenyl]-1,6-naphthyridin-5-yl}propane-1,3-diamine
ChEMBLCHEMBL30678
DrugBank
ZINCZINC000003816697
PDB chain5cxz Chain A Residue 703 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5cxz Orally bioavailable Syk inhibitors with activity in a rat PK/PD model.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		L377 A400 M450 A451 G454 P455 L501 D512
Binding residue
(residue number reindexed from 1)		L15 A38 M83 A84 G87 P88 L134 D145
Annotation score1
Binding affinityMOAD: ic50=552nM
PDBbind-CN: -logKd/Ki=6.26,IC50=552nM
BindingDB: IC50=34nM
Enzymatic activity
Catalytic site (original residue number in PDB) D494 A496 R498 N499 D512 K533
Catalytic site (residue number reindexed from 1) D127 A129 R131 N132 D145 K165
Enzyme Commision number 2.7.10.2: non-specific protein-tyrosine kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004713 protein tyrosine kinase activity
GO:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5cxz, PDBe:5cxz, PDBj:5cxz
PDBsum5cxz
PubMed26320624
UniProtP43405|KSYK_HUMAN Tyrosine-protein kinase SYK (Gene Name=SYK)

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