Structure of PDB 5lmb Chain B Binding Site BS01

Receptor Information
>5lmb Chain B (length=262) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVAVKILKNEANDPAL
KDELLAEANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQN
RHVKDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDF
GLSKALRADENYYKAWPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSY
GQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPG
FAAVELRLRNYY
Ligand information
Ligand ID6ZF
InChIInChI=1S/C20H25N7/c1-27(2)18-6-5-15(13-24-18)16-10-17-19(23-9-8-22-17)20(26-16)25-12-14-4-3-7-21-11-14/h5-6,8-10,13-14,21H,3-4,7,11-12H2,1-2H3,(H,25,26)/t14-/m0/s1
InChIKeyCLKZDZYGBHNPSM-AWEZNQCLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.5CN(C)c1ccc(cn1)c2cc3c(c(n2)NCC4CCCNC4)nccn3
CACTVS 3.385CN(C)c1ccc(cn1)c2cc3nccnc3c(NC[CH]4CCCNC4)n2
CACTVS 3.385CN(C)c1ccc(cn1)c2cc3nccnc3c(NC[C@H]4CCCNC4)n2
OpenEye OEToolkits 2.0.5CN(C)c1ccc(cn1)c2cc3c(c(n2)NC[C@H]4CCCNC4)nccn3
FormulaC20 H25 N7
Name7-[6-(dimethylamino)pyridin-3-yl]-~{N}-[[(3~{S})-piperidin-3-yl]methyl]pyrido[3,4-b]pyrazin-5-amine
ChEMBLCHEMBL4528289
DrugBank
ZINCZINC000203741615
PDB chain5lmb Chain B 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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PDB5lmb Optimisation of a novel series of potent and orally bioavailable azanaphthyridine SYK inhibitors.
Resolution1.95 Å
Binding residue
(original residue number in PDB)		L377 A400 M448 M450 A451 G454 P455 R498 N499 L501 D512
Binding residue
(residue number reindexed from 1)		L14 A37 M85 M87 A88 G91 P92 R135 N136 L138 D149
Annotation score1
Binding affinityMOAD: ic50=16nM
BindingDB: IC50=16nM
Enzymatic activity
Catalytic site (original residue number in PDB) D494 A496 R498 N499 D512
Catalytic site (residue number reindexed from 1) D131 A133 R135 N136 D149
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:5lmb, PDBe:5lmb, PDBj:5lmb
PDBsum5lmb
PubMed27578246
UniProtP43405|KSYK_HUMAN Tyrosine-protein kinase SYK (Gene Name=SYK)

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