Structure of PDB 4at5 Chain A Binding Site BS01

Receptor Information
>4at5 Chain A (length=294) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GAMDTFVQHIKRHNIVLKRELGEGAFGKVFLAECYNLKILVAVKTLKDAS
DNARKDFHREAELLTNLQHEHIVKFYGVCVEGDPLIMVFEYMKHGDLNKF
LRAHGPDAVLMAEGNPPTELTQSQMLHIAQQIAAGMVYLASQHFVHRDLA
TRNCLVGENLLVKIGDFGMSRDVYSTDYYRVGGHTMLPIRWMPPESIMYR
KFTTESDVWSLGVVLWEIFTYGKQPWYQLSNNEVIECITQGRVLQRPRTC
PQEVYELMLGCWQREPHMRKNIKGIHTLLQNLAKASPVYLDILG
Ligand information
Ligand IDMUJ
InChIInChI=1S/C20H22N4O3/c1-25-16-6-3-13(4-7-16)12-27-17-8-5-14(10-18(17)26-2)9-15-11-23-20(22)24-19(15)21/h3-8,10-11H,9,12H2,1-2H3,(H4,21,22,23,24)
InChIKeyMYQAUKPBNJWPIE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2COc1ccc(cc1)COc2ccc(cc2OC)Cc3cnc(nc3N)N
CACTVS 3.385COc1ccc(COc2ccc(Cc3cnc(N)nc3N)cc2OC)cc1
ACDLabs 12.01n1c(N)c(cnc1N)Cc3ccc(OCc2ccc(OC)cc2)c(OC)c3
FormulaC20 H22 N4 O3
Name5-{3-methoxy-4-[(4-methoxybenzyl)oxy]benzyl}pyrimidine-2,4-diamine
ChEMBLCHEMBL261849
DrugBank
ZINCZINC000013985942
PDB chain4at5 Chain A Residue 1839 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4at5 The Crystal Structures of Trka and Trkb Suggest Key Regions for Achieving Selective Inhibition.
Resolution1.71 Å
Binding residue
(original residue number in PDB)		A586 L608 V617 F633 Y635 M636 F688 N697 L699 G709 D710 F711
Binding residue
(residue number reindexed from 1)		A42 L64 V73 F89 Y91 M92 F144 N153 L155 G165 D166 F167
Annotation score1
Binding affinityMOAD: ic50=0.038uM
PDBbind-CN: -logKd/Ki=7.42,IC50=0.038uM
BindingDB: Kd=36nM
Enzymatic activity
Catalytic site (original residue number in PDB) D692 A694 R696 N697 D710 S719 L731
Catalytic site (residue number reindexed from 1) D148 A150 R152 N153 D166 S175 L187
Enzyme Commision number 2.7.10.1: receptor protein-tyrosine kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004713 protein tyrosine kinase activity
GO:0004714 transmembrane receptor protein tyrosine kinase activity
GO:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation
GO:0007169 cell surface receptor protein tyrosine kinase signaling pathway
Cellular Component
GO:0016020 membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4at5, PDBe:4at5, PDBj:4at5
PDBsum4at5
PubMed22902478
UniProtQ16620|NTRK2_HUMAN BDNF/NT-3 growth factors receptor (Gene Name=NTRK2)

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