Structure of PDB 6dkg Chain A

Receptor sequence

>6dkgA (length=276) Species: 9606 (Homo sapiens)

ACVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLPEQDKMLVAVKALKEA
SESARQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHGDLNR
FLRSHGPDGPLGLGQLLAVASQVAAGMVYLAGLHFVHRDLATRNCLVGQG
LVVKIGDFGYSTDYYRTMLPIRWMPPESILYRKFTTESDVWSFGVVLWEI
FTYGKQPWYQLSNTEAIDCITQGRELERPRACPPEVYAIMRGCWQREPQQ
RHSIKDVHARLQALAQAPPVYLDVLG

3D structure

• PDB: 6dkg Discovery of Potent, Selective, and Peripherally Restricted Pan-Trk Kinase Inhibitors for the Treatment of Pain.
• Chain: A
• Resolution: 2.53 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): D650 R654 N655 D668
• Catalytic site (residue number reindexed from 1): D139 R143 N144 D157
• Enzyme Commision number: 2.7.10.1: receptor protein-tyrosine kinase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	22L	A	K513 W514 E515	K14 W15 E16
BS02	GO7	A	L516 V524 A542 L564 F589 Y591 M592 F646 H648 L657 I666 G667 D668 F669	L17 V25 A43 L65 F90 Y92 M93 F135 H137 L146 I155 G156 D157 F158	PDBbind-CN: -logKd/Ki=8.59,Kd=2.6nM BindingDB: IC50=7700nM,Kd=1.1nM

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

External links

• PDB: RCSB:6dkg, PDBe:6dkg, PDBj:6dkg
• PDBsum: 6dkg
• PubMed: 29944371
• UniProt: P04629|NTRK1_HUMAN High affinity nerve growth factor receptor (Gene Name=NTRK1)