Structure of PDB 6kzc Chain A Binding Site BS01

Receptor Information
>6kzc Chain A (length=281) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TYVQHIKRRDIVLKRELGEGAFGKVFLAECYNLSPTKDKMLVAVKALKDP
TLAARKDFQREAELLTNLQHEHIVKFYGVCGDGDPLIMVFEYMKHGDLNK
FLRAHGPDAGELGLSQMLHIASQIASGMVYLASQHFVHRDLATRNCLVGA
NLLVKIGDFGMSRVYSTDYYRLHTMLPIRWMPPESIMYRKFTTESDVWSF
GVILWEIFTYGKQPWFQLSNTEVIECITQGRVLERPRVCPKEVYDVMLGC
WQREPQQRLNIKEIYKILHALGKATPIYLDI
Ligand information
Ligand IDDZC
InChIInChI=1S/C28H25F3N6O/c1-19-20(6-7-23-17-33-26-18-32-8-9-37(23)26)4-3-5-25(19)27(38)34-22-14-21(28(29,30)31)15-24(16-22)36-12-10-35(2)11-13-36/h3-5,8-9,14-18H,10-13H2,1-2H3,(H,34,38)
InChIKeyMFTCKIGOHVOPIP-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CN1CCN(CC1)c2cc(NC(=O)c3cccc(C#Cc4cnc5cnccn45)c3C)cc(c2)C(F)(F)F
OpenEye OEToolkits 2.0.7Cc1c(cccc1C(=O)Nc2cc(cc(c2)N3CCN(CC3)C)C(F)(F)F)C#Cc4cnc5n4ccnc5
FormulaC28 H25 F3 N6 O
Name3-(2-imidazo[1,2-a]pyrazin-3-ylethynyl)-2-methyl-~{N}-[3-(4-methylpiperazin-1-yl)-5-(trifluoromethyl)phenyl]benzamide
ChEMBL
DrugBank
ZINC
PDB chain6kzc Chain A Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6kzc Design, synthesis and biological evaluation of 3-(imidazo[1,2-a]pyrazin-3-ylethynyl)-2-methylbenzamides as potent and selective pan-tropomyosin receptor kinase (TRK) inhibitors.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		L544 A570 K572 E588 L591 L592 V601 F617 E618 Y619 M620 H677 L686 G696 D697 F698
Binding residue
(residue number reindexed from 1)		L17 A43 K45 E61 L64 L65 V74 F90 E91 Y92 M93 H138 L147 G157 D158 F159
Annotation score1
Binding affinityMOAD: ic50=11.46nM
PDBbind-CN: -logKd/Ki=7.94,IC50=11.46nM
Enzymatic activity
Catalytic site (original residue number in PDB) D679 R683 N684 D697
Catalytic site (residue number reindexed from 1) D140 R144 N145 D158
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:6kzc, PDBe:6kzc, PDBj:6kzc
PDBsum6kzc
PubMed31271959
UniProtQ16288|NTRK3_HUMAN NT-3 growth factor receptor (Gene Name=NTRK3)

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