Structure of PDB 6nec Chain C Binding Site BS01

Receptor Information
>6nec Chain C (length=284) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GPLSLSVDAFKILEDPKWEFPRKNLVLGKTLGEGEFGKVVKATAFHLKGR
AGYTTVAVKMLKENASPSELRDLLSEFNVLKQVNHPHVIKLYGACSQDGP
LLLIVEYAKYGSLRGFLRESRKVERALTMGDLISFAWQISQGMQYLAEMK
LVHRDLAARNILVAEGRKMKISDFGLSRDVSQGRIPVKWMAIESLFDHIY
TTQSDVWSFGVLLWEIVTLGGNPYPGIPPERLFNLLKTGHRMERPDNCSE
EMYRLMLQCWKQEPDKRPVFADISKDLEKMMVKR
Ligand information
Ligand IDXIN
InChIInChI=1S/C31H33N5O4/c1-34-15-17-36(18-16-34)20-27(37)35(2)24-12-10-23(11-13-24)32-29(21-7-5-4-6-8-21)28-25-14-9-22(31(39)40-3)19-26(25)33-30(28)38/h4-14,19,32H,15-18,20H2,1-3H3,(H,33,38)/b29-28-
InChIKeyXZXHXSATPCNXJR-ZIADKAODSA-N
SMILES
SoftwareSMILES
CACTVS 3.341COC(=O)c1ccc\2c(NC(=O)C\2=C(Nc3ccc(cc3)N(C)C(=O)CN4CCN(C)CC4)/c5ccccc5)c1
OpenEye OEToolkits 1.5.0CN1CCN(CC1)CC(=O)N(C)c2ccc(cc2)NC(=C3c4ccc(cc4NC3=O)C(=O)OC)c5ccccc5
CACTVS 3.341COC(=O)c1ccc2c(NC(=O)C2=C(Nc3ccc(cc3)N(C)C(=O)CN4CCN(C)CC4)c5ccccc5)c1
ACDLabs 10.04O=C(OC)c1cc2c(cc1)/C(C(=O)N2)=C(\c3ccccc3)Nc4ccc(cc4)N(C(=O)CN5CCN(C)CC5)C
OpenEye OEToolkits 1.5.0CN1CCN(CC1)CC(=O)N(C)c2ccc(cc2)N/C(=C\3/c4ccc(cc4NC3=O)C(=O)OC)/c5ccccc5
FormulaC31 H33 N5 O4
Namemethyl (3Z)-3-{[(4-{methyl[(4-methylpiperazin-1-yl)acetyl]amino}phenyl)amino](phenyl)methylidene}-2-oxo-2,3-dihydro-1H-indole-6-carboxylate
ChEMBLCHEMBL502835
DrugBankDB09079
ZINCZINC000100014909
PDB chain6nec Chain C Residue 1102 [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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PDB6nec Structural basis of resistance of mutant RET protein-tyrosine kinase to its inhibitors nintedanib and vandetanib.
Resolution1.87 Å
Binding residue
(original residue number in PDB)		K728 T729 L730 G731 V738 A756 K758 E775 I788 V804 E805 Y806 A807 G810 L881 S891 D892
Binding residue
(residue number reindexed from 1)		K29 T30 L31 G32 V39 A57 K59 E76 I89 V105 E106 Y107 A108 G111 L162 S172 D173
Annotation score1
Binding affinityBindingDB: Kd=31nM
Enzymatic activity
Catalytic site (original residue number in PDB) D874 A876 R878 N879 D892
Catalytic site (residue number reindexed from 1) D155 A157 R159 N160 D173
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:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6nec, PDBe:6nec, PDBj:6nec
PDBsum6nec
PubMed31118272
UniProtP07949|RET_HUMAN Proto-oncogene tyrosine-protein kinase receptor Ret (Gene Name=RET)

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