Structure of PDB 4ckr Chain A Binding Site BS01

Receptor Information
>4ckr Chain A (length=295) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MPRVDFPRSRLRFKEKLGEGQFGEVHLCEVDSPQDLVSLDFPLNVRKGHP
LLVAVKILRPDATKNARNDFLKEVKIMSRLKDPNIIRLLGVCVQDDPLCM
ITDYMENGDLNQFLSAHQLEDPTISYPMLLHVAAQIASGMRYLATLNFVH
RDLATRNCLVGENFTIKIADFGMSRNLYAGDYYRVVLPIRWMAWECILMG
KFTTASDVWAFGVTLWEVLMLCRAQPFGQLTDEQVIENAGEFFRDQGRQV
YLSRPPACPQGLYELMLRCWSRESEQRPPFSQLHRFLAEDALNTV
Ligand information
Ligand IDDI1
InChIInChI=1S/C30H31F3N4O3/c1-3-36-10-12-37(13-11-36)18-21-6-5-20(15-25(21)30(31,32)33)29(39)34-23-7-4-19(2)27(17-23)40-24-8-9-26-22(14-24)16-28(38)35-26/h4-9,14-15,17H,3,10-13,16,18H2,1-2H3,(H,34,39)(H,35,38)
InChIKeyAOZPVMOOEJAZGK-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCN1CCN(CC1)Cc2ccc(cc2C(F)(F)F)C(=O)Nc3ccc(C)c(Oc4ccc5NC(=O)Cc5c4)c3
ACDLabs 12.01O=C5Nc4c(cc(Oc1c(ccc(c1)NC(=O)c2ccc(c(c2)C(F)(F)F)CN3CCN(CC)CC3)C)cc4)C5
OpenEye OEToolkits 1.9.2CCN1CCN(CC1)Cc2ccc(cc2C(F)(F)F)C(=O)Nc3ccc(c(c3)Oc4ccc5c(c4)CC(=O)N5)C
FormulaC30 H31 F3 N4 O3
Name4-[(4-ethylpiperazin-1-yl)methyl]-n-{4-methyl-3-[(2-oxo-2,3-dihydro-1h-indol-5-yl)oxy]phenyl}-3-(trifluoromethyl)benzamide
ChEMBLCHEMBL3421914
DrugBank
ZINCZINC000096174842
PDB chain4ckr Chain A Residue 1000 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4ckr Discovery of a Potent and Selective Ddr1 Receptor Tyrosine Kinase Inhibitor.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		A653 K655 E672 M676 T701 Y703 M704 V763 H764 R765 L773 I782 A783 D784 F785
Binding residue
(residue number reindexed from 1)		A54 K56 E73 M77 T102 Y104 M105 V149 H150 R151 L159 I168 A169 D170 F171
Annotation score1
Binding affinityMOAD: ic50=105nM
PDBbind-CN: -logKd/Ki=6.98,IC50=105nM
BindingDB: IC50=105nM,EC50=86nM
Enzymatic activity
Catalytic site (original residue number in PDB) D766 R770 N771 D784 A793
Catalytic site (residue number reindexed from 1) D152 R156 N157 D170 A179
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:4ckr, PDBe:4ckr, PDBj:4ckr
PDBsum4ckr
PubMed23899692
UniProtQ08345|DDR1_HUMAN Epithelial discoidin domain-containing receptor 1 (Gene Name=DDR1)

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