Structure of PDB 6fil Chain A Binding Site BS01

Receptor Information
>6fil Chain A (length=287) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DFPRSRLRFKEKLGEGQFGEVHLCEVDSPPLLVAVKILRPDATKNARNDF
LKEVKIMSRLKDPNIIRLLGVCVQDDPLCMITDYMENGDLNQFLSAHQLE
DKAAEGAPGDPTISYPMLLHVAAQIASGMRYLATLNFVHRDLATRNCLVG
ENFTIKIADFGMSRNLYAGDYYRVQGRAVLPIRWMAWECILMGKFTTASD
VWAFGVTLWEVLMLCRAQPFGQLTDEQVIENAGEFFRDQGRQVYLSRPPA
CPQGLYELMLRCWSRESEQRPPFSQLHRFLAEDALNT
Ligand information
Ligand IDD6W
InChIInChI=1S/C24H26N6O3/c1-25-21(31)15-29-16-30(19-5-3-2-4-6-19)24(23(29)33)9-11-28(12-10-24)22(32)17-7-8-20-18(13-17)14-26-27-20/h2-8,13-14H,9-12,15-16H2,1H3,(H,25,31)(H,26,27)
InChIKeyQDMKAQVMVBLGFR-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CNC(=O)CN1CN(c2ccccc2)C3(CCN(CC3)C(=O)c4ccc5n[nH]cc5c4)C1=O
OpenEye OEToolkits 2.0.6CNC(=O)CN1CN(C2(C1=O)CCN(CC2)C(=O)c3ccc4c(c3)c[nH]n4)c5ccccc5
FormulaC24 H26 N6 O3
Name2-[8-(2~{H}-indazol-5-ylcarbonyl)-4-oxidanylidene-1-phenyl-1,3,8-triazaspiro[4.5]decan-3-yl]-~{N}-methyl-ethanamide
ChEMBLCHEMBL4646682
DrugBank
ZINC
PDB chain6fil Chain A Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6fil DNA-Encoded Library-Derived DDR1 Inhibitor Prevents Fibrosis and Renal Function Loss in a Genetic Mouse Model of Alport Syndrome.
Resolution1.73 Å
Binding residue
(original residue number in PDB)		V624 A653 K655 E672 M676 I685 M699 T701 M704 L767 A777 D778 F779
Binding residue
(residue number reindexed from 1)		V21 A34 K36 E53 M57 I66 M80 T82 M85 L148 A158 D159 F160
Annotation score1
Binding affinityMOAD: ic50=1.41uM
PDBbind-CN: -logKd/Ki=5.85,IC50=1.41uM
Enzymatic activity
Catalytic site (original residue number in PDB) D760 R764 N765 D778
Catalytic site (residue number reindexed from 1) D141 R145 N146 D159
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:6fil, PDBe:6fil, PDBj:6fil
PDBsum6fil
PubMed30452219
UniProtQ08345|DDR1_HUMAN Epithelial discoidin domain-containing receptor 1 (Gene Name=DDR1)

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