Structure of PDB 6fer Chain A Binding Site BS01

Receptor Information
>6fer Chain A (length=271) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VAVEEFPRKLLTFKEKLGEGQFGEVHLCEVEGPVLVAVKMLRADANKNAR
NDFLKEIKIMSRLKDPNIIHLLAVCITDDPLCMITEYMENGDLNQFLSRH
TVSYTNLKFMATQIASGMKYLSSLNFVHRDLATRNCLVGKNYTIKIADFG
MSRNLYSGDYYRIQGRAVLPIRWMSWESILLGKFTTASDVWAFGVTLWET
FTFCQEQPYSQLSDEQVIENTGEFFRDQGRQTYLPQPAICPDSVYKLMLS
CWRRDTKNRPSFQEIHLLLLQ
Ligand information
Ligand IDD6Q
InChIInChI=1S/C23H19F5N6O3/c24-14-1-2-15-17(18(14)25)22(21(37)34(15)10-16(35)30-11-23(26,27)28)3-5-33(6-4-22)20(36)13-7-12-9-31-32-19(12)29-8-13/h1-2,7-9H,3-6,10-11H2,(H,30,35)(H,29,31,32)
InChIKeyIJPAFYMYOCLEBL-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Fc1ccc2N(CC(=O)NCC(F)(F)F)C(=O)C3(CCN(CC3)C(=O)c4cnc5[nH]ncc5c4)c2c1F
OpenEye OEToolkits 2.0.6c1cc(c(c2c1N(C(=O)C23CCN(CC3)C(=O)c4cc5cn[nH]c5nc4)CC(=O)NCC(F)(F)F)F)F
FormulaC23 H19 F5 N6 O3
Name2-[4,5-bis(fluoranyl)-2-oxidanylidene-1'-(1~{H}-pyrazolo[3,4-b]pyridin-5-ylcarbonyl)spiro[indole-3,4'-piperidine]-1-yl]-~{N}-[2,2,2-tris(fluoranyl)ethyl]ethanamide
ChEMBL
DrugBank
ZINC
PDB chain6fer Chain A Residue 1001 [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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PDB6fer DNA-Encoded Library-Derived DDR1 Inhibitor Prevents Fibrosis and Renal Function Loss in a Genetic Mouse Model of Alport Syndrome.
Resolution2.87 Å
Binding residue
(original residue number in PDB)		L616 V624 M676 I685 M699 T701 Y703 M704 F753 L764 A774 D775 F776
Binding residue
(residue number reindexed from 1)		L17 V25 M60 I69 M83 T85 Y87 M88 F126 L137 A147 D148 F149
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.36,IC50=44.1uM
Enzymatic activity
Catalytic site (original residue number in PDB) D757 R761 N762 D775
Catalytic site (residue number reindexed from 1) D130 R134 N135 D148
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:6fer, PDBe:6fer, PDBj:6fer
PDBsum6fer
PubMed30452219
UniProtQ16832|DDR2_HUMAN Discoidin domain-containing receptor 2 (Gene Name=DDR2)

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