Structure of PDB 4pms Chain A Binding Site BS01

Receptor Information
>4pms Chain A (length=283) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
CVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLDKMLVAVKALKESARQD
FQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHGDLNRFLRSHGP
DAKLLAGGEDVAPGPLGLGQLLAVASQVAAGMVYLAGLHFVHRDLATRNC
LVGQGLVVKIGDFGMSRDIYSTDYYRVRTMLPIRWMPPESILYRKFTTES
DVWSFGVVLWEIFTYGKQPWYQLSNTEAIDCITQGRELERPRACPPEVYA
IMRGCWQREPQQRHSIKDVHARLQALAQAHHHH
Ligand information
Ligand ID31X
InChIInChI=1S/C27H18N4O3/c32-27(33)23-15-21-22(31(23)16-24-29-26(34-30-24)18-8-2-1-3-9-18)13-14-28-25(21)20-12-6-10-17-7-4-5-11-19(17)20/h1-15H,16H2,(H,32,33)
InChIKeyBUVASZPZZZNEAY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2c1ccc(cc1)c2nc(no2)Cn3c4ccnc(c4cc3C(=O)O)c5cccc6c5cccc6
ACDLabs 12.01O=C(O)c1cc6c(n1Cc2nc(on2)c3ccccc3)ccnc6c5c4ccccc4ccc5
CACTVS 3.385OC(=O)c1cc2c(ccnc2c3cccc4ccccc34)n1Cc5noc(n5)c6ccccc6
FormulaC27 H18 N4 O3
Name4-(naphthalen-1-yl)-1-[(5-phenyl-1,2,4-oxadiazol-3-yl)methyl]-1H-pyrrolo[3,2-c]pyridine-2-carboxylic acid
ChEMBLCHEMBL3298162
DrugBank
ZINCZINC000098208379
PDB chain4pms Chain A Residue 801 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4pms Maximizing diversity from a kinase screen: identification of novel and selective pan-Trk inhibitors for chronic pain.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		V524 K544 L564 V573 F589 L657 D668 F669 G670 M671
Binding residue
(residue number reindexed from 1)		V24 K41 L58 V67 F83 L151 D162 F163 G164 M165
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.10,Kd=7.9nM
BindingDB: IC50=2300nM,Kd=7.9nM
Enzymatic activity
Catalytic site (original residue number in PDB) D650 A652 R654 N655 D668 S677 L689
Catalytic site (residue number reindexed from 1) D144 A146 R148 N149 D162 S171 L181
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:4pms, PDBe:4pms, PDBj:4pms
PDBsum4pms
PubMed24914455
UniProtP04629|NTRK1_HUMAN High affinity nerve growth factor receptor (Gene Name=NTRK1)

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