Structure of PDB 6p3d Chain A Binding Site BS01

Receptor Information
>6p3d Chain A (length=264) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KMDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQL
QAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHASE
TKFEMKKLIDIARQTARGMDYLHAKSIIHRDLKSNNIFLHEDNTVKIGDF
GLATESGSILWMAPEVIRMQDSNPYSFQSDVYAFGIVLYELMTGQLPYSN
INNRDQIIEMVGRGSLSPDLSKVRSNCPKRMKRLMAECLKKKRDERPSFP
RILAEIEELARELS
Ligand information
Ligand ID0LI
InChIInChI=1S/C29H27F3N6O/c1-20-5-6-22(16-21(20)8-10-25-18-33-27-4-3-11-34-38(25)27)28(39)35-24-9-7-23(26(17-24)29(30,31)32)19-37-14-12-36(2)13-15-37/h3-7,9,11,16-18H,12-15,19H2,1-2H3,(H,35,39)
InChIKeyPHXJVRSECIGDHY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CN1CCN(CC1)Cc2ccc(NC(=O)c3ccc(C)c(c3)C#Cc4cnc5cccnn45)cc2C(F)(F)F
ACDLabs 12.01FC(F)(F)c1cc(ccc1CN2CCN(C)CC2)NC(=O)c5cc(C#Cc3cnc4cccnn34)c(cc5)C
OpenEye OEToolkits 1.7.6Cc1ccc(cc1C#Cc2cnc3n2nccc3)C(=O)Nc4ccc(c(c4)C(F)(F)F)CN5CCN(CC5)C
FormulaC29 H27 F3 N6 O
Name3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-N-{4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl}benzam ide;
Ponatinib
ChEMBLCHEMBL1171837
DrugBankDB08901
ZINCZINC000036701290
PDB chain6p3d 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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PDB6p3d Inhibitors of BRAF dimers using an allosteric site.
Resolution2.11 Å
Binding residue
(original residue number in PDB)		A481 K483 E501 L514 I527 T529 W531 C532 I573 H574 F583 G593 D594 F595
Binding residue
(residue number reindexed from 1)		A36 K38 E56 L69 I82 T84 W86 C87 I128 H129 F138 G148 D149 F150
Annotation score1
Binding affinityMOAD: ic50=14nM
Enzymatic activity
Catalytic site (original residue number in PDB) D576 K578 N580 N581 D594 S616
Catalytic site (residue number reindexed from 1) D131 K133 N135 N136 D149 S158
Enzyme Commision number 2.7.11.1: non-specific serine/threonine protein kinase.
Gene Ontology
Molecular Function
GO:0004672 protein 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:6p3d, PDBe:6p3d, PDBj:6p3d
PDBsum6p3d
PubMed32873792
UniProtP15056|BRAF_HUMAN Serine/threonine-protein kinase B-raf (Gene Name=BRAF)

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