Structure of PDB 1y57 Chain A Binding Site BS01

Receptor Information
>1y57 Chain A (length=452) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MVTTFVALYDYESRTETDLSFKKGERLQIVNNTEGDWWLAHSLSTGQTGY
IPSNYVAPSDSIQAEEWYFGKITRRESERLLLNAENPRGTFLVRESETTK
GAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFNSLQQLVAYYS
KHADGLCHRLTTVCPTSKPQTQGLAKDAWEIPRESLRLEVKLGQGCFGEV
WMGTWNGTTRVAIKTLKPGTMSPEAFLQEAQVMKKLRHEKLVQLYAVVSE
EPIYIVTEYMSKGSLLDFLKGETGKYLRLPQLVDMAAQIASGMAYVERMN
YVHRDLRAANILVGENLVCKVADFGLARLIEDNEYTARQGAKFPIKWTAP
EAALYGRFTIKSDVWSFGILLTELTTKGRVPYPGMVNREVLDQVERGYRM
PCPPECPESLHDLMCQCWRKEPEERPTFEYLQAFLEDYFTSTEPQYQPGE
NL
Ligand information
Ligand IDMPZ
InChIInChI=1S/C28H29N7O/c1-34-14-16-35(17-15-34)20-21-7-9-22(10-8-21)27(36)31-24-5-2-6-25(18-24)32-28-30-13-11-26(33-28)23-4-3-12-29-19-23/h2-13,18-19H,14-17,20H2,1H3,(H,31,36)(H,30,32,33)
InChIKeyJHMBUEWQJDGKGS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CN1CCN(CC1)Cc2ccc(cc2)C(=O)Nc3cccc(c3)Nc4nccc(n4)c5cccnc5
CACTVS 3.341CN1CCN(CC1)Cc2ccc(cc2)C(=O)Nc3cccc(Nc4nccc(n4)c5cccnc5)c3
ACDLabs 10.04O=C(Nc3cccc(Nc2nc(c1cccnc1)ccn2)c3)c4ccc(cc4)CN5CCN(CC5)C
FormulaC28 H29 N7 O
Name4-[(4-METHYLPIPERAZIN-1-YL)METHYL]-N-{3-[(4-PYRIDIN-3-YLPYRIMIDIN-2-YL)AMINO]PHENYL}BENZAMIDE;
4-[(4-METHYL-1-PIPERAZINYL)METHYL]-N-[3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]AMINO]PHENYL]-BENZAMIDE
ChEMBLCHEMBL56904
DrugBankDB04739
ZINCZINC000022794841
PDB chain1y57 Chain A Residue 600 [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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PDB1y57 The Crystal Structure of a c-Src Complex in an Active Conformation Suggests Possible Steps in c-Src Activation
Resolution1.91 Å
Binding residue
(original residue number in PDB)		L273 Q275 V281 A293 Y340 M341 G344 L393
Binding residue
(residue number reindexed from 1)		L192 Q194 V200 A212 Y259 M260 G263 L312
Annotation score1
Binding affinityMOAD: ic50=1633nM
PDBbind-CN: -logKd/Ki=5.79,IC50=1633nM
BindingDB: IC50=7800nM
Enzymatic activity
Catalytic site (original residue number in PDB) D386 R388 A390 N391 D404 F424
Catalytic site (residue number reindexed from 1) D305 R307 A309 N310 D323 F343
Enzyme Commision number 2.7.10.2: non-specific protein-tyrosine kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004713 protein tyrosine 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:1y57, PDBe:1y57, PDBj:1y57
PDBsum1y57
PubMed15939018
UniProtP12931|SRC_HUMAN Proto-oncogene tyrosine-protein kinase Src (Gene Name=SRC)

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