1Y57

Structure of unphosphorylated c-Src in complex with an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.213
  • R-Value Work: 0.188

Literature

Macromolecules
Sequence Display for 1Y57

Classification: TRANSFERASE

Total Structure Weight: 52589.48

Macromolecule Entities
Molecule Chains Length Organism Details
Proto-oncogene tyrosine-protein kinase Src A 452 Homo sapiens EC#: 2.7.10.2 IUBMB
Fragment: SH3 SH2 and KINASE domains
Gene Name(s): SRC Gene View SRC1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MPZ
Query on MPZ

A 4-[(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 (Synonym)
C28 H29 N7 O
JHMBUEWQJDGKGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
MPZ IC50: 7800 nM (100) BindingDB

IC50: 1633 nM  BindingMOAD
IC50: 1633 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.213
  • R-Value Work: 0.188
  • Space Group: P 41 21 2

Unit Cell:

Length (Å) Angle (°)
a = 106.21 α = 90.00
b = 106.21 β = 90.00
c = 123.73 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-12-02
  • Released Date: 2005-06-21
  • Deposition author(s): Cowan-Jacob, S.W., Fendrich, G., Manley, P.W., Jahnke, W., Fabbro, D., Liebetanz, J., Meyer, T.

Revision History

  • Version 1_0: 2005-06-21

    Type: Initial release

  • Version 1_1: 2008-04-30

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Advisory, Version format compliance

  • Version 1_3: 2015-04-15

    Type: Database references