2O63

Crystal structure of Pim1 with Myricetin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.193

Literature

Macromolecules
Sequence Display for 2O63

Classification: TRANSFERASE

Total Structure Weight: 34357.81

Macromolecule Entities
Molecule Chains Length Organism Details
Proto-oncogene serine/threonine-protein kinase Pim-1 A 293 Homo sapiens EC#: 2.7.11.1 IUBMB
Fragment: CATALYTIC DOMAIN
Gene Name(s): PIM1 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A 3,5,7-TRIHYDROXY-2-(3,4,5-TRIHYDROXYPHENYL)- 4H-CHROMEN-4-ONE
4, (Synonym)
C15 H10 O8
IKMDFBPHZNJCSN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IMD
Query on IMD

A IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
MYC IC50: 776 - 780 nM (100) BindingDB

Kd: 780 nM  BindingMOAD
IC50: 780 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.193
  • Space Group: P 65

Unit Cell:

Length (Å) Angle (°)
a = 98.71 α = 90.00
b = 98.71 β = 90.00
c = 80.60 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-12-06
  • Released Date: 2007-02-13
  • Deposition author(s): Holder, S., Zemskova, M., Zhang, C., Tabrizizad, M., Bremer, R., Neidigh, J.W., Lilly, M.B.

Revision History

  • Version 1_0: 2007-02-13

    Type: Initial release

  • Version 1_1: 2008-05-01

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Version format compliance