1XWS

Crystal Structure of the human PIM1 kinase domain

Structural Biology Knowledgebase: 1XWS SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.213
  • R-Value Work: 0.180

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1XWS

Classification: TRANSFERASE

Total Structure Weight: 36241.61

Macromolecule Entities
Molecule Chains Length Organism Details
Proto-oncogene serine/threonine-protein kinase Pim-1 A 313 Homo sapiens EC#: 2.7.11.1 IUBMB
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
BI1
Query on BI1

A 3-{1-[3-(DIMETHYLAMINO)PROPYL]-1H-INDOL-3- YL}-4-(1H-INDOL-3-YL)-1H-PYRROLE-2,5-DIONE
RBT205 INHIBITOR (Synonym)
C25 H24 N4 O2
QMGUOJYZJKLOLH-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
BI1 IC50: 27 - 150 nM (100) BindingDB
Kd: 10 nM (100) BindingDB
ΔG: -43.5 kJ/mol (100) BindingDB
-TΔS: 16.1 kJ/mol (100) BindingDB

N/A in BindingMoad
Kd: 10 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.213
  • R-Value Work: 0.180
  • Space Group: P 65
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 99.55 α = 90.00
b = 99.55 β = 90.00
c = 80.06 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-11-02
  • Released Date: 2004-11-16
  • Deposition author(s): Knapp, S., Debreczeni, J., Bullock, A., von Delft, F., Sundstrom, M., Arrowsmith, C., Edwards, A., Guo, K.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor