5KGD

Crystal structure of PIM1 with inhibitor: 2-pyridin-3-yl-1~{H}-benzimidazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure of PIM1 in complex with inhibitor

Ferguson, A.D.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase pim-1
A
276Homo sapiensMutation(s): 0 
Gene Names: PIM1
EC: 2.7.11.1
Find proteins for P11309 (Homo sapiens)
Go to Gene View: PIM1
Go to UniProtKB:  P11309
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
6SL
Query on 6SL

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Download CCD File 
A
2-pyridin-3-yl-1~{H}-benzimidazole
C12 H9 N3
BOUOQESVDURNSB-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.162 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 97.585α = 90.00
b = 97.585β = 90.00
c = 80.962γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
SCALAdata scaling
BUSTERrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-06-13 
  • Released Date: 2017-08-09 
  • Deposition Author(s): Ferguson, A.D.

Revision History 

  • Version 1.0: 2017-08-09
    Type: Initial release