3CY3

Crystal structure of human proto-oncogene serine threonine kinase (PIM1) in complex with a consensus peptide and the JNK inhibitor V


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Proto-oncogene serine threonine kinase (PIM1) in complex with a consensus peptide and the JNK inhibitor V.

Filippakopoulos, P.Bullock, A.Fedorov, O.Pike, A.C.W.von Delft, F.Arrowsmith, C.H.Edwards, A.M.Bountra, C.Knapp, S.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proto-oncogene serine/threonine-protein kinase Pim-1, Isoform 2
A
314Homo sapiensGene Names: PIM1
EC: 2.7.11.1
Find proteins for P11309 (Homo sapiens)
Go to Gene View: PIM1
Go to UniProtKB:  P11309
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Pimtide peptide
B
14N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JN5
Query on JN5

Download SDF File 
Download CCD File 
A
(2S)-1,3-benzothiazol-2-yl{2-[(2-pyridin-3-ylethyl)amino]pyrimidin-4-yl}ethanenitrile
C20 H16 N6 S
RCYPVQCPYKNSTG-OAHLLOKOSA-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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
JN5IC50: 80 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.163 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 98.239α = 90.00
b = 98.239β = 90.00
c = 80.723γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement
CrystalCleardata collection
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Author supporting evidence