2BIL

The human protein kinase Pim1 in complex with its consensus peptide Pimtide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history


Literature

The Human Protein Kinase Pim1 in Complex with its Consensus Peptide Pimtide

Knapp, S.Debreczeni, J.Bullock, A.von Delft, F.Sundstrom, M.Arrowsmith, C.Edwards, A.Guo, K.

To be published.

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CONSENSUS PIM1 PEPTIDE PIMTIDE14Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE PIM-1313Homo sapiensMutation(s): 1 
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P11309 (Homo sapiens)
Explore P11309 
Go to UniProtKB:  P11309
PHAROS:  P11309
GTEx:  ENSG00000137193 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11309
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BI1
Query on BI1

Download Ideal Coordinates CCD File 
C [auth B]3-{1-[3-(DIMETHYLAMINO)PROPYL]-1H-INDOL-3-YL}-4-(1H-INDOL-3-YL)-1H-PYRROLE-2,5-DIONE
C25 H24 N4 O2
QMGUOJYZJKLOLH-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
BI1 BindingDB:  2BIL Kd: 10 (nM) from 1 assay(s)
IC50: min: 27, max: 150 (nM) from 2 assay(s)
-TΔS: 16.08 (kJ/mol) from 1 assay(s)
ΔG: -4.35e+1 (kJ/mol) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.1α = 90
b = 98.1β = 90
c = 80.04γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-02-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Database references, Structure summary
  • Version 1.3: 2019-03-06
    Changes: Data collection, Experimental preparation
  • Version 1.4: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 1.5: 2019-10-23
    Changes: Data collection, Database references, Other
  • Version 1.6: 2023-12-13
    Changes: Data collection, Database references, Refinement description