2BIL

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

• PDB DOI: https://doi.org/10.2210/pdb2BIL/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2005-01-22 Released: 2005-02-07 
• Deposition Author(s): Knapp, S., Debreczeni, J., Bullock, A., von Delft, F., Sundstrom, M., Arrowsmith, C., Edwards, A., Guo, K.

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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

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 37.64 kDa 
• Atom Count: 2,343 
• Modelled Residue Count: 281 
• Deposited Residue Count: 327 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CONSENSUS PIM1 PEPTIDE PIMTIDE	A	14	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE PIM-1	B	313	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BI1	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
ID	Source	Binding 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 = 98.1	α = 90
b = 98.1	β = 90
c = 80.04	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-02-07 
Deposition Author(s): Knapp, S., Debreczeni, J., Bullock, A., von Delft, F., Sundstrom, M., Arrowsmith, C., Edwards, A., Guo, K.

Revision History  

• 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