3QF9 | pdb_00003qf9

Crystal structure of human proto-oncogene serine threonine kinase (PIM1) in complex with a consensus peptide and a furan-thiazolidinedione ligand

• PDB DOI: https://doi.org/10.2210/pdb3QF9/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2011-01-21 Released: 2011-03-02 
• Deposition Author(s): Filippakopoulos, P., Bullock, A.N., Fedorov, O., Miduturu, C.V., von Delft, F., Arrowsmith, C.H., Weigelt, J., Edwards, A., Bountra, C., Grey, N., Knapp, S., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.227 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human proto-oncogene serine threonine kinase (PIM1) in complex with a consensus peptide and a furan-thiazolidinedione ligand

Filippakopoulos, P., Bullock, A.N., Fedorov, O., Miduturu, C.V., von Delft, F., Arrowsmith, C.H., Weigelt, J., Edwards, A., Bountra, C., Grey, N., Knapp, S., Structural Genomics Consortium (SGC)

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 PISA (software)

Macromolecule Content 

• Total Structure Weight: 37.88 kDa 
• Atom Count: 2,471 
• Modeled Residue Count: 283 
• Deposited Residue Count: 327 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene serine/threonine-protein kinase pim-1	A	313	Homo sapiens	Mutation(s): 1  Gene Names: PIM1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P11309 (Homo sapiens) Explore P11309  Go to UniProtKB:  P11309
PHAROS:  P11309 GTEx:  ENSG00000137193

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
pimtide	B	14	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NM8	C [auth A]	6-{5-[(Z)-(2,4-dioxo-1,3-thiazolidin-5-ylidene)methyl]furan-2-yl}-N-{3-[(4-ethylpiperazin-1-yl)methyl]-5-(trifluoromethyl)phenyl}naphthalene-1-carboxamide C33 H29 F3 N4 O4 S QFKROKXEJOKXGQ-MIXAMLLLSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.227 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.843	α = 90
b = 97.843	β = 90
c = 80.428	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-02 
Deposition Author(s): Filippakopoulos, P., Bullock, A.N., Fedorov, O., Miduturu, C.V., von Delft, F., Arrowsmith, C.H., Weigelt, J., Edwards, A., Bountra, C., Grey, N., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2011-03-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Refinement description