5N4V

Crystal structure of human Pim-1 kinase in complex with a consensuspeptide and fragment like molekule 2-cyclopropyl-4,5-dimethylthieno[5,4-d]pyrimidine-6-carboxylic acid

• PDB DOI: https://doi.org/10.2210/pdb5N4V/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-02-11 Released: 2018-02-28 
• Deposition Author(s): Siefker, C., Heine, A., Klebe, G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.187 
• R-Value Work: 0.164 
• R-Value Observed: 0.165 

Starting Model: experimental

Literature

A crystallographic fragment study with human Pim-1 kinase

Siefker, C., Heine, A., Hardes, K., Steinmetzer, A., Klebe, G.

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: 37.57 kDa 
• Atom Count: 2,469 
• Modelled Residue Count: 282 
• Deposited Residue Count: 327 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
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 [auth D]	14	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8MW	C [auth A]	2-cyclopropyl-4,5-dimethyl-thieno[2,3-d]pyrimidine-6-carboxylic acid C12 H12 N2 O2 S SQXQFDZJONADBV-UHFFFAOYSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.187 
• R-Value Work: 0.164 
• R-Value Observed: 0.165 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.055	α = 90
b = 98.055	β = 90
c = 80.493	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-02-28 
Deposition Author(s): Siefker, C., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2018-02-28
  Type: Initial release
  
• Version 1.1: 2019-08-14
  Changes: Data collection
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description