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


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
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A crystallographic fragment study with human Pim-1 kinase

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

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase pim-1313Homo sapiensMutation(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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11309
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PimtideB [auth D]14Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8MW
Query on 8MW

Download Ideal Coordinates CCD File 
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
Query on GOL

Download Ideal Coordinates CCD File 
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 = 98.055α = 90
b = 98.055β = 90
c = 80.493γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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