5N4R

Crystal structure of human Pim-1 kinase in complex with a consensus peptide and fragment like molecule 2-(azepan-1-yl)-1-(1H-indol-3-yl)propan-1-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase pim-1
A
313Homo sapiensMutation(s): 1 
Gene Names: PIM1
EC: 2.7.11.1
Find proteins for P11309 (Homo sapiens)
Go to Gene View: PIM1
Go to UniProtKB:  P11309
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Pimtide
E
14N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
8MQ
Query on 8MQ

Download SDF File 
Download CCD File 
A
2-(azepan-1-yl)-1-(1~{H}-indol-3-yl)propan-1-one
C17 H22 N2 O
OLYBVEMMSRDXDJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.160 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 98.121α = 90.00
b = 98.121β = 90.00
c = 80.457γ = 120.00
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
PHENIXrefinement
Cootmodel building
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2019-08-14
    Type: Data collection