5NDT

Crystal structure of human Pim-1 kinase in complex with a consensus peptide and fragment like molecule (E)-3-(2-(thiophen-2-yl)vinyl)-3,4-dihydroquinoxalin-2(1H)-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.985 Å
  • R-Value Free: 0.194 
  • 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
B
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
8UB
Query on 8UB

Download SDF File 
Download CCD File 
A
3-(2-thiophen-2-ylethenyl)-1~{H}-quinoxalin-2-one
C14 H10 N2 O S
DPAFRZPZFHBARE-UHFFFAOYSA-N
 Ligand Interaction
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.985 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.160 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 98.528α = 90.00
b = 98.528β = 90.00
c = 80.378γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
Cootmodel building
PHENIXrefinement
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 1.1: 2019-08-14
    Type: Data collection