8R0H | pdb_00008r0h

Pim1 in complex with (E)-3-(2-(thiophen-2-yl)vinyl)-3,4-dihydroquinoxalin-2(1H)-one and Pimtide

• PDB DOI: https://doi.org/10.2210/pdb8R0H/pdb

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


• Deposited: 2023-10-31 Released: 2024-11-13 
• Deposition Author(s): Hochban, P.M.M., Heine, A., Diederich, W.E.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 
  0.174 (Depositor), 0.173 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.153 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Starting Model: experimental

Literature

Pim1 in complex with (E)-3-(2-(thiophen-2-yl)vinyl)-3,4-dihydroquinoxalin-2(1H)-one and Pimtide

Hochban, P.M.M., Heyder, L., Heine, A., Diederich, W.E.

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: 37.7 kDa 
• Atom Count: 2,546 
• Modeled 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	14	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8UB (Subject of Investigation/LOI)	E [auth A]	3-(2-thiophen-2-ylethenyl)-1~{H}-quinoxalin-2-one C14 H10 N2 O S DPAFRZPZFHBARE-UHFFFAOYSA-N
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free:  0.174 (Depositor), 0.173 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.153 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.304	α = 90
b = 98.304	β = 90
c = 80.339	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-13 
Deposition Author(s): Hochban, P.M.M., Heine, A., Diederich, W.E.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-11-13
  Type: Initial release