6L16

Crystal structure of Ser/Thr kinase Pim1 in complex with 10-DEBC derivatives

• PDB DOI: https://doi.org/10.2210/pdb6L16/pdb

• Classification: TRANSFERASE/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-09-27 Released: 2020-05-27 
• Deposition Author(s): Zhang, W., Xie, Y., Cao, R., Huang, N., Zhou, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.218 
• R-Value Work: 0.198 
• R-Value Observed: 0.199 

Starting Model: experimental

Literature

Structure-Based Optimization of 10-DEBC Derivatives as Potent and Selective Pim-1 Kinase Inhibitors.

Li, G., Zhang, W., Xie, Y., Li, Y., Cao, R., Zheng, G., Huang, N., Zhou, Y.

(2020) J Chem Inf Model 60: 3287-3294

• PubMed: 32407627 
• DOI: https://doi.org/10.1021/acs.jcim.0c00245
• Primary Citation of Related Structures:  
  6KZI, 6L11, 6L12, 6L13, 6L14, 6L15, 6L16, 6L17


• PubMed Abstract: 
  

  Pim-1 kinase has been widely regarded as an attractive target for anticancer drugs. Here, we reported our continued efforts in structure-based optimization of compound 10-DEBC, a previously identified micromolar Pim-1 inhibitor. Guided by the Site Identification by Ligand Competitive Saturation (SILCS) method, we quickly obtained a series of 10-DEBC derivatives with significantly improved activity and selectivity. In particular, compound 26 exhibited an IC ₅₀ value of 0.9 nM, as well as 220- and 8-fold selectivity over Pim-2 and Pim-3 kinases, respectively.

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Organizational Affiliation: 

State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing 100029, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 33.67 kDa 
• Atom Count: 2,258 
• Modelled Residue Count: 270 
• Deposited Residue Count: 289 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase pim-1	A	289	Homo sapiens	Mutation(s): 0  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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E2U (Subject of Investigation/LOI)	B [auth A]	2-[4-[2-(7-chloranylpyrido[3,4-b][1,4]benzoxazin-5-yl)ethyl]piperidin-1-yl]ethanamine C20 H25 Cl N4 O JTIZNTMOQMLDDF-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: 2.10 Å
• R-Value Free: 0.218 
• R-Value Work: 0.198 
• R-Value Observed: 0.199 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.031	α = 90
b = 98.031	β = 90
c = 80.915	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SCALEPACK	data scaling
PHASES	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-05-27 
Deposition Author(s): Zhang, W., Xie, Y., Cao, R., Huang, N., Zhou, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	21807007

Revision History  

• Version 1.0: 2020-05-27
  Type: Initial release
  
• Version 1.1: 2020-07-08
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Advisory, Data collection, Database references, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary