6L11 | pdb_00006l11

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

• PDB DOI: https://doi.org/10.2210/pdb6L11/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: 2.05 Å
• R-Value Free: 
  0.240 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

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 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.
National Institute of Biological Sciences, Beijing, Beijing 102206, China.
Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, 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: 33.65 kDa 
• Atom Count: 2,370 
• Modeled Residue Count: 273 
• 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
E2C (Subject of Investigation/LOI)	B [auth A]	5-(2-chloranylphenoxazin-10-yl)-~{N},~{N}-diethyl-pentan-1-amine C21 H27 Cl N2 O UVWATVYWPWOHHD-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: 2.05 Å
• R-Value Free:  0.240 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.915	α = 90
b = 97.915	β = 90
c = 80.718	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: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary