3BGQ

Human Pim-1 kinase in complex with an triazolo pyridazine inhibitor VX2

• PDB DOI: https://doi.org/10.2210/pdb3BGQ/pdb

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


• Deposited: 2007-11-27 Released: 2007-12-11 
• Deposition Author(s): Jacobs, M.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.230 
• R-Value Work: 0.212 
• R-Value Observed: 0.213 

Literature

Docking study yields four novel inhibitors of the protooncogene pim-1 kinase.

Pierce, A.C., Jacobs, M., Stuver-Moody, C.

(2008) J Med Chem 51: 1972-1975

• PubMed: 18290603 
• DOI: https://doi.org/10.1021/jm701248t
• Primary Citation of Related Structures:  
  3BGP, 3BGQ, 3BGZ


• PubMed Abstract: 
  

  To supplement the hits from a high throughput screen, docking was performed against Pim-1 kinase. Glide docking was augmented with a filter to require traditional or aromatic CH..O hydrogen bonds to the kinase hinge. Four diverse actives, of 96 molecules assayed, had K(i) values between 0.091 and 4.5 microM. This gives a 14-fold enrichment over the earlier HTS run, and the two crystal structures solved confirmed the binding modes predicted by docking.

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Organizational Affiliation: 

Vertex Pharmaceuticals Incorporated, 130 Waverly Street, Cambridge, MA 02139, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 38.35 kDa 
• Atom Count: 2,359 
• Modelled Residue Count: 273 
• Deposited Residue Count: 333 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene serine/threonine-protein kinase Pim-1	A	333	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
VX2	B [auth A]	N-cyclohexyl-3-[3-(trifluoromethyl)phenyl][1,2,4]triazolo[4,3-b]pyridazin-6-amine C18 H18 F3 N5 XYYDXQCAYXOGQT-UHFFFAOYSA-N

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

Binding Affinity Annotations
ID	Source	Binding Affinity
VX2	BindingDB:  3BGQ	Ki: 11 (nM) from 1 assay(s)
	PDBBind:  3BGQ	Ki: 11 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.230 
• R-Value Work: 0.212 
• R-Value Observed: 0.213 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.34	α = 90
b = 98.34	β = 90
c = 81.35	γ = 120

Software Package:

Software Name	Purpose
d*TREK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
d*TREK	data reduction
CNX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-11 
Deposition Author(s): Jacobs, M.D.

Revision History  

• Version 1.0: 2007-12-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary