6NO9

PIM1 in complex with Cpd16 (5-amino-N-(5-((4R,5R)-4-amino-5-fluoroazepan-1-yl)-1-methyl-1H-pyrazol-4-yl)-2-(2,6-difluorophenyl)thiazole-4-carboxamide)

• PDB DOI: https://doi.org/10.2210/pdb6NO9/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-01-15 Released: 2019-02-27 
• Deposition Author(s): Murray, J.M., Noland, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 0.205 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 

Starting Model: experimental

Literature

Optimization of Pan-Pim Kinase Activity and Oral Bioavailability Leading to Diaminopyrazole (GDC-0339) for the Treatment of Multiple Myeloma.

Wang, X., Blackaby, W., Allen, V., Chan, G.K.Y., Chang, J.H., Chiang, P.C., Diene, C., Drummond, J., Do, S., Fan, E., Harstad, E.B., Hodges, A., Hu, H., Jia, W., Kofie, W., Kolesnikov, A., Lyssikatos, J.P., Ly, J., Matteucci, M., Moffat, J.G., Munugalavadla, V., Murray, J., Nash, D., Noland, C.L., Del Rosario, G., Ross, L., Rouse, C., Sharpe, A., Slaga, D., Sun, M., Tsui, V., Wallweber, H., Yu, S.F., Ebens, A.J.

(2019) J Med Chem 62: 2140-2153

• PubMed: 30715878 
• DOI: https://doi.org/10.1021/acs.jmedchem.8b01857
• Primary Citation of Related Structures:  
  6NO9


• PubMed Abstract: 
  

  Pim kinases have been targets of interest for a number of therapeutic areas. Evidence of durable single-agent efficacy in human clinical trials validated Pim kinase inhibition as a promising therapeutic approach for multiple myeloma patients. Here, we report the compound optimization leading to GDC-0339 (16), a potent, orally bioavailable, and well tolerated pan-Pim kinase inhibitor that proved efficacious in RPMI8226 and MM.1S human multiple myeloma xenograft mouse models and has been evaluated as an early development candidate.

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Organizational Affiliation: 

Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 32.27 kDa 
• Atom Count: 2,405 
• Modelled Residue Count: 273 
• Deposited Residue Count: 273 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase pim-1	A	273	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KUV	E [auth A]	5-amino-N-{5-[(4R,5R)-4-amino-5-fluoroazepan-1-yl]-1-methyl-1H-pyrazol-4-yl}-2-(2,6-difluorophenyl)-1,3-thiazole-4-carboxamide C20 H22 F3 N7 O S NHXVGMQFCYBLTL-ZWNOBZJWSA-N
PO4	C [auth A], D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
KUV	BindingDB:  6NO9	Ki: min: 0.03, max: 0.04 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 0.205 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.632	α = 90
b = 96.632	β = 90
c = 80.703	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-02-27 
Deposition Author(s): Murray, J.M., Noland, C.

Revision History  

• Version 1.0: 2019-02-27
  Type: Initial release
  
• Version 1.1: 2019-03-13
  Changes: Data collection, Database references
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description