6PDI

Human PIM1 bound to benzothiophene inhibitor 224

• PDB DOI: https://doi.org/10.2210/pdb6PDI/pdb

• Classification: TRANSFERASE/TRANSFERASE Inhibitor
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-06-19 Released: 2019-07-24 
• Deposition Author(s): Godoi, P.H.C., Fala, A.M., Santiago, A.S., Ramos, P.Z., Sriranganadane, D., Mascarello, A., Segretti, N., Azevedo, H., Guimaraes, C.R.W., Arruda, P., Elkins, J.M., Counago, R.M., Structural Genomics Consortium (SGC)
• Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.193 
• R-Value Work: 0.161 
• R-Value Observed: 0.163 

Literature

Human PIM1

Godoi, P.H.C., Santiago, A.S., Fala, A.M., Ramos, P.Z., Sriranganadane, D., Mascarello, A., Segretti, N., Azevedo, H., Guimaraes, C.R.W., Arruda, P., Elkins, J.M., Counago, R.M.

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: 38.08 kDa 
• Atom Count: 2,497 
• Modelled Residue Count: 284 
• 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): 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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide	B	14	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OCJ (Subject of Investigation/LOI)	C [auth A]	4-(5-{[(3-aminophenyl)methyl]carbamoyl}thiophen-2-yl)-1-benzothiophene-2-carboxamide C21 H17 N3 O2 S2 SDZHQRUPXPKDOD-UHFFFAOYSA-N
GOL	D [auth A], E [auth A], F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	H [auth A], I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.193 
• R-Value Work: 0.161 
• R-Value Observed: 0.163 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.961	α = 90
b = 96.961	β = 90
c = 80.065	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-07-24 
Deposition Author(s): Godoi, P.H.C., Fala, A.M., Santiago, A.S., Ramos, P.Z., Sriranganadane, D., Mascarello, A., Segretti, N., Azevedo, H., Guimaraes, C.R.W., Arruda, P., Elkins, J.M., Counago, R.M., Structural Genomics Consortium (SGC)

---

Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	13/50724-5

Revision History  

• Version 1.0: 2019-07-24
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references