Download MendeleyHuman 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.
6PDN
Human PIM1 bound to benzothiophene inhibitor 292
- PDB DOI: https://doi.org/10.2210/pdb6PDN/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
- Funding Organization(s): Sao Paulo Research Foundation (FAPESP)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.223
- R-Value Work: 0.188
- R-Value Observed: 0.190
This is version 1.2 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Serine/threonine-protein kinase pim-1 | 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 Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P11309 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| peptide | 14 | synthetic construct | Mutation(s): 0 |  | |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| OD4 (Subject of Investigation/LOI) Query on OD4 | C [auth A] | 4-{5-[(3-aminopropyl)carbamoyl]thiophen-2-yl}-1-benzothiophene-2-carboxylic acid C17 H16 N2 O3 S2 PPVOHCUEWCXUEU-UHFFFAOYSA-N |  | ||
| GOL Query on GOL | D [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| SEP Query on SEP | A | L-PEPTIDE LINKING | C3 H8 N O6 P |  | SER |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.223
- R-Value Work: 0.188
- R-Value Observed: 0.190
- Space Group: P 65
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 98.001 | α = 90 |
| b = 98.001 | β = 90 |
| c = 80.248 | γ = 120 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2019-07-24 Deposition Author(s): 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., Structural Genomics Consortium (SGC)
| Funding Organization | Location | Grant Number |
|---|---|---|
| Sao Paulo Research Foundation (FAPESP) | Brazil | 13/50724-5 |
Revision History (Full details and data files)
- Version 1.0: 2019-07-24
Type: Initial release - Version 1.1: 2020-01-01
Changes: Author supporting evidence - Version 1.2: 2024-10-23
Changes: Data collection, Database references, Structure summary
