Download MendeleyA crystallographic fragment study with human Pim-1 kinase
Siefker, C., Heine, A., Hardes, K., Steinmetzer, A., Klebe, G.To be published.
5N4R
Crystal structure of human Pim-1 kinase in complex with a consensus peptide and fragment like molecule 2-(azepan-1-yl)-1-(1H-indol-3-yl)propan-1-one
- PDB DOI: https://doi.org/10.2210/pdb5N4R/pdb
- Classification: TRANSFERASE
- Organism(s): Homo sapiens
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes
- Deposited: 2017-02-11 Released: 2018-02-28
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.13 Å
- R-Value Free: 0.193
- R-Value Work: 0.160
- R-Value Observed: 0.162
Starting Model: experimental
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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): 1 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 | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Pimtide | B [auth E] | 14 | Homo sapiens | 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 | |
| 8MQ Query on 8MQ | D [auth A] | 2-(azepan-1-yl)-1-(1~{H}-indol-3-yl)propan-1-one C17 H22 N2 O OLYBVEMMSRDXDJ-UHFFFAOYSA-N |  | ||
| GOL Query on GOL | C [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.13 Å
- R-Value Free: 0.193
- R-Value Work: 0.160
- R-Value Observed: 0.162
- Space Group: P 65
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 98.121 | α = 90 |
| b = 98.121 | β = 90 |
| c = 80.457 | γ = 120 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| XDS | data scaling |
| PHASER | phasing |
| Coot | model building |
Entry History
Deposition Data
- Released Date: 2018-02-28 Deposition Author(s): Siefker, C., Heine, A., Klebe, G.
Revision History (Full details and data files)
- Version 1.0: 2018-02-28
Type: Initial release - Version 1.1: 2019-08-14
Changes: Data collection - Version 1.2: 2024-01-17
Changes: Data collection, Database references, Refinement description
