› 7z6u

X-ray diffraction
2.28Å resolution

Pim1 in complex with (E)-4-((6-amino-2-oxoindolin-3-ylidene)methyl)benzoic acid and Pimtide

Released:
DOI: 10.2210/pdb7z6u/pdb
Model geometry
Fit model/data
PDB entry 7z6u coloured by chain, front view.
PDB entry 7z6u coloured by chain, side view.
PDB entry 7z6u coloured by chain, top view.
Source organisms:
Primary publication:
Pose, duplicate, then elaborate: Steps towards increased affinity for inhibitors targeting the specificity surface of the Pim-1 kinase.
Heyder L, Hochban PMM, Taylor C, Chevillard F, Siefker C, Iking C, Borchardt H, Aigner A, Klebe G, Heine A, Kolb P, Diederich WE
Eur J Med Chem 245 114914 (2023)
PMID: 36410167

Function and Biology Details

Reaction catalysed: 
ATP + a protein = ADP + a phosphoprotein
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-273161 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Serine/threonine-protein kinase pim-1 Chain: A
Molecule details ›
Chain: A
Length: 313 amino acids
Theoretical weight: 35.71 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P11309 (Residues: 1-313; Coverage: 100%)
Gene name: PIM1
Sequence domains: Protein kinase domain
Pimtide Chain: D
Molecule details ›
Chain: D
Length: 14 amino acids
Theoretical weight: 1.59 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand GOL 1 x GOL
Ligand IJB 1 x IJB
1 modified residue:
Ligand SEP 1 x SEP

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P65
Unit cell:
a: 97.797Å b: 97.797Å c: 80.067Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.163 0.162 0.191
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

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