› 1z5m

X-ray diffraction
2.17Å resolution

Crystal Structure Of N1-[3-[[5-bromo-2-[[3-[(1-pyrrolidinylcarbonyl)amino]phenyl]amino]-4-pyrimidinyl]amino]propyl]-2,2-dimethylpropanediamide Complexed with Human PDK1

Released:
DOI: 10.2210/pdb1z5m/pdb
PDB entry 1z5m coloured by chain, front view.
PDB entry 1z5m coloured by chain, side view.
PDB entry 1z5m coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Novel small molecule inhibitors of 3-phosphoinositide-dependent kinase-1.
Feldman RI, Wu JM, Polokoff MA, Kochanny MJ, Dinter H, Zhu D, Biroc SL, Alicke B, Bryant J, Yuan S, Buckman BO, Lentz D, Ferrer M, Whitlow M, Adler M, Finster S, Chang Z, Arnaiz DO
J Biol Chem 280 19867-74 (2005)
PMID: 15772071

Function and Biology Details

Reaction catalysed: 
ATP + a protein = ADP + a phosphoprotein
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-127511 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
3-phosphoinositide-dependent protein kinase 1 Chain: A
Molecule details ›
Chain: A
Length: 286 amino acids
Theoretical weight: 33.13 KDa
Source organism: Homo sapiens
Expression system: unidentified baculovirus
UniProt:
  • Canonical: O15530 (Residues: 74-359; Coverage: 51%)
Gene names: PDK1, PDPK1
Sequence domains: Protein kinase domain
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand SO4 1 x SO4
Ligand CL 1 x CL
Ligand LI8 1 x LI8
Ligand GOL 3 x GOL
1 modified residue:
Ligand SEP 1 x SEP

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.1
Spacegroup: P3221
Unit cell:
a: 124.61Å b: 124.61Å c: 46.97Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.232 0.212 0.269
Expression system: unidentified baculovirus

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Citations

26 review citations

Ras/Raf/MEK/ERK and PI3K/PTEN/Akt/mTOR inhibitors: rationale and importance to inhibiting these pathways in human health.
Chappell et al. (2011)
25 more

5 mentions without citation

Design, Synthesis and Biological Activity Evaluation of S-Substituted 1H-5-Mercapto-1,2,4-Triazole Derivatives as Antiproliferative Agents in Colorectal Cancer.
Mioc et al. (2018)
4 more