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 5BMS | pdb_00005bms

Crystal structure of P21-activated kinase 4 in complex with an inhibitor compound 29


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.230 (Depositor), 0.236 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 

Literature

Structure-Guided Design of Group I Selective p21-Activated Kinase Inhibitors.

Crawford, J.J., Lee, W., Aliagas, I., Mathieu, S., Hoeflich, K.P., Zhou, W., Wang, W., Rouge, L., Murray, L., La, H., Liu, N., Fan, P.W., Cheong, J., Heise, C.E., Ramaswamy, S., Mintzer, R., Liu, Y., Chao, Q., Rudolph, J.

(2015) J Med Chem 58: 5121-5136

  • DOI: https://doi.org/10.1021/acs.jmedchem.5b00572
  • Primary Citation Related Structures: 
    4ZY4, 4ZY5, 4ZY6, 5BMS

  • PubMed Abstract: 

    The p21-activated kinases (PAKs) play important roles in cytoskeletal organization, cellular morphogenesis, and survival and have generated significant attention as potential therapeutic targets for cancer. Following a high-throughput screen, we identified an aminopyrazole scaffold-based series that was optimized to yield group I selective PAK inhibitors. A structure-based design effort aimed at targeting the ribose pocket for both potency and selectivity led to much-improved group I vs II selectivity. Early lead compounds contained a basic primary amine, which was found to be a major metabolic soft spot with in vivo clearance proceeding predominantly via N-acetylation. We succeeded in identifying replacements with improved metabolic stability, leading to compounds with lower in vivo rodent clearance and excellent group I PAK selectivity.


  • Organizational Affiliation: 
    • #Shanghai Chempartner Inc., 998 Halei Road, Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai 201203, People's Republic of China.

Macromolecule Content 

  • Total Structure Weight: 33.45 kDa 
  • Atom Count: 2,326 
  • Modeled Residue Count: 291 
  • Deposited Residue Count: 293 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PAK 4293Homo sapiensMutation(s): 0 
Gene Names: PAK4, KIAA1142
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O96013 (Homo sapiens)
Explore O96013 
Go to UniProtKB:  O96013
PHAROS:  O96013
GTEx:  ENSG00000130669 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO96013
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4T6

Query on 4T6



Download:Ideal Coordinates CCD File
B [auth A]N~2~-[(7-chloro-1H-benzimidazol-6-yl)methyl]-N~4~-(5-cyclopropyl-1H-pyrazol-3-yl)pyrimidine-2,4-diamine
C18 H17 Cl N8
DYLHVDVCWIEYSA-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains Modified ResidueModification TypeFormula2D Diagram
SEP
Query on SEP
SERPhosphorylationC3 H8 N O6 P

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.230 (Depositor), 0.236 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.412α = 90
b = 64.412β = 90
c = 185.146γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-01
    Type: Initial release
  • Version 1.1: 2015-07-15
    Changes: Database references
  • Version 1.2: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary