Crystal structure of HCK complexed with a pyrrolo-pyrimidine inhibitor (S)-2-(((1r,4S)-4-(4-amino-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)cyclohexyl)amino)-N,N,4-trimethylpentanamide

Experimental Data Snapshot

  • Resolution: 1.72 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

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This is version 1.2 of the entry. See complete history


Activity cliff for 7-substituted pyrrolo-pyrimidine inhibitors of HCK explained in terms of predicted basicity of the amine nitrogen.

Yuki, H.Kikuzato, K.Koda, Y.Mikuni, J.Tomabechi, Y.Kukimoto-Niino, M.Tanaka, A.Shirai, F.Shirouzu, M.Koyama, H.Honma, T.

(2017) Bioorg Med Chem 25: 4259-4264

  • DOI: https://doi.org/10.1016/j.bmc.2017.05.053
  • Primary Citation of Related Structures:  
    5H09, 5H0B, 5H0E, 5H0G, 5H0H

  • PubMed Abstract: 

    We previously reported the structure-based design of a highly potent hematopoietic cell kinase (HCK) inhibitor, a pyrrolo-pyrimidine compound designated RK-20449, for treatment of recurrent leukemia. Herein we report the synthesis and structure-activity relationships of some amino acid derivatives of 7-substituted pyrrolo-pyrimidine. Although these derivatives had the same predicted binding conformation as RK-20449, their IC 50 values were 100-1000 times larger than that of the parent compound. We assumed that the basicity of the amine nitrogen, which formed an ionic bond with Asp348 of HCK, markedly affected inhibitory activity against HCK. The pKa values of the nitrogen were predicted by means of an ab initio quantum mechanical method, and complexes of the derivatives with HCK were analyzed by X-ray crystallography. We observed a significant correlation between the predicted pKa and IC 50 values, and the crystal structures of the less potent derivatives showed various types of defects around the ionic bond.

  • Organizational Affiliation

    Drug Discovery Computational Chemistry Platform Unit, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase HCK454Homo sapiensMutation(s): 3 
Gene Names: HCK
UniProt & NIH Common Fund Data Resources
Find proteins for P08631 (Homo sapiens)
Explore P08631 
Go to UniProtKB:  P08631
PHAROS:  P08631
GTEx:  ENSG00000101336 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08631
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on OOV

Download Ideal Coordinates CCD File 
B [auth A](2~{S})-2-[[4-[4-azanyl-5-(4-phenoxyphenyl)pyrrolo[2,3-d]pyrimidin-7-yl]cyclohexyl]amino]-~{N},~{N},4-trimethyl-pentanamide
C32 H40 N6 O2
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on PTR
Binding Affinity Annotations 
IDSourceBinding Affinity
OOV BindingDB:  5H0H IC50: min: 686, max: 692 (nM) from 2 assay(s)
Binding MOAD:  5H0H IC50: 686 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.72 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.113α = 90
b = 85.623β = 90
c = 129.01γ = 90
Software Package:
Software NamePurpose
DENZOdata collection
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-04
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2023-11-15
    Changes: Data collection