ISDA

Deposition Date 2016-10-04

Release Date 2017-10-04

Last Version Date 2024-10-23

Entry Detail

PDB ID:

5H0H

Keywords:

TRANSFERASE/TRANSFERASE INHIBITOR

Title:

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

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)

Host Organism:

Spodoptera frugiperda

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.72 Å

R-Value Free:

0.22

R-Value Work:

0.18

R-Value Observed:

0.18

Space Group:

P 21 21 21

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Tyrosine-protein kinase HCK
Gene (Uniprot):HCK
Mutations:Q523E, Q524E, Q525I
Chain IDs:A
Chain Length:454
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P08631 Pfam ID:PF00018, PF00017, PF07714 EC:2.7.10.2

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
PTR	A	TYR	modified residue

Ligand Molecules

OOV

Primary Citation

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.Show

Bioorg. Med. Chem. 25 4259 4264 (2017)

PMID: 28662963 DOI: 10.1016/j.bmc.2017.05.053

Abstact

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 IC50 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 IC50 values, and the crystal structures of the less potent derivatives showed various types of defects around the ionic bond.

Legend

Protein

Chemical

Disease

Primary Citation of related structures