Crystal structures of human CDK2 complexed with inhibitor

The image shows two crystal structures of human CDK2 in complex with inhibitors (1Y8Y, 2C6L). Structural interaction fingerprints (SIFts) were clustered (based on UniProt accession of the protein) and these two ligands were found to be neighbouring leaves on the same node. The structures can be loaded into PyMOL, aligned and the interactions visualised with command below. The resulting PyMOL scene can be downloaded from the bottom of this page.

from credopymol import *
 
In [1]: l1 = LigandAdaptor().fetchByLigandID(105120)
In [2]: l2 = LigandAdaptor().fetchByLigandID(126047)
 
In [3]: l1, l2
Out[3]: (Ligand(401, CT7, A), Ligand(1299, DT4, A))
 
In [4]: l1.Structure.title
Out[4]: 'CRYSTAL STRUCTURE OF HUMAN CDK2 COMPLEXED WITH A PYRAZOLO[1,5-A]PYRIMIDINE INHIBITOR'
 
In [5]: n = l1.getUniProtSIFtNode()
In [6]: n
Out[6]: <UniProtSIFtNode('P24941', -269L)>
 
# l1 and l2 are neighbours in SIFt clustering
In [7]: n.getChildren()
Out[7]: [Ligand(401, CT7, A), Ligand(1299, DT4, A)] 
 
# tanimoto similarity of node leaves
In [8]: n.Properties.tanimoto
Out[8]: 0.517
 
# USR shape similarity of node leaves
In [9]: n.Properties.usr
Out[9]: 0.568
 
In [10]: l1.Structure.load()
In [11]: l2.Structure.load()
 
In [12]: l1.Structure.Chains[0].align(l2.Structure.Chains[0])
 
In [13]: l1.showContacts()
In [14]: l2.showContacts()
 
In [15]: pymol.set('grid_mode',1)

Crystal structures of human CDK2 complexed with inhibitor
AttachmentSize
1Y8Y-2C6L-SIFt-GRID.pse1.52 MB