Alignment of CDK2 and JNK crystal structures complexed with inhibitors

The image shows the structural interactions of the bound inhibitors in the aligned chains 'A' of 2C4G and 2P33. Both ligands were found to be leaves of the same node in a SCOP-based SIFt clustering.

In [1]: from credopymol import *
In [2]: s = StructureAdaptor().fetchByPDB('2p33')
In [3]: l = s.Ligands[0]
 
# Get node based on SCOP-based SIFt clustering
In [4]: node = l.getScopSIFtNode()
In [5]: node
Out[5]: <ScopSIFtNode('88854', -1276L)>
 
# Return all leaves for this node (ligands)
In [6]: leaves = node.getLeaves()
In [7]: leaves
Out[7]:
[Ligand(1904, PP2, A),
 Ligand(507, J07, A),
 Ligand(306, 514, A),
 Ligand(2020, IRE, A),
 Ligand(501, 39Z, A),
 Ligand(501, 517, A)]
 
In [8]: x = leaves[2]
In [9]: x
Out[9]: Ligand(306, 514, A)
 
In [10]: s.load()
In [11]: x.Structure.load()
 
# Align chains
In [12]: s.Chains[0].align(x.Structure.Chains[0])
 
In [13]: l.showContacts()
In [14]: x.showContacts()
 
In [15]: pymol.set('grid_mode',1)

Alignment of CDK2 and JNK crystal structures complexed with inhibitors
AttachmentSize
2P33-2C4G-SCOP-SIFT.pse3.63 MB