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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Interaction pattern similarity measured by Grim
You can zoom onto the graph by using the mouse to make a selection

Binding Modes are compared using Grim.
For more information, please see the following publication: Desaphy J. et al. Encoding Protein-Ligand Interaction Patterns in Fingerprints and Graphs J. Chem. Inf. Model., 2013, 53 (3), pp 623-637
Binding modes are considered as similar when the similarity value is greater than 0.65


Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
3zpu M8B Gag-Pol polyprotein 3.4.23.16

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3zpu M8BGag-Pol polyprotein 3.4.23.16 1.433
3zpt M8YGag-Pol polyprotein 3.4.23.16 1.258
3zps EQMGag-Pol polyprotein 3.4.23.16 1.230
2xye CXGGag-Pol polyprotein / 1.041
2xyf G40Gag-Pol polyprotein / 1.025
2aqu DR7Gag-Pol polyprotein 3.4.23.16 0.821
4a6c QG9Gag-Pol polyprotein 3.4.23.16 0.818
2wkz 5AHGag-Pol polyprotein / 0.792
2uxz HI1Gag-Pol polyprotein 3.4.23.16 0.791
3oxx DR7Gag-Pol polyprotein 3.4.23.16 0.791
3em4 DR7Gag-Pol polyprotein 3.4.23.16 0.780
1ec2 BEJGag-Pol polyprotein 3.4.23.16 0.751
1ec3 MS3Gag-Pol polyprotein 3.4.23.16 0.748
1fg6 2NCGag-Pol polyprotein 3.4.23.16 0.739
3nyg 2NCGag-Pol polyprotein 3.4.23.16 0.737
3ekw DR7Gag-Pol polyprotein 3.4.23.16 0.736
4a4q UX9Pol protein / 0.734
2q5k AB1Protease / 0.732
1ffi 2NCGag-Pol polyprotein 3.4.23.16 0.730
1fgc 2NCGag-Pol polyprotein 3.4.23.16 0.728
3bxr DRRGag-Pol polyprotein 3.4.23.16 0.728
1ebk 0Q4Gag-Pol polyprotein 3.4.23.16 0.725
3el9 DR7Gag-Pol polyprotein 3.4.23.16 0.724
3nwx KVSGag-Pol polyprotein 3.4.23.16 0.723
2q54 MU1Protease / 0.721
3dck KVIProtease / 0.719
4a6b QG8Gag-Pol polyprotein 3.4.23.16 0.717
1hvi A77Protease / 0.714
3s85 LK0Gag-Pol polyprotein / 0.714
2cem 2AHPol protein / 0.712
2wl0 5AHGag-Pol polyprotein / 0.712
3tof 076Gag-Pol polyprotein 2.7.7.49 0.712
1izh Q50Protease / 0.711
3gga GGWGag-Pol polyprotein / 0.708
1a8k 0Q4Gag-Pol polyprotein 3.4.23.16 0.707
1hxw RITGag-Pol polyprotein / 0.706
2cen 4AHProtease / 0.705
1ff0 2NCGag-Pol polyprotein 3.4.23.16 0.704
3kfn 3TLGag-Pol polyprotein / 0.702
1hvl A76Gag-Pol polyprotein / 0.699
2b60 RITPol polyprotein / 0.699
3nwq 2NCGag-Pol polyprotein 3.4.23.16 0.699
3ndw RITGag-Pol polyprotein 3.4.23.16 0.698
3i2l 2NCProtease / 0.697
4k4p 3TLGag-Pol polyprotein / 0.697
3hzc 2NCProtease / 0.695
1daz 0Q4Gag-Pol polyprotein 3.4.23.16 0.694
1k2c 0Q4Gag-Pol polyprotein 3.4.23.16 0.694
1k2b 0Q4Gag-Pol polyprotein 3.4.23.16 0.693
3bvb 017Gag-Pol polyprotein 3.4.23.16 0.693
1m0b 0ZQGag-Pol polyprotein 3.4.23.16 0.692
2aoe 0Q4Gag-Pol polyprotein 3.4.23.16 0.691
1ebw BEIGag-Pol polyprotein 3.4.23.16 0.690
2qhc AB1Protease / 0.690
4njv RITProtease / 0.690
2ieo 017Protease / 0.689
1fej 2NCGag-Pol polyprotein 3.4.23.16 0.685
3d1x ROCGag-Pol polyprotein 3.4.23.16 0.685
1fmb HYBPol polyprotein / 0.684
3s54 017Protease / 0.683
3eky DR7Gag-Pol polyprotein 3.4.23.16 0.681
3nxe 2NCProtease / 0.681
3kf0 3TLGag-Pol polyprotein / 0.679
3jvy 017Gag-Pol polyprotein 3.4.23.16 0.678
2bqv A1AProtease / 0.676
2avm 2NCGag-Pol polyprotein 3.4.23.16 0.675
3d1y ROCGag-Pol polyprotein 3.4.23.16 0.675
3dcr KVSProtease / 0.674
1ec1 BEEGag-Pol polyprotein 3.4.23.16 0.673
1ida 0POGag-Pol polyprotein 3.4.23.47 0.673
3bva 2NCGag-Pol polyprotein 3.4.23.16 0.673
1hii C20Gag-Pol polyprotein / 0.671
2pk6 O33V-1 protease / 0.670
3kfr 3TLGag-Pol polyprotein / 0.670
3o9a K14Pol polyprotein / 0.669
3tl9 ROCGag-Pol polyprotein 3.4.23.16 0.669
2az9 3TLGag-Pol polyprotein 3.4.23.16 0.668
2p3c 3TLProtease / 0.668
3ggu 017Gag-Pol polyprotein 3.4.23.16 0.668
2f81 017Gag-Pol polyprotein 3.4.23.16 0.667
1zsr 0ZTGag-Pol polyprotein 3.4.23.16 0.666
3s56 ROCProtease / 0.665
1hos PHPGag-Pol polyprotein / 0.663
1a94 0Q4Gag-Pol polyprotein 3.4.23.16 0.662
1msn JE2Gag-Pol polyprotein 3.4.23.16 0.662
2z54 AB1Gag-Pol polyprotein 3.4.23.16 0.662
3mws 017Pol protein / 0.662
1hvs A77Gag-Pol polyprotein / 0.660
3el4 ROCGag-Pol polyprotein 3.4.23.16 0.660
3ggx GGXGag-Pol polyprotein / 0.660
1fff 0Q4Gag-Pol polyprotein 3.4.23.16 0.659
2fxe DR7Gag-Pol polyprotein 3.4.23.16 0.659
3el1 DR7Gag-Pol polyprotein 3.4.23.16 0.659
3sa7 55AProtease / 0.658
3slz 3TLPutative gag-pro-pol polyprotein / 0.658
3ndu ROCGag-Pol polyprotein 3.4.23.16 0.656
1sbg IM1Gag-Pol polyprotein / 0.655
3bxs DRSGag-Pol polyprotein 3.4.23.16 0.655
2fxd DR7Pol polyprotein / 0.654
3o9f K2DGag-Pol polyprotein / 0.654
1odw 0E8Gag-Pol polyprotein 3.4.23.16 0.653
1b11 3TLPol polyprotein / 0.652
1bdq IM1Gag-Pol polyprotein 3.4.23.16 0.652
3d20 017Gag-Pol polyprotein 3.4.23.16 0.652
3sa3 23XProtease / 0.651
2fdd 385Pol protein / 0.650
3tog 079Gag-Pol polyprotein 2.7.7.49 0.650