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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
3tog 079 Gag-Pol polyprotein 2.7.7.49

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3tog 079Gag-Pol polyprotein 2.7.7.49 1.335
3toh 079Gag-Pol polyprotein 2.7.7.49 0.954
3tof 076Gag-Pol polyprotein 2.7.7.49 0.891
2pk5 075Protease / 0.828
2a1e IPFGag-Pol polyprotein 3.4.23.16 0.827
3ekw DR7Gag-Pol polyprotein 3.4.23.16 0.818
2qi5 MZ7Gag-Pol polyprotein / 0.809
1hpx KNIGag-Pol polyprotein / 0.801
3ndt ROCGag-Pol polyprotein 3.4.23.16 0.796
3ndu ROCGag-Pol polyprotein 3.4.23.16 0.795
3dcr KVSProtease / 0.788
3kfr 3TLGag-Pol polyprotein / 0.784
2p3b 3TLV-1 PROTEASE protein / 0.772
2p3b 3TLV-1 protease / 0.772
3i2l 2NCProtease / 0.770
1vik BAYGag-Pol polyprotein / 0.769
2cen 4AHProtease / 0.769
3sa3 23XProtease / 0.766
1d4l PI9Gag-Pol polyprotein 3.4.23.16 0.765
1hxb ROCGag-Pol polyprotein 3.4.23.16 0.764
3tl9 ROCGag-Pol polyprotein 3.4.23.16 0.764
1hvs A77Gag-Pol polyprotein / 0.761
2aqu DR7Gag-Pol polyprotein 3.4.23.16 0.758
4k4p 3TLGag-Pol polyprotein / 0.752
3gi6 D78Gag-Pol polyprotein / 0.750
2fxe DR7Gag-Pol polyprotein 3.4.23.16 0.746
2pk6 O33V-1 protease / 0.745
3kf0 3TLGag-Pol polyprotein / 0.744
2q54 MU1Protease / 0.743
3sa7 55AProtease / 0.743
3fx5 KNIGag-Pol polyprotein 3.4.23.16 0.741
2wl0 5AHGag-Pol polyprotein / 0.739
1hvk A79Gag-Pol polyprotein / 0.737
2p3d 3TLProtease / 0.734
1fff 0Q4Gag-Pol polyprotein 3.4.23.16 0.732
1ida 0POGag-Pol polyprotein 3.4.23.47 0.732
3ekp 478Gag-Pol polyprotein 3.4.23.16 0.731
3nyg 2NCGag-Pol polyprotein 3.4.23.16 0.728
3kfs 3TLGag-Pol polyprotein / 0.727
2p3a 3TLPol protein / 0.726
3gga GGWGag-Pol polyprotein / 0.726
3em4 DR7Gag-Pol polyprotein 3.4.23.16 0.725
3el4 ROCGag-Pol polyprotein 3.4.23.16 0.723
3d1y ROCGag-Pol polyprotein 3.4.23.16 0.722
1hvj A78Gag-Pol polyprotein / 0.721
3cyx ROCGag-Pol polyprotein 3.4.23.16 0.719
9hvp 0E9Gag-Pol polyprotein / 0.719
2wkz 5AHGag-Pol polyprotein / 0.718
1ody LP1Gag-Pol polyprotein 3.4.23.16 0.716
3el1 DR7Gag-Pol polyprotein 3.4.23.16 0.716
1ivq 0PXGag-Pol polyprotein / 0.714
3el9 DR7Gag-Pol polyprotein 3.4.23.16 0.714
3slz 3TLPutative gag-pro-pol polyprotein / 0.714
1ebk 0Q4Gag-Pol polyprotein 3.4.23.16 0.712
1zsf 0ZSGag-Pol polyprotein 3.4.23.16 0.712
1ffi 2NCGag-Pol polyprotein 3.4.23.16 0.711
1sh9 RITGag-Pol polyprotein 3.4.23.16 0.711
3sab F78Protease / 0.711
1n49 RITGag-Pol polyprotein 3.4.23.16 0.710
1fej 2NCGag-Pol polyprotein 3.4.23.16 0.708
1hvi A77Protease / 0.708
4a4q UX9Pol protein / 0.707
1jld 0PPGag-Pol polyprotein / 0.706
1hos PHPGag-Pol polyprotein / 0.703
1a94 0Q4Gag-Pol polyprotein 3.4.23.16 0.702
2cem 2AHPol protein / 0.702
1a9m U0EGag-Pol polyprotein / 0.701
1dif A85Gag-Pol polyprotein / 0.701
3bxs DRSGag-Pol polyprotein 3.4.23.16 0.701
1hih C20Gag-Pol polyprotein / 0.700
3tlh 3TLGag-Pol polyprotein 3.4.23.16 0.700
3zps EQMGag-Pol polyprotein 3.4.23.16 0.700
2bqv A1AProtease / 0.699
3zpt M8YGag-Pol polyprotein 3.4.23.16 0.699
3ndx RITGag-Pol polyprotein 3.4.23.16 0.698
2fmb LP1Reverse transcriptase / 0.696
2qi1 MZ4Gag-Pol polyprotein / 0.696
1fg6 2NCGag-Pol polyprotein 3.4.23.16 0.695
1hxw RITGag-Pol polyprotein / 0.695
2az8 3TLGag-Pol polyprotein 3.4.23.16 0.695
3ndw RITGag-Pol polyprotein 3.4.23.16 0.695
3eky DR7Gag-Pol polyprotein 3.4.23.16 0.694
1fgc 2NCGag-Pol polyprotein 3.4.23.16 0.693
1rl8 RITGag-Pol polyprotein 3.4.23.16 0.693
3ekq ROCGag-Pol polyprotein 3.4.23.16 0.693
4njv RITProtease / 0.693
3sa6 F71Protease / 0.692
1iiq 0ZRGag-Pol polyprotein 3.4.23.16 0.691
2qhc AB1Protease / 0.691
1hiv 1ZKGag-Pol polyprotein / 0.690
3nwx KVSGag-Pol polyprotein 3.4.23.16 0.690
2q55 MU0Protease / 0.689
3d1x ROCGag-Pol polyprotein 3.4.23.16 0.689
3ggx GGXGag-Pol polyprotein / 0.689
1fg8 0Q4Gag-Pol polyprotein 3.4.23.16 0.684
3kfn 3TLGag-Pol polyprotein / 0.684
2nnp ROCProtease / 0.683
1izh Q50Protease / 0.682
1mrx K57Gag-Pol polyprotein 3.4.23.16 0.682
2nmy ROCProtease / 0.681
3bva 2NCGag-Pol polyprotein 3.4.23.16 0.681
1ec1 BEEGag-Pol polyprotein 3.4.23.16 0.680
2z54 AB1Gag-Pol polyprotein 3.4.23.16 0.680
3pwr ROCGag-Pol polyprotein 3.4.23.16 0.679
1k2b 0Q4Gag-Pol polyprotein 3.4.23.16 0.677
4hdf G52Gag-Pol polyprotein 3.4.23.16 0.676
2fxd DR7Pol polyprotein / 0.675
3nwq 2NCGag-Pol polyprotein 3.4.23.16 0.675
3o9e A60Pol polyprotein / 0.674
2uy0 HV1Gag-Pol polyprotein 3.4.23.16 0.673
3pwm 017Gag-Pol polyprotein 3.4.23.16 0.673
2qnp QN2Gag-Pol polyprotein 3.4.23.16 0.672
1a8g 2Z4Gag-Pol polyprotein 3.4.23.16 0.671
1hii C20Gag-Pol polyprotein / 0.671
1xe5 5FEPlasmepsin-2 3.4.23.39 0.671
2p3c 3TLProtease / 0.671
2rkg AB1Pol protein / 0.671
3nxe 2NCProtease / 0.671
2ien 017Gag-Pol polyprotein 3.4.23.16 0.668
1z1r HBHGag-Pol polyprotein 3.4.23.16 0.666
3hzc 2NCProtease / 0.666
3k4v ROCGag-Pol polyprotein 3.4.23.16 0.666
1k2c 0Q4Gag-Pol polyprotein 3.4.23.16 0.664
4kb9 G79Protease / 0.664
2az9 3TLGag-Pol polyprotein 3.4.23.16 0.663
1b6l PI4Gag-Pol polyprotein 3.4.23.16 0.662
1ebw BEIGag-Pol polyprotein 3.4.23.16 0.662
1w5x BE5Gag-Pol polyprotein 3.4.23.16 0.662
1a8k 0Q4Gag-Pol polyprotein 3.4.23.16 0.660
3dck KVIProtease / 0.659
3oxx DR7Gag-Pol polyprotein 3.4.23.16 0.659
1dw6 0Q4Gag-Pol polyprotein 3.4.23.16 0.658
1zj7 0ZTGag-Pol polyprotein 3.4.23.16 0.658
2a4f AAUV-1 protease / 0.658
3gi4 K60Gag-Pol polyprotein / 0.658
1yt9 OISGag-Pol polyprotein / 0.657
4a6b QG8Gag-Pol polyprotein 3.4.23.16 0.656
1fmb HYBPol polyprotein / 0.655
2azb 3TLGag-Pol polyprotein 3.4.23.16 0.654
3i6o GR6Gag-Pol polyprotein 3.4.23.16 0.654
2i0a MUIProtease / 0.653
3lix E17Protease / 0.653
4heg G52Gag-Pol polyprotein 3.4.23.16 0.653
1ec3 MS3Gag-Pol polyprotein 3.4.23.16 0.652
1siv PSIGag-Pol polyprotein / 0.652
2fle AIProtease / 0.652
3el5 1UNGag-Pol polyprotein / 0.652
1fb7 ROCGag-Pol polyprotein / 0.651
3kfp 3TLGag-Pol polyprotein / 0.650
3liq E14Protease / 0.650
3zpu M8BGag-Pol polyprotein 3.4.23.16 0.650