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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
2fxd DR7 Pol polyprotein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2fxd DR7Pol polyprotein / 1.477
2fxe DR7Gag-Pol polyprotein 3.4.23.16 1.075
3oxx DR7Gag-Pol polyprotein 3.4.23.16 1.035
3el1 DR7Gag-Pol polyprotein 3.4.23.16 1.034
3em4 DR7Gag-Pol polyprotein 3.4.23.16 1.028
3el9 DR7Gag-Pol polyprotein 3.4.23.16 0.991
2aqu DR7Gag-Pol polyprotein 3.4.23.16 0.990
3eky DR7Gag-Pol polyprotein 3.4.23.16 0.988
3ekw DR7Gag-Pol polyprotein 3.4.23.16 0.923
1hih C20Gag-Pol polyprotein / 0.920
3kfn 3TLGag-Pol polyprotein / 0.910
3kf0 3TLGag-Pol polyprotein / 0.889
3slz 3TLPutative gag-pro-pol polyprotein / 0.867
3s85 LK0Gag-Pol polyprotein / 0.846
3kfr 3TLGag-Pol polyprotein / 0.845
3gga GGWGag-Pol polyprotein / 0.842
4k4p 3TLGag-Pol polyprotein / 0.825
2a1e IPFGag-Pol polyprotein 3.4.23.16 0.807
2p3b 3TLV-1 PROTEASE protein / 0.796
2p3b 3TLV-1 protease / 0.796
3kfs 3TLGag-Pol polyprotein / 0.789
2cem 2AHPol protein / 0.788
3dck KVIProtease / 0.786
1hvj A78Gag-Pol polyprotein / 0.778
1hii C20Gag-Pol polyprotein / 0.776
2p3c 3TLProtease / 0.776
1hvl A76Gag-Pol polyprotein / 0.774
1fgc 2NCGag-Pol polyprotein 3.4.23.16 0.773
2qi5 MZ7Gag-Pol polyprotein / 0.773
2xyf G40Gag-Pol polyprotein / 0.771
1ffi 2NCGag-Pol polyprotein 3.4.23.16 0.769
1k2b 0Q4Gag-Pol polyprotein 3.4.23.16 0.769
3bva 2NCGag-Pol polyprotein 3.4.23.16 0.768
3sa9 A68Protease / 0.768
2avm 2NCGag-Pol polyprotein 3.4.23.16 0.767
2q54 MU1Protease / 0.766
1z1h HBBGag-Pol polyprotein 3.4.23.16 0.763
2rkf AB1Pol protein / 0.757
1hos PHPGag-Pol polyprotein / 0.754
2q63 1UNGag-Pol polyprotein 3.4.23.16 0.754
3nxe 2NCProtease / 0.747
1ida 0POGag-Pol polyprotein 3.4.23.47 0.746
1dw6 0Q4Gag-Pol polyprotein 3.4.23.16 0.742
1ff0 2NCGag-Pol polyprotein 3.4.23.16 0.740
3liq E14Protease / 0.739
1ody LP1Gag-Pol polyprotein 3.4.23.16 0.735
2p3a 3TLPol protein / 0.734
2z54 AB1Gag-Pol polyprotein 3.4.23.16 0.734
2f3k RO1Protease / 0.733
1fff 0Q4Gag-Pol polyprotein 3.4.23.16 0.731
2wkz 5AHGag-Pol polyprotein / 0.730
3hzc 2NCProtease / 0.730
3lin E13Protease / 0.730
3toh 079Gag-Pol polyprotein 2.7.7.49 0.730
1k2c 0Q4Gag-Pol polyprotein 3.4.23.16 0.729
2cej 1AHPol protein / 0.729
3dcr KVSProtease / 0.729
1fg8 0Q4Gag-Pol polyprotein 3.4.23.16 0.728
3o9f K2DGag-Pol polyprotein / 0.727
3tl9 ROCGag-Pol polyprotein 3.4.23.16 0.727
2qi0 MZ3Gag-Pol polyprotein / 0.726
3nyg 2NCGag-Pol polyprotein 3.4.23.16 0.726
2rkg AB1Pol protein / 0.724
3bxr DRRGag-Pol polyprotein 3.4.23.16 0.723
1hpx KNIGag-Pol polyprotein / 0.722
2b60 RITPol polyprotein / 0.722
2nmy ROCProtease / 0.721
1hvs A77Gag-Pol polyprotein / 0.720
3ekx 1UNGag-Pol polyprotein 3.4.23.16 0.720
2xye CXGGag-Pol polyprotein / 0.719
3zps EQMGag-Pol polyprotein 3.4.23.16 0.717
3lit E15Protease / 0.714
3sa3 23XProtease / 0.714
1izi Q50Gag-Pol polyprotein 3.4.23.16 0.712
2p3d 3TLProtease / 0.712
3nwx KVSGag-Pol polyprotein 3.4.23.16 0.712
1izh Q50Protease / 0.711
3sa7 55AProtease / 0.711
2cen 4AHProtease / 0.710
2qhc AB1Protease / 0.709
1hvi A77Protease / 0.708
1vik BAYGag-Pol polyprotein / 0.708
3lix E17Protease / 0.708
3o9h K2EGag-Pol polyprotein / 0.708
1d4l PI9Gag-Pol polyprotein 3.4.23.16 0.707
3nwq 2NCGag-Pol polyprotein 3.4.23.16 0.707
1a94 0Q4Gag-Pol polyprotein 3.4.23.16 0.706
1kzk JE2Gag-Pol polyprotein 3.4.23.16 0.706
1daz 0Q4Gag-Pol polyprotein 3.4.23.16 0.705
3liv E16Protease / 0.705
3ggx GGXGag-Pol polyprotein / 0.703
2pym 1UNGag-Pol polyprotein 3.4.23.16 0.700
2q55 MU0Protease / 0.700
4kb9 G79Protease / 0.700
2hs2 017Protease / 0.697
2wl0 5AHGag-Pol polyprotein / 0.697
3vfa 031Gag-Pol polyprotein 3.4.23.16 0.697
1jld 0PPGag-Pol polyprotein / 0.695
2f8g 017Gag-Pol polyprotein 3.4.23.16 0.695
4hdp G52Gag-Pol polyprotein 3.4.23.16 0.694
1b6k PI5Gag-Pol polyprotein 3.4.23.16 0.692
1hxw RITGag-Pol polyprotein / 0.692
3ndx RITGag-Pol polyprotein 3.4.23.16 0.692
4djp M73Pol polyprotein / 0.692
1fmb HYBPol polyprotein / 0.691
3ndt ROCGag-Pol polyprotein 3.4.23.16 0.691
1a8g 2Z4Gag-Pol polyprotein 3.4.23.16 0.690
1fej 2NCGag-Pol polyprotein 3.4.23.16 0.690
1a8k 0Q4Gag-Pol polyprotein 3.4.23.16 0.689
3i2l 2NCProtease / 0.688
4dqe 017Gag-Pol polyprotein / 0.688
1hiv 1ZKGag-Pol polyprotein / 0.687
1tcx IM1Gag-Pol polyprotein 3.4.23.16 0.686
3cyx ROCGag-Pol polyprotein 3.4.23.16 0.686
1fg6 2NCGag-Pol polyprotein 3.4.23.16 0.685
1siv PSIGag-Pol polyprotein / 0.685
2qd8 065Gag-Pol polyprotein 3.4.23.16 0.685
3lzu 017Gag-Pol polyprotein 3.4.23.16 0.685
3zpt M8YGag-Pol polyprotein 3.4.23.16 0.685
3ogq AB1Pol polyprotein / 0.684
3tof 076Gag-Pol polyprotein 2.7.7.49 0.684
3em6 017Gag-Pol polyprotein 3.4.23.16 0.683
2qhy MZ1Gag-Pol polyprotein / 0.682
3vf7 031Gag-Pol polyprotein 3.4.23.16 0.681
4dfg 0JVGag-Pol polyprotein 3.4.23.16 0.681
3ecg 065Gag-Pol polyprotein 3.4.23.47 0.679
2i4u DJRProtease / 0.678
1xe5 5FEPlasmepsin-2 3.4.23.39 0.677
2b7z MK1Gag-Pol polyprotein / 0.676
3el5 1UNGag-Pol polyprotein / 0.676
3ndw RITGag-Pol polyprotein 3.4.23.16 0.676
1w6h TITPlasmepsin-2 3.4.23.39 0.675
2q5k AB1Protease / 0.675
3tog 079Gag-Pol polyprotein 2.7.7.49 0.675
1mrw K57Gag-Pol polyprotein 3.4.23.16 0.674
4hdb G52Gag-Pol polyprotein 3.4.23.16 0.674
2hs1 017Protease / 0.673
4dqh 017Gag-Pol polyprotein / 0.673
4j5j 478Gag-Pol polyprotein 3.4.23.16 0.673
2nnp ROCProtease / 0.672
3bxs DRSGag-Pol polyprotein 3.4.23.16 0.672
3r4b 74TGag-Pol polyprotein / 0.672
3t3c 017Gag-Pol polyprotein 3.4.23.16 0.672
2f81 017Gag-Pol polyprotein 3.4.23.16 0.671
3el4 ROCGag-Pol polyprotein 3.4.23.16 0.671
3st5 G89Gag-Pol polyprotein 3.4.23.16 0.671
3ucb 017Gag-Pol polyprotein / 0.671
1rl8 RITGag-Pol polyprotein 3.4.23.16 0.670
3jvy 017Gag-Pol polyprotein 3.4.23.16 0.670
1hxb ROCGag-Pol polyprotein 3.4.23.16 0.669
3d1x ROCGag-Pol polyprotein 3.4.23.16 0.669
1mrx K57Gag-Pol polyprotein 3.4.23.16 0.668
2r5q 1UNGag-Pol polyprotein / 0.668
1bai 0Q4Gag-Pro polyprotein / 0.667
3ggu 017Gag-Pol polyprotein 3.4.23.16 0.667
2fdd 385Pol protein / 0.666
3ec0 GRLGag-Pol polyprotein 3.4.23.47 0.666
2bqv A1AProtease / 0.665
1gvv 0GMEndothiapepsin 3.4.23.22 0.664
1ivp 1ZKGag-Pol polyprotein / 0.664
2f80 017Gag-Pol polyprotein 3.4.23.16 0.664
2bb9 AKCGag-Pol polyprotein 3.4.23.16 0.663
4hdf G52Gag-Pol polyprotein 3.4.23.16 0.663
4njs G08Protease / 0.663
2qd7 065Gag-Pol polyprotein 3.4.23.16 0.662
3oxw 017Gag-Pol polyprotein 3.4.23.16 0.662
3saa 77FProtease / 0.662
3jw2 017Gag-Pol polyprotein 3.4.23.16 0.661
1ebk 0Q4Gag-Pol polyprotein 3.4.23.16 0.660
1k1u 0Q4Gag-Pol polyprotein 3.4.23.16 0.660
3o9a K14Pol polyprotein / 0.660
4j54 G52Gag-Pol polyprotein 3.4.23.16 0.660
2fde 385Gag-Pol polyprotein 3.4.23.16 0.659
3s54 017Protease / 0.659
2jji 0QSEndothiapepsin 3.4.23.22 0.658
3mws 017Pol protein / 0.657
1z1r HBHGag-Pol polyprotein 3.4.23.16 0.656
3mxe K54Gag-Pol polyprotein 3.4.23.16 0.656
2nnk ROCProtease / 0.655
3o99 K13Pol polyprotein / 0.655
3sm2 478Putative gag-pro-pol polyprotein / 0.655
4heg G52Gag-Pol polyprotein 3.4.23.16 0.655
1wbm BLLPol protein / 0.654
3zpu M8BGag-Pol polyprotein 3.4.23.16 0.654
1b6m PI6Gag-Pol polyprotein 3.4.23.16 0.653
2qhz MZ2Gag-Pol polyprotein / 0.653
3ekt 017Gag-Pol polyprotein 3.4.23.16 0.653
3k4v ROCGag-Pol polyprotein 3.4.23.16 0.653
3pwr ROCGag-Pol polyprotein 3.4.23.16 0.653
3qaa G04Gag-Pol polyprotein 3.4.23.16 0.652
3vfb 031Gag-Pol polyprotein 3.4.23.16 0.652
3em3 478Gag-Pol polyprotein 3.4.23.16 0.651
3s43 478Protease / 0.651
9hvp 0E9Gag-Pol polyprotein / 0.651