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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
3sab F78 Protease

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3sab F78Protease / 1.393
4djp M73Pol polyprotein / 1.117
3sa9 A68Protease / 1.091
3o9a K14Pol polyprotein / 1.089
3o9f K2DGag-Pol polyprotein / 1.081
4kb9 G79Protease / 1.073
3st5 G89Gag-Pol polyprotein 3.4.23.16 1.072
3o9h K2EGag-Pol polyprotein / 1.068
2qi5 MZ7Gag-Pol polyprotein / 1.059
3sa8 K83Protease / 1.052
3gi4 K60Gag-Pol polyprotein / 1.043
2qci 065Gag-Pol polyprotein 3.4.23.16 1.040
3sa5 A69Protease / 1.040
4djo MK5Pol polyprotein / 1.038
3o9c K20Pol polyprotein / 1.033
4hdf G52Gag-Pol polyprotein 3.4.23.16 1.032
4hdp G52Gag-Pol polyprotein 3.4.23.16 1.030
2i0a MUIProtease / 1.027
3vfa 031Gag-Pol polyprotein 3.4.23.16 1.027
3mxd K53Gag-Pol polyprotein 3.4.23.16 1.025
4heg G52Gag-Pol polyprotein 3.4.23.16 1.022
3saa 77FProtease / 1.017
3ok9 G52Gag-Pol polyprotein 3.4.23.16 1.016
3r4b 74TGag-Pol polyprotein / 1.013
3ecg 065Gag-Pol polyprotein 3.4.23.47 1.012
4dfg 0JVGag-Pol polyprotein 3.4.23.16 1.012
2qd8 065Gag-Pol polyprotein 3.4.23.16 1.008
3qaa G04Gag-Pol polyprotein 3.4.23.16 1.008
4djq M86Pol polyprotein / 1.008
4hdb G52Gag-Pol polyprotein 3.4.23.16 1.007
2hb3 GRLProtease / 1.004
3pwm 017Gag-Pol polyprotein 3.4.23.16 1.000
2qi0 MZ3Gag-Pol polyprotein / 0.998
2qhy MZ1Gag-Pol polyprotein / 0.997
1t3r 017Gag-Pol polyprotein 3.4.23.16 0.996
2qd7 065Gag-Pol polyprotein 3.4.23.16 0.996
2z4o 065Gag-Pol polyprotein 3.4.23.16 0.996
3o9i A61Gag-Pol polyprotein / 0.996
3ekv 478Gag-Pol polyprotein 3.4.23.16 0.995
3sa7 55AProtease / 0.994
3vf5 031Gag-Pol polyprotein 3.4.23.16 0.994
2qi7 MZ9Gag-Pol polyprotein / 0.989
3gi5 K62Gag-Pol polyprotein / 0.987
3dk1 G05Gag-Pol polyprotein 3.4.23.16 0.986
3oy4 017Gag-Pol polyprotein 3.4.23.16 0.981
3o9g F53Gag-Pol polyprotein / 0.980
2i4d QFIProtease / 0.979
3gi6 D78Gag-Pol polyprotein / 0.979
3o9e A60Pol polyprotein / 0.979
3o9d K19Pol polyprotein / 0.978
3o9b K2APol polyprotein / 0.975
3vf7 031Gag-Pol polyprotein 3.4.23.16 0.968
4dqh 017Gag-Pol polyprotein / 0.968
2i4u DJRProtease / 0.962
2qi4 MZ6Gag-Pol polyprotein / 0.959
2i4x KGQProtease / 0.958
3o99 K13Pol polyprotein / 0.956
4njs G08Protease / 0.955
4j54 G52Gag-Pol polyprotein 3.4.23.16 0.951
4dqb 017Gag-Pol polyprotein / 0.948
3djk G55Gag-Pol polyprotein 3.4.23.16 0.945
3oxv 478Gag-Pol polyprotein 3.4.23.16 0.940
4dqc 017Gag-Pol polyprotein / 0.938
4q1w 017Gag-Pol polyprotein 3.4.23.16 0.937
2qi6 MZ8Gag-Pol polyprotein / 0.935
4djr 0KJPol polyprotein / 0.935
4dqe 017Gag-Pol polyprotein / 0.934
3eky DR7Gag-Pol polyprotein 3.4.23.16 0.933
2i0d MUTProtease / 0.924
1t7i 017Gag-Pol polyprotein 3.4.23.16 0.922
2hs1 017Protease / 0.921
2f80 017Gag-Pol polyprotein 3.4.23.16 0.917
3lzv 017Gag-Pol polyprotein 3.4.23.16 0.917
2i4w KGQProtease / 0.915
3lzu 017Gag-Pol polyprotein 3.4.23.16 0.913
4ye3 G04Gag-Pol polyprotein 3.4.23.16 0.912
3ec0 GRLGag-Pol polyprotein 3.4.23.47 0.911
4q1x 017Gag-Pol polyprotein 3.4.23.16 0.910
4dqf 017Gag-Pol polyprotein / 0.909
3em3 478Gag-Pol polyprotein 3.4.23.16 0.908
3nuo 478Gag-Pol polyprotein 3.4.23.16 0.903
2fdd 385Pol protein / 0.902
3nu9 478Gag-Pol polyprotein 3.4.23.16 0.900
2idw 017Protease / 0.896
1z1h HBBGag-Pol polyprotein 3.4.23.16 0.894
2psu MUUProtease / 0.893
3ucb 017Gag-Pol polyprotein / 0.893
4j55 031Gag-Pol polyprotein 3.4.23.16 0.891
3d20 017Gag-Pol polyprotein 3.4.23.16 0.890
3em4 DR7Gag-Pol polyprotein 3.4.23.16 0.888
2ien 017Gag-Pol polyprotein 3.4.23.16 0.885
3vfb 031Gag-Pol polyprotein 3.4.23.16 0.884
2i4v DJRV-1 protease / 0.881
3nu4 478Gag-Pol polyprotein 3.4.23.16 0.880
2ieo 017Protease / 0.878
2qd6 065Gag-Pol polyprotein 3.4.23.16 0.878
2f81 017Gag-Pol polyprotein 3.4.23.16 0.876
3mws 017Pol protein / 0.874
3s54 017Protease / 0.874
3el9 DR7Gag-Pol polyprotein 3.4.23.16 0.871
3nu3 478Gag-Pol polyprotein 3.4.23.16 0.871
3nu6 478Gag-Pol polyprotein 3.4.23.16 0.870
3nu5 478Gag-Pol polyprotein 3.4.23.16 0.867
2qi3 MZ5Gag-Pol polyprotein / 0.862
3nuj 478Gag-Pol polyprotein 3.4.23.16 0.859
3sa4 F72Protease / 0.856
1hpv 478Gag-Pol polyprotein / 0.855
3oxw 017Gag-Pol polyprotein 3.4.23.16 0.855
2hs2 017Protease / 0.854
3s43 478Protease / 0.854
4i8z G08Gag-Pol polyprotein 3.4.23.16 0.854
4q1y 017Gag-Pol polyprotein 3.4.23.16 0.854
3t3c 017Gag-Pol polyprotein 3.4.23.16 0.853
3em6 017Gag-Pol polyprotein 3.4.23.16 0.843
3sa3 23XProtease / 0.842
4rvj 478Protease / 0.838
3sac AF8Protease / 0.835
3cyw 017Gag-Pol polyprotein 3.4.23.16 0.832
3ggu 017Gag-Pol polyprotein 3.4.23.16 0.830
2f8g 017Gag-Pol polyprotein 3.4.23.16 0.829
3oxx DR7Gag-Pol polyprotein 3.4.23.16 0.827
3jvy 017Gag-Pol polyprotein 3.4.23.16 0.826
3ekt 017Gag-Pol polyprotein 3.4.23.16 0.823
3jw2 017Gag-Pol polyprotein 3.4.23.16 0.821
3lzs 017Gag-Pol polyprotein 3.4.23.16 0.821
1izh Q50Protease / 0.820
2fde 385Gag-Pol polyprotein 3.4.23.16 0.820
3el1 DR7Gag-Pol polyprotein 3.4.23.16 0.819
3i6o GR6Gag-Pol polyprotein 3.4.23.16 0.817
3d1z 017Gag-Pol polyprotein 3.4.23.16 0.816
1d4l PI9Gag-Pol polyprotein 3.4.23.16 0.815
2psv MUVProtease / 0.815
1z1r HBHGag-Pol polyprotein 3.4.23.16 0.806
3i7e DJRGag-Pol polyprotein / 0.793
3toh 079Gag-Pol polyprotein 2.7.7.49 0.792
3gga GGWGag-Pol polyprotein / 0.789
2fle AIProtease / 0.787
1sbg IM1Gag-Pol polyprotein / 0.784
3sa6 F71Protease / 0.783
2cem 2AHPol protein / 0.782
2q63 1UNGag-Pol polyprotein 3.4.23.16 0.780
2qak 1UNGag-Pol polyprotein 3.4.23.16 0.780
4hla 017Gag-Pol polyprotein 3.4.23.16 0.780
2avs MK1Gag-Pol polyprotein 3.4.23.16 0.779
2avv MK1Gag-Pol polyprotein 3.4.23.16 0.778
1ec3 MS3Gag-Pol polyprotein 3.4.23.16 0.776
2p3c 3TLProtease / 0.776
1hvr XK2Gag-Pol polyprotein / 0.775
3sm2 478Putative gag-pro-pol polyprotein / 0.774
1b6k PI5Gag-Pol polyprotein 3.4.23.16 0.763
3ufn ROCGag-Pol polyprotein / 0.761
2p3a 3TLPol protein / 0.758
3k4v ROCGag-Pol polyprotein 3.4.23.16 0.757
3kfr 3TLGag-Pol polyprotein / 0.756
1b6m PI6Gag-Pol polyprotein 3.4.23.16 0.753
1b6p PI7Gag-Pol polyprotein 3.4.23.16 0.753
1npa 3NHGag-Pol polyprotein 3.4.23.16 0.752
1npw LGZGag-Pol polyprotein 3.4.23.16 0.752
3kf0 3TLGag-Pol polyprotein / 0.752
1d4i BEGGag-Pol polyprotein 3.4.23.16 0.749
2avm 2NCGag-Pol polyprotein 3.4.23.16 0.749
2pym 1UNGag-Pol polyprotein 3.4.23.16 0.748
3kdd JZQGag-Pol polyprotein 3.4.23.16 0.748
3ndx RITGag-Pol polyprotein 3.4.23.16 0.747
2a1e IPFGag-Pol polyprotein 3.4.23.16 0.746
1sdt MK1Gag-Pol polyprotein 3.4.23.16 0.745
1w5x BE5Gag-Pol polyprotein 3.4.23.16 0.745
2cen 4AHProtease / 0.744
3kfn 3TLGag-Pol polyprotein / 0.744
1t7j 478Gag-Pol polyprotein 3.4.23.16 0.743
3bvb 017Gag-Pol polyprotein 3.4.23.16 0.743
3ekx 1UNGag-Pol polyprotein 3.4.23.16 0.739
3el4 ROCGag-Pol polyprotein 3.4.23.16 0.739
3s56 ROCProtease / 0.739
4k4p 3TLGag-Pol polyprotein / 0.738
3i2l 2NCProtease / 0.737
4njt 017Protease / 0.737
1iiq 0ZRGag-Pol polyprotein 3.4.23.16 0.733
3bxr DRRGag-Pol polyprotein 3.4.23.16 0.733
1sdu MK1Gag-Pol polyprotein 3.4.23.16 0.732
1sdv MK1Gag-Pol polyprotein 3.4.23.16 0.732
2nmy ROCProtease / 0.732
3d1y ROCGag-Pol polyprotein 3.4.23.16 0.732
3tl9 ROCGag-Pol polyprotein 3.4.23.16 0.732
4j5j 478Gag-Pol polyprotein 3.4.23.16 0.732
2rkf AB1Pol protein / 0.731
3ekw DR7Gag-Pol polyprotein 3.4.23.16 0.731
1ec1 BEEGag-Pol polyprotein 3.4.23.16 0.725
1hvi A77Protease / 0.724
1w5v BE3Gag-Pol polyprotein 3.4.23.16 0.721
2fxe DR7Gag-Pol polyprotein 3.4.23.16 0.721
1pro A88Gag-Pol polyprotein / 0.720
3ekp 478Gag-Pol polyprotein 3.4.23.16 0.720
1k6t XN1Gag-Pol polyprotein 3.4.23.16 0.719
2bb9 AKCGag-Pol polyprotein 3.4.23.16 0.718
2bpx MK1Gag-Pol polyprotein 3.4.23.16 0.714
2f3k RO1Protease / 0.713
3tog 079Gag-Pol polyprotein 2.7.7.49 0.711
1t7k BH0Gag-Pol polyprotein 3.4.23.16 0.710
2b60 RITPol polyprotein / 0.710
2p3d 3TLProtease / 0.710
1mtr PI6Gag-Pol polyprotein 3.4.23.16 0.709
1qbr XV6Gag-Pol polyprotein 3.4.23.16 0.709
1a94 0Q4Gag-Pol polyprotein 3.4.23.16 0.708
1mrw K57Gag-Pol polyprotein 3.4.23.16 0.708
3dcr KVSProtease / 0.708
3hzc 2NCProtease / 0.707
3slz 3TLPutative gag-pro-pol polyprotein / 0.706
1ajv NMBGag-Pol polyprotein 3.4.23.16 0.705
1ebw BEIGag-Pol polyprotein 3.4.23.16 0.705
1ida 0POGag-Pol polyprotein 3.4.23.47 0.705
2q54 MU1Protease / 0.705
1bdq IM1Gag-Pol polyprotein 3.4.23.16 0.704
2nnk ROCProtease / 0.703
3nxe 2NCProtease / 0.702
1tcx IM1Gag-Pol polyprotein 3.4.23.16 0.701
1m0b 0ZQGag-Pol polyprotein 3.4.23.16 0.700
4qgi ROCGag-Pol polyprotein 3.4.23.16 0.700
2r43 G3GGag-Pol polyprotein 3.4.23.16 0.699
1hvk A79Gag-Pol polyprotein / 0.698
3ndu ROCGag-Pol polyprotein 3.4.23.16 0.698
2nnp ROCProtease / 0.696
2qhz MZ2Gag-Pol polyprotein / 0.693
1d4h BEHGag-Pol polyprotein 3.4.23.16 0.692
1ohr 1UNV-1 PROTEASE protein / 0.692
3bxs DRSGag-Pol polyprotein 3.4.23.16 0.691
3ndw RITGag-Pol polyprotein 3.4.23.16 0.690
2pyn 1UNGag-Pol polyprotein 3.4.23.16 0.689
2q55 MU0Protease / 0.689
1ajx AH1Gag-Pol polyprotein 3.4.23.16 0.688
1hvs A77Gag-Pol polyprotein / 0.688
2q64 1UNGag-Pol polyprotein 3.4.23.16 0.688
3cyx ROCGag-Pol polyprotein 3.4.23.16 0.688
2hc0 AB2Protease / 0.686
3bva 2NCGag-Pol polyprotein 3.4.23.16 0.686
3kfs 3TLGag-Pol polyprotein / 0.686
3nls 016Gag-Pol polyprotein 3.4.23.16 0.686
3nwx KVSGag-Pol polyprotein 3.4.23.16 0.686
2bbb HH1Gag-Pol polyprotein 3.4.23.16 0.684
4a4q UX9Pol protein / 0.684
1yt9 OISGag-Pol polyprotein / 0.682
1zsr 0ZTGag-Pol polyprotein 3.4.23.16 0.681
2aoe 0Q4Gag-Pol polyprotein 3.4.23.16 0.681
2bqv A1AProtease / 0.680
2q5k AB1Protease / 0.679
1qbt 146Gag-Pol polyprotein 3.4.23.16 0.678
2aqu DR7Gag-Pol polyprotein 3.4.23.16 0.678
2bpw 1INGag-Pol polyprotein 3.4.23.16 0.677
1hos PHPGag-Pol polyprotein / 0.675
1k6c MK1Gag-Pol polyprotein 3.4.23.16 0.675
1c6z ROCProtease / 0.674
1fg6 2NCGag-Pol polyprotein 3.4.23.16 0.673
1hxw RITGag-Pol polyprotein / 0.671
1w5y BE6Gag-Pol polyprotein 3.4.23.16 0.671
3nwq 2NCGag-Pol polyprotein 3.4.23.16 0.671
3pwr ROCGag-Pol polyprotein 3.4.23.16 0.671
1fff 0Q4Gag-Pol polyprotein 3.4.23.16 0.669
1zsf 0ZSGag-Pol polyprotein 3.4.23.16 0.668
2p4j 23IBeta-secretase 1 3.4.23.46 0.668
1w5w BE4Gag-Pol polyprotein 3.4.23.16 0.667
2qnp QN2Gag-Pol polyprotein 3.4.23.16 0.666
1a9m U0EGag-Pol polyprotein / 0.665
1ffi 2NCGag-Pol polyprotein 3.4.23.16 0.665
1k6v XN2Gag-Pol polyprotein 3.4.23.16 0.665
1daz 0Q4Gag-Pol polyprotein 3.4.23.16 0.664
1mrx K57Gag-Pol polyprotein 3.4.23.16 0.664
1npv L27Gag-Pol polyprotein 3.4.23.16 0.664
1wbm BLLPol protein / 0.664
1a8g 2Z4Gag-Pol polyprotein 3.4.23.16 0.662
3ixj 586Beta-secretase 1 3.4.23.46 0.662
1bv7 XV6Gag-Pol polyprotein 3.4.23.16 0.661
3qrm NK7Gag-Pol polyprotein 3.4.23.16 0.660
1kzk JE2Gag-Pol polyprotein 3.4.23.16 0.659
2pk6 O33V-1 protease / 0.659
2wkz 5AHGag-Pol polyprotein / 0.659
1bdr IM1Gag-Pol polyprotein 3.4.23.16 0.658
2qnq QN3Gag-Pol polyprotein 3.4.23.16 0.658
1ebz BECGag-Pol polyprotein 3.4.23.16 0.657
2qhc AB1Protease / 0.657
1fej 2NCGag-Pol polyprotein 3.4.23.16 0.656
1siv PSIGag-Pol polyprotein / 0.655
1c70 L75Protease / 0.654
1rl8 RITGag-Pol polyprotein 3.4.23.16 0.653
3s85 LK0Gag-Pol polyprotein / 0.653
1fgc 2NCGag-Pol polyprotein 3.4.23.16 0.652
1hpx KNIGag-Pol polyprotein / 0.652
1k2b 0Q4Gag-Pol polyprotein 3.4.23.16 0.651
1eag A70Candidapepsin-2 3.4.23.24 0.650