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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
3sa3 23X Protease

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3sa3 23XProtease / 1.371
2qi5 MZ7Gag-Pol polyprotein / 1.154
3sa7 55AProtease / 1.149
3sa9 A68Protease / 1.141
3o9d K19Pol polyprotein / 1.007
3o9c K20Pol polyprotein / 0.981
4djp M73Pol polyprotein / 0.980
2qi7 MZ9Gag-Pol polyprotein / 0.972
3o9i A61Gag-Pol polyprotein / 0.968
3o9h K2EGag-Pol polyprotein / 0.967
3o9a K14Pol polyprotein / 0.966
4djr 0KJPol polyprotein / 0.966
3sa5 A69Protease / 0.963
2i0a MUIProtease / 0.961
3mxe K54Gag-Pol polyprotein 3.4.23.16 0.961
2qhy MZ1Gag-Pol polyprotein / 0.958
4kb9 G79Protease / 0.954
4hdp G52Gag-Pol polyprotein 3.4.23.16 0.952
4djo MK5Pol polyprotein / 0.951
4heg G52Gag-Pol polyprotein 3.4.23.16 0.951
3eky DR7Gag-Pol polyprotein 3.4.23.16 0.950
3o9f K2DGag-Pol polyprotein / 0.946
3sa4 F72Protease / 0.943
3r4b 74TGag-Pol polyprotein / 0.937
2qi6 MZ8Gag-Pol polyprotein / 0.935
1t3r 017Gag-Pol polyprotein 3.4.23.16 0.931
3o9b K2APol polyprotein / 0.926
3oy4 017Gag-Pol polyprotein 3.4.23.16 0.925
3mxd K53Gag-Pol polyprotein 3.4.23.16 0.923
3sa8 K83Protease / 0.923
4dfg 0JVGag-Pol polyprotein 3.4.23.16 0.921
2qi0 MZ3Gag-Pol polyprotein / 0.920
3saa 77FProtease / 0.920
4djq M86Pol polyprotein / 0.920
3o9e A60Pol polyprotein / 0.919
3gi6 D78Gag-Pol polyprotein / 0.916
2hb3 GRLProtease / 0.915
3ekv 478Gag-Pol polyprotein 3.4.23.16 0.914
3gi5 K62Gag-Pol polyprotein / 0.907
4hdf G52Gag-Pol polyprotein 3.4.23.16 0.903
4dqh 017Gag-Pol polyprotein / 0.902
3lzv 017Gag-Pol polyprotein 3.4.23.16 0.900
3nu4 478Gag-Pol polyprotein 3.4.23.16 0.898
3pwm 017Gag-Pol polyprotein 3.4.23.16 0.897
3em3 478Gag-Pol polyprotein 3.4.23.16 0.896
2qi4 MZ6Gag-Pol polyprotein / 0.893
3st5 G89Gag-Pol polyprotein 3.4.23.16 0.893
1z1h HBBGag-Pol polyprotein 3.4.23.16 0.891
2qi3 MZ5Gag-Pol polyprotein / 0.890
4dqe 017Gag-Pol polyprotein / 0.890
2qd7 065Gag-Pol polyprotein 3.4.23.16 0.888
3oxv 478Gag-Pol polyprotein 3.4.23.16 0.887
3ecg 065Gag-Pol polyprotein 3.4.23.47 0.886
3o9g F53Gag-Pol polyprotein / 0.884
3dk1 G05Gag-Pol polyprotein 3.4.23.16 0.883
4q1w 017Gag-Pol polyprotein 3.4.23.16 0.883
2qd8 065Gag-Pol polyprotein 3.4.23.16 0.882
3o99 K13Pol polyprotein / 0.882
3ok9 G52Gag-Pol polyprotein 3.4.23.16 0.882
3vf5 031Gag-Pol polyprotein 3.4.23.16 0.882
2f80 017Gag-Pol polyprotein 3.4.23.16 0.881
2psu MUUProtease / 0.881
3qaa G04Gag-Pol polyprotein 3.4.23.16 0.879
4dqf 017Gag-Pol polyprotein / 0.875
3nuo 478Gag-Pol polyprotein 3.4.23.16 0.874
4dqc 017Gag-Pol polyprotein / 0.873
2qci 065Gag-Pol polyprotein 3.4.23.16 0.872
4njs G08Protease / 0.868
3vfa 031Gag-Pol polyprotein 3.4.23.16 0.867
3nu9 478Gag-Pol polyprotein 3.4.23.16 0.864
2psv MUVProtease / 0.863
4j54 G52Gag-Pol polyprotein 3.4.23.16 0.862
2z4o 065Gag-Pol polyprotein 3.4.23.16 0.861
3nu3 478Gag-Pol polyprotein 3.4.23.16 0.860
3d1z 017Gag-Pol polyprotein 3.4.23.16 0.858
3oxw 017Gag-Pol polyprotein 3.4.23.16 0.858
4dqb 017Gag-Pol polyprotein / 0.857
2i4d QFIProtease / 0.856
3ec0 GRLGag-Pol polyprotein 3.4.23.47 0.856
2i4x KGQProtease / 0.855
3gi4 K60Gag-Pol polyprotein / 0.853
2qd6 065Gag-Pol polyprotein 3.4.23.16 0.846
1ida 0POGag-Pol polyprotein 3.4.23.47 0.845
1d4l PI9Gag-Pol polyprotein 3.4.23.16 0.844
2f81 017Gag-Pol polyprotein 3.4.23.16 0.844
2i4v DJRV-1 protease / 0.842
3oxx DR7Gag-Pol polyprotein 3.4.23.16 0.842
3sab F78Protease / 0.842
3i6o GR6Gag-Pol polyprotein 3.4.23.16 0.839
3vf7 031Gag-Pol polyprotein 3.4.23.16 0.838
2i0d MUTProtease / 0.837
3mws 017Pol protein / 0.836
2f8g 017Gag-Pol polyprotein 3.4.23.16 0.835
3s43 478Protease / 0.835
2i4u DJRProtease / 0.834
3nu6 478Gag-Pol polyprotein 3.4.23.16 0.834
3em6 017Gag-Pol polyprotein 3.4.23.16 0.833
1z1r HBHGag-Pol polyprotein 3.4.23.16 0.831
3nuj 478Gag-Pol polyprotein 3.4.23.16 0.831
3nu5 478Gag-Pol polyprotein 3.4.23.16 0.830
3djk G55Gag-Pol polyprotein 3.4.23.16 0.829
4k4p 3TLGag-Pol polyprotein / 0.828
2fxe DR7Gag-Pol polyprotein 3.4.23.16 0.826
3toh 079Gag-Pol polyprotein 2.7.7.49 0.825
2hs1 017Protease / 0.824
3k4v ROCGag-Pol polyprotein 3.4.23.16 0.824
2fdd 385Pol protein / 0.822
2ien 017Gag-Pol polyprotein 3.4.23.16 0.820
3sa6 F71Protease / 0.815
3t3c 017Gag-Pol polyprotein 3.4.23.16 0.815
3s54 017Protease / 0.813
4ye3 G04Gag-Pol polyprotein 3.4.23.16 0.812
2qhz MZ2Gag-Pol polyprotein / 0.811
3s56 ROCProtease / 0.811
3dcr KVSProtease / 0.810
4q1y 017Gag-Pol polyprotein 3.4.23.16 0.809
2fle AIProtease / 0.806
1t7i 017Gag-Pol polyprotein 3.4.23.16 0.803
3ucb 017Gag-Pol polyprotein / 0.803
3d20 017Gag-Pol polyprotein 3.4.23.16 0.801
3el4 ROCGag-Pol polyprotein 3.4.23.16 0.799
3tof 076Gag-Pol polyprotein 2.7.7.49 0.798
4hdb G52Gag-Pol polyprotein 3.4.23.16 0.798
3em4 DR7Gag-Pol polyprotein 3.4.23.16 0.797
3i7e DJRGag-Pol polyprotein / 0.792
2idw 017Protease / 0.790
2nmy ROCProtease / 0.790
3i2l 2NCProtease / 0.790
3sac AF8Protease / 0.790
3vfb 031Gag-Pol polyprotein 3.4.23.16 0.790
2cen 4AHProtease / 0.789
2nnk ROCProtease / 0.789
2nnp ROCProtease / 0.789
4j5j 478Gag-Pol polyprotein 3.4.23.16 0.788
3ekw DR7Gag-Pol polyprotein 3.4.23.16 0.786
3d1x ROCGag-Pol polyprotein 3.4.23.16 0.785
1fg6 2NCGag-Pol polyprotein 3.4.23.16 0.784
1npv L27Gag-Pol polyprotein 3.4.23.16 0.784
3jvy 017Gag-Pol polyprotein 3.4.23.16 0.784
3d1y ROCGag-Pol polyprotein 3.4.23.16 0.782
3lzu 017Gag-Pol polyprotein 3.4.23.16 0.782
2q54 MU1Protease / 0.781
2hs2 017Protease / 0.780
2aqu DR7Gag-Pol polyprotein 3.4.23.16 0.777
3ufn ROCGag-Pol polyprotein / 0.777
2ieo 017Protease / 0.776
3bxr DRRGag-Pol polyprotein 3.4.23.16 0.773
3nwx KVSGag-Pol polyprotein 3.4.23.16 0.773
4q1x 017Gag-Pol polyprotein 3.4.23.16 0.773
3tl9 ROCGag-Pol polyprotein 3.4.23.16 0.770
2avv MK1Gag-Pol polyprotein 3.4.23.16 0.767
3cyw 017Gag-Pol polyprotein 3.4.23.16 0.767
4j55 031Gag-Pol polyprotein 3.4.23.16 0.767
1iiq 0ZRGag-Pol polyprotein 3.4.23.16 0.766
3ekt 017Gag-Pol polyprotein 3.4.23.16 0.766
3tog 079Gag-Pol polyprotein 2.7.7.49 0.766
3dck KVIProtease / 0.763
1siv PSIGag-Pol polyprotein / 0.762
2avs MK1Gag-Pol polyprotein 3.4.23.16 0.762
2pym 1UNGag-Pol polyprotein 3.4.23.16 0.762
3kfs 3TLGag-Pol polyprotein / 0.762
3el1 DR7Gag-Pol polyprotein 3.4.23.16 0.761
1tcx IM1Gag-Pol polyprotein 3.4.23.16 0.759
2q63 1UNGag-Pol polyprotein 3.4.23.16 0.759
2qak 1UNGag-Pol polyprotein 3.4.23.16 0.759
1hpv 478Gag-Pol polyprotein / 0.758
4rvj 478Protease / 0.758
1a8g 2Z4Gag-Pol polyprotein 3.4.23.16 0.755
1sbg IM1Gag-Pol polyprotein / 0.755
1ohr 1UNV-1 PROTEASE protein / 0.751
2wl0 5AHGag-Pol polyprotein / 0.750
1npa 3NHGag-Pol polyprotein 3.4.23.16 0.749
1npw LGZGag-Pol polyprotein 3.4.23.16 0.749
2a1e IPFGag-Pol polyprotein 3.4.23.16 0.749
3ekq ROCGag-Pol polyprotein 3.4.23.16 0.748
4njt 017Protease / 0.748
2bb9 AKCGag-Pol polyprotein 3.4.23.16 0.744
1fej 2NCGag-Pol polyprotein 3.4.23.16 0.742
3el9 DR7Gag-Pol polyprotein 3.4.23.16 0.742
3fx5 KNIGag-Pol polyprotein 3.4.23.16 0.742
4hla 017Gag-Pol polyprotein 3.4.23.16 0.741
1sdu MK1Gag-Pol polyprotein 3.4.23.16 0.739
3lzs 017Gag-Pol polyprotein 3.4.23.16 0.739
1hvs A77Gag-Pol polyprotein / 0.737
3sm2 478Putative gag-pro-pol polyprotein / 0.735
4i8z G08Gag-Pol polyprotein 3.4.23.16 0.735
1fgc 2NCGag-Pol polyprotein 3.4.23.16 0.733
1k6t XN1Gag-Pol polyprotein 3.4.23.16 0.732
2f3k RO1Protease / 0.732
1mtr PI6Gag-Pol polyprotein 3.4.23.16 0.731
3gga GGWGag-Pol polyprotein / 0.731
1ffi 2NCGag-Pol polyprotein 3.4.23.16 0.729
3pwr ROCGag-Pol polyprotein 3.4.23.16 0.729
1sdv MK1Gag-Pol polyprotein 3.4.23.16 0.728
1hii C20Gag-Pol polyprotein / 0.727
2q64 1UNGag-Pol polyprotein 3.4.23.16 0.725
3bxs DRSGag-Pol polyprotein 3.4.23.16 0.724
1hih C20Gag-Pol polyprotein / 0.723
3ndw RITGag-Pol polyprotein 3.4.23.16 0.723
1ebw BEIGag-Pol polyprotein 3.4.23.16 0.722
1k2b 0Q4Gag-Pol polyprotein 3.4.23.16 0.722
1b6l PI4Gag-Pol polyprotein 3.4.23.16 0.720
1fff 0Q4Gag-Pol polyprotein 3.4.23.16 0.716
1jld 0PPGag-Pol polyprotein / 0.716
2wkz 5AHGag-Pol polyprotein / 0.715
3kfr 3TLGag-Pol polyprotein / 0.715
2fxd DR7Pol polyprotein / 0.714
1bdq IM1Gag-Pol polyprotein 3.4.23.16 0.713
2a4f AAUV-1 protease / 0.713
2fde 385Gag-Pol polyprotein 3.4.23.16 0.713
1a94 0Q4Gag-Pol polyprotein 3.4.23.16 0.712
1izh Q50Protease / 0.712
1sdt MK1Gag-Pol polyprotein 3.4.23.16 0.712
2p3b 3TLV-1 PROTEASE protein / 0.712
2p3b 3TLV-1 protease / 0.712
1hiv 1ZKGag-Pol polyprotein / 0.710
1ody LP1Gag-Pol polyprotein 3.4.23.16 0.710
2cem 2AHPol protein / 0.710
3jw2 017Gag-Pol polyprotein 3.4.23.16 0.708
1bdr IM1Gag-Pol polyprotein 3.4.23.16 0.707
1qbt 146Gag-Pol polyprotein 3.4.23.16 0.707
4qgi ROCGag-Pol polyprotein 3.4.23.16 0.707
3kfn 3TLGag-Pol polyprotein / 0.706
1ec3 MS3Gag-Pol polyprotein 3.4.23.16 0.705
3ndu ROCGag-Pol polyprotein 3.4.23.16 0.705
3s85 LK0Gag-Pol polyprotein / 0.705
1ec2 BEJGag-Pol polyprotein 3.4.23.16 0.704
1ff0 2NCGag-Pol polyprotein 3.4.23.16 0.702
3ggu 017Gag-Pol polyprotein 3.4.23.16 0.700
1b6p PI7Gag-Pol polyprotein 3.4.23.16 0.699
1b6m PI6Gag-Pol polyprotein 3.4.23.16 0.698
3ggx GGXGag-Pol polyprotein / 0.698
1hos PHPGag-Pol polyprotein / 0.694
3slz 3TLPutative gag-pro-pol polyprotein / 0.694
3kf0 3TLGag-Pol polyprotein / 0.693
3tlh 3TLGag-Pol polyprotein 3.4.23.16 0.693
3hzc 2NCProtease / 0.692
2b60 RITPol polyprotein / 0.690
2cej 1AHPol protein / 0.690
2pyn 1UNGag-Pol polyprotein 3.4.23.16 0.690
1fg8 0Q4Gag-Pol polyprotein 3.4.23.16 0.689
3cyx ROCGag-Pol polyprotein 3.4.23.16 0.688
1bv7 XV6Gag-Pol polyprotein 3.4.23.16 0.685
2r3t G4GGag-Pol polyprotein 3.4.23.16 0.685
2bpw 1INGag-Pol polyprotein 3.4.23.16 0.683
2aoe 0Q4Gag-Pol polyprotein 3.4.23.16 0.681
2bqv A1AProtease / 0.681
2az8 3TLGag-Pol polyprotein 3.4.23.16 0.678
1ajv NMBGag-Pol polyprotein 3.4.23.16 0.676
1mrw K57Gag-Pol polyprotein 3.4.23.16 0.676
1hpx KNIGag-Pol polyprotein / 0.675
1b11 3TLPol polyprotein / 0.674
1ivq 0PXGag-Pol polyprotein / 0.673
1yt9 OISGag-Pol polyprotein / 0.673
1fb7 ROCGag-Pol polyprotein / 0.672
1fmb HYBPol polyprotein / 0.672
1g35 AHFGag-Pol polyprotein 3.4.23.16 0.672
1daz 0Q4Gag-Pol polyprotein 3.4.23.16 0.671
1izi Q50Gag-Pol polyprotein 3.4.23.16 0.671
2hc0 AB2Protease / 0.671
1rl8 RITGag-Pol polyprotein 3.4.23.16 0.665
3zpt M8YGag-Pol polyprotein 3.4.23.16 0.665
1ec1 BEEGag-Pol polyprotein 3.4.23.16 0.664
1hxb ROCGag-Pol polyprotein 3.4.23.16 0.664
1n49 RITGag-Pol polyprotein 3.4.23.16 0.664
3el0 1UNGag-Pol polyprotein 3.4.23.16 0.664
3kfp 3TLGag-Pol polyprotein / 0.664
1d4i BEGGag-Pol polyprotein 3.4.23.16 0.663
1a9m U0EGag-Pol polyprotein / 0.662
2qnq QN3Gag-Pol polyprotein 3.4.23.16 0.662
1k1u 0Q4Gag-Pol polyprotein 3.4.23.16 0.661
1hvk A79Gag-Pol polyprotein / 0.660
2fmb LP1Reverse transcriptase / 0.660
2i4w KGQProtease / 0.660
2qnp QN2Gag-Pol polyprotein 3.4.23.16 0.660
3so9 017Pol protein / 0.660
1ebk 0Q4Gag-Pol polyprotein 3.4.23.16 0.659
1m0b 0ZQGag-Pol polyprotein 3.4.23.16 0.659
1ppk IVVPenicillopepsin-1 3.4.23.20 0.658
2uxz HI1Gag-Pol polyprotein 3.4.23.16 0.658
1wbk 568Pol protein / 0.657
1bwa XV6Gag-Pol polyprotein 3.4.23.16 0.656
2bbb HH1Gag-Pol polyprotein 3.4.23.16 0.656
3bvb 017Gag-Pol polyprotein 3.4.23.16 0.656
1b6k PI5Gag-Pol polyprotein 3.4.23.16 0.655
3nwq 2NCGag-Pol polyprotein 3.4.23.16 0.654
3nxe 2NCProtease / 0.654
1d4h BEHGag-Pol polyprotein 3.4.23.16 0.652
1t7k BH0Gag-Pol polyprotein 3.4.23.16 0.652
3nyg 2NCGag-Pol polyprotein 3.4.23.16 0.652
3zpu M8BGag-Pol polyprotein 3.4.23.16 0.651
1wbm BLLPol protein / 0.650