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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
3i2l 2NC Protease

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity
Align
3i2l 2NCProtease / 1.604
3nwq 2NCGag-Pol polyprotein 3.4.23.16 1.211
3nyg 2NCGag-Pol polyprotein 3.4.23.16 1.181
3nxe 2NCProtease / 1.161
2avm 2NCGag-Pol polyprotein 3.4.23.16 1.125
1fej 2NCGag-Pol polyprotein 3.4.23.16 1.109
1fg6 2NCGag-Pol polyprotein 3.4.23.16 1.093
3dck KVIProtease / 1.084
3dcr KVSProtease / 1.084
3hzc 2NCProtease / 1.076
1ffi 2NCGag-Pol polyprotein 3.4.23.16 1.065
3bva 2NCGag-Pol polyprotein 3.4.23.16 1.064
3nwx KVSGag-Pol polyprotein 3.4.23.16 1.037
1fgc 2NCGag-Pol polyprotein 3.4.23.16 1.025
1ff0 2NCGag-Pol polyprotein 3.4.23.16 0.996
2aoe 0Q4Gag-Pol polyprotein 3.4.23.16 0.991
1daz 0Q4Gag-Pol polyprotein 3.4.23.16 0.932
1iiq 0ZRGag-Pol polyprotein 3.4.23.16 0.927
1a94 0Q4Gag-Pol polyprotein 3.4.23.16 0.918
1k1u 0Q4Gag-Pol polyprotein 3.4.23.16 0.911
1k2c 0Q4Gag-Pol polyprotein 3.4.23.16 0.907
1dw6 0Q4Gag-Pol polyprotein 3.4.23.16 0.904
1k2b 0Q4Gag-Pol polyprotein 3.4.23.16 0.888
3bxr DRRGag-Pol polyprotein 3.4.23.16 0.882
3el1 DR7Gag-Pol polyprotein 3.4.23.16 0.870
3em4 DR7Gag-Pol polyprotein 3.4.23.16 0.863
1izh Q50Protease / 0.857
2a1e IPFGag-Pol polyprotein 3.4.23.16 0.848
1izi Q50Gag-Pol polyprotein 3.4.23.16 0.846
3oxx DR7Gag-Pol polyprotein 3.4.23.16 0.846
1m0b 0ZQGag-Pol polyprotein 3.4.23.16 0.845
1fff 0Q4Gag-Pol polyprotein 3.4.23.16 0.837
1ody LP1Gag-Pol polyprotein 3.4.23.16 0.831
2p3c 3TLProtease / 0.829
1fg8 0Q4Gag-Pol polyprotein 3.4.23.16 0.827
1hvi A77Protease / 0.819
3kf0 3TLGag-Pol polyprotein / 0.814
2cem 2AHPol protein / 0.812
3el9 DR7Gag-Pol polyprotein 3.4.23.16 0.810
1a8k 0Q4Gag-Pol polyprotein 3.4.23.16 0.802
3ekw DR7Gag-Pol polyprotein 3.4.23.16 0.802
1b6p PI7Gag-Pol polyprotein 3.4.23.16 0.800
1hvj A78Gag-Pol polyprotein / 0.799
3gga GGWGag-Pol polyprotein / 0.798
2wkz 5AHGag-Pol polyprotein / 0.794
1ec1 BEEGag-Pol polyprotein 3.4.23.16 0.793
3kfr 3TLGag-Pol polyprotein / 0.792
3sa3 23XProtease / 0.790
1bai 0Q4Gag-Pro polyprotein / 0.786
3kfs 3TLGag-Pol polyprotein / 0.786
2aqu DR7Gag-Pol polyprotein 3.4.23.16 0.784
1d4l PI9Gag-Pol polyprotein 3.4.23.16 0.783
1sbg IM1Gag-Pol polyprotein / 0.782
1ebk 0Q4Gag-Pol polyprotein 3.4.23.16 0.780
2qi5 MZ7Gag-Pol polyprotein / 0.779
3kfn 3TLGag-Pol polyprotein / 0.778
1hos PHPGag-Pol polyprotein / 0.776
2cen 4AHProtease / 0.776
1hvs A77Gag-Pol polyprotein / 0.772
1dif A85Gag-Pol polyprotein / 0.770
3tog 079Gag-Pol polyprotein 2.7.7.49 0.770
1siv PSIGag-Pol polyprotein / 0.768
2uy0 HV1Gag-Pol polyprotein 3.4.23.16 0.768
2q54 MU1Protease / 0.765
3sa9 A68Protease / 0.761
3jw2 017Gag-Pol polyprotein 3.4.23.16 0.759
3ndw RITGag-Pol polyprotein 3.4.23.16 0.755
1zsr 0ZTGag-Pol polyprotein 3.4.23.16 0.754
1rl8 RITGag-Pol polyprotein 3.4.23.16 0.753
3tof 076Gag-Pol polyprotein 2.7.7.49 0.753
1hxw RITGag-Pol polyprotein / 0.752
3ndx RITGag-Pol polyprotein 3.4.23.16 0.752
1hvl A76Gag-Pol polyprotein / 0.751
4k4p 3TLGag-Pol polyprotein / 0.751
1mtr PI6Gag-Pol polyprotein 3.4.23.16 0.749
2wl0 5AHGag-Pol polyprotein / 0.749
1b6m PI6Gag-Pol polyprotein 3.4.23.16 0.748
2fxe DR7Gag-Pol polyprotein 3.4.23.16 0.748
2z4o 065Gag-Pol polyprotein 3.4.23.16 0.748
1ec3 MS3Gag-Pol polyprotein 3.4.23.16 0.745
1hiv 1ZKGag-Pol polyprotein / 0.745
1zj7 0ZTGag-Pol polyprotein 3.4.23.16 0.743
3ok9 G52Gag-Pol polyprotein 3.4.23.16 0.743
3qaa G04Gag-Pol polyprotein 3.4.23.16 0.742
1bdq IM1Gag-Pol polyprotein 3.4.23.16 0.741
1ec2 BEJGag-Pol polyprotein 3.4.23.16 0.741
2qci 065Gag-Pol polyprotein 3.4.23.16 0.737
3sab F78Protease / 0.737
4dqc 017Gag-Pol polyprotein / 0.737
2p3a 3TLPol protein / 0.735
3eky DR7Gag-Pol polyprotein 3.4.23.16 0.734
3vf5 031Gag-Pol polyprotein 3.4.23.16 0.734
3toh 079Gag-Pol polyprotein 2.7.7.49 0.732
2uxz HI1Gag-Pol polyprotein 3.4.23.16 0.731
3sa5 A69Protease / 0.731
1ebz BECGag-Pol polyprotein 3.4.23.16 0.726
1d4i BEGGag-Pol polyprotein 3.4.23.16 0.724
1w5w BE4Gag-Pol polyprotein 3.4.23.16 0.724
1a9m U0EGag-Pol polyprotein / 0.723
1w5x BE5Gag-Pol polyprotein 3.4.23.16 0.722
4heg G52Gag-Pol polyprotein 3.4.23.16 0.721
1bdr IM1Gag-Pol polyprotein 3.4.23.16 0.720
1n49 RITGag-Pol polyprotein 3.4.23.16 0.720
2ien 017Gag-Pol polyprotein 3.4.23.16 0.719
1npa 3NHGag-Pol polyprotein 3.4.23.16 0.718
1npw LGZGag-Pol polyprotein 3.4.23.16 0.718
1z1h HBBGag-Pol polyprotein 3.4.23.16 0.718
3i6o GR6Gag-Pol polyprotein 3.4.23.16 0.718
3st5 G89Gag-Pol polyprotein 3.4.23.16 0.718
3el4 ROCGag-Pol polyprotein 3.4.23.16 0.717
3pwm 017Gag-Pol polyprotein 3.4.23.16 0.717
3r4b 74TGag-Pol polyprotein / 0.717
4dfg 0JVGag-Pol polyprotein 3.4.23.16 0.717
4njv RITProtease / 0.717
2cej 1AHPol protein / 0.715
1ec0 BEDGag-Pol polyprotein 3.4.23.16 0.714
3d1y ROCGag-Pol polyprotein 3.4.23.16 0.713
1hih C20Gag-Pol polyprotein / 0.711
3sa7 55AProtease / 0.709
2f8g 017Gag-Pol polyprotein 3.4.23.16 0.708
3d20 017Gag-Pol polyprotein 3.4.23.16 0.708
1b6k PI5Gag-Pol polyprotein 3.4.23.16 0.707
2hs2 017Protease / 0.705
1hvk A79Gag-Pol polyprotein / 0.704
1w5y BE6Gag-Pol polyprotein 3.4.23.16 0.704
4hdf G52Gag-Pol polyprotein 3.4.23.16 0.704
3d1x ROCGag-Pol polyprotein 3.4.23.16 0.703
3el5 1UNGag-Pol polyprotein / 0.703
1hii C20Gag-Pol polyprotein / 0.702
2p3d 3TLProtease / 0.702
3bxs DRSGag-Pol polyprotein 3.4.23.16 0.702
4i8z G08Gag-Pol polyprotein 3.4.23.16 0.702
1a8g 2Z4Gag-Pol polyprotein 3.4.23.16 0.701
2i4w KGQProtease / 0.701
2pk5 075Protease / 0.701
9hvp 0E9Gag-Pol polyprotein / 0.701
1eby BEBGag-Pol polyprotein 3.4.23.16 0.700
1zsf 0ZSGag-Pol polyprotein 3.4.23.16 0.700
1tcx IM1Gag-Pol polyprotein 3.4.23.16 0.699
1d4y TPVGag-Pol polyprotein 3.4.23.16 0.698
4a4q UX9Pol protein / 0.698
3zpu M8BGag-Pol polyprotein 3.4.23.16 0.697
4hdb G52Gag-Pol polyprotein 3.4.23.16 0.695
2bpw 1INGag-Pol polyprotein 3.4.23.16 0.694
2fde 385Gag-Pol polyprotein 3.4.23.16 0.694
1pro A88Gag-Pol polyprotein / 0.693
4q1w 017Gag-Pol polyprotein 3.4.23.16 0.693
1odw 0E8Gag-Pol polyprotein 3.4.23.16 0.692
3mws 017Pol protein / 0.692
1sdu MK1Gag-Pol polyprotein 3.4.23.16 0.691
2f80 017Gag-Pol polyprotein 3.4.23.16 0.691
2rkg AB1Pol protein / 0.691
3fx5 KNIGag-Pol polyprotein 3.4.23.16 0.691
3tl9 ROCGag-Pol polyprotein 3.4.23.16 0.691
1kzk JE2Gag-Pol polyprotein 3.4.23.16 0.690
1sdt MK1Gag-Pol polyprotein 3.4.23.16 0.690
2i4d QFIProtease / 0.689
2rkf AB1Pol protein / 0.689
3bvb 017Gag-Pol polyprotein 3.4.23.16 0.689
3em3 478Gag-Pol polyprotein 3.4.23.16 0.689
3lzv 017Gag-Pol polyprotein 3.4.23.16 0.689
2fxd DR7Pol polyprotein / 0.688
3lzs 017Gag-Pol polyprotein 3.4.23.16 0.688
1msm JE2Gag-Pol polyprotein 3.4.23.16 0.687
2bqv A1AProtease / 0.687
2pk6 O33V-1 protease / 0.687
2qhc AB1Protease / 0.687
3t3c 017Gag-Pol polyprotein 3.4.23.16 0.687
4hdp G52Gag-Pol polyprotein 3.4.23.16 0.685
1fmb HYBPol polyprotein / 0.684
2pyn 1UNGag-Pol polyprotein 3.4.23.16 0.684
2qak 1UNGag-Pol polyprotein 3.4.23.16 0.684
3vf7 031Gag-Pol polyprotein 3.4.23.16 0.684
1hsh MK1Gag-Pol polyprotein / 0.683
3cyw 017Gag-Pol polyprotein 3.4.23.16 0.683
1msn JE2Gag-Pol polyprotein 3.4.23.16 0.682
2f3k RO1Protease / 0.682
3pwr ROCGag-Pol polyprotein 3.4.23.16 0.682
1vij BAYGag-Pol polyprotein / 0.681
2i4u DJRProtease / 0.681
3ggu 017Gag-Pol polyprotein 3.4.23.16 0.681
1ida 0POGag-Pol polyprotein 3.4.23.47 0.679
1ivp 1ZKGag-Pol polyprotein / 0.679
2a4f AAUV-1 protease / 0.679
2q64 1UNGag-Pol polyprotein 3.4.23.16 0.679
2o4p TPVProtease / 0.678
3el0 1UNGag-Pol polyprotein 3.4.23.16 0.678
3ndt ROCGag-Pol polyprotein 3.4.23.16 0.678
2nnp ROCProtease / 0.677
1ohr 1UNV-1 PROTEASE protein / 0.676
4dqh 017Gag-Pol polyprotein / 0.676
1jld 0PPGag-Pol polyprotein / 0.675
3nls 016Gag-Pol polyprotein 3.4.23.16 0.675
4dqb 017Gag-Pol polyprotein / 0.675
3o9a K14Pol polyprotein / 0.674
3o9c K20Pol polyprotein / 0.674
1npv L27Gag-Pol polyprotein 3.4.23.16 0.673
2b60 RITPol polyprotein / 0.673
2bpx MK1Gag-Pol polyprotein 3.4.23.16 0.673
3o9b K2APol polyprotein / 0.673
4dqe 017Gag-Pol polyprotein / 0.673
4nju TPVProtease / 0.673
4rvj 478Protease / 0.673
1k6p XN3Gag-Pol polyprotein 3.4.23.16 0.672
3jvy 017Gag-Pol polyprotein 3.4.23.16 0.672
3o9e A60Pol polyprotein / 0.672
1sh9 RITGag-Pol polyprotein 3.4.23.16 0.671
3em6 017Gag-Pol polyprotein 3.4.23.16 0.671
3oxv 478Gag-Pol polyprotein 3.4.23.16 0.671
3o9d K19Pol polyprotein / 0.670
3o9f K2DGag-Pol polyprotein / 0.670
3o9h K2EGag-Pol polyprotein / 0.670
1wbm BLLPol protein / 0.669
3i7e DJRGag-Pol polyprotein / 0.669
1hpv 478Gag-Pol polyprotein / 0.668
1sdv MK1Gag-Pol polyprotein 3.4.23.16 0.668
3ekp 478Gag-Pol polyprotein 3.4.23.16 0.668
3nuj 478Gag-Pol polyprotein 3.4.23.16 0.668
1hsg MK1Gag-Pol polyprotein / 0.667
2r5p MK1Gag-Pol polyprotein / 0.667
3ufn ROCGag-Pol polyprotein / 0.666
2r5q 1UNGag-Pol polyprotein / 0.665
2xye CXGGag-Pol polyprotein / 0.665
3k4v ROCGag-Pol polyprotein 3.4.23.16 0.665
2q5k AB1Protease / 0.663
1mrx K57Gag-Pol polyprotein 3.4.23.16 0.662
3ekv 478Gag-Pol polyprotein 3.4.23.16 0.662
4fiv LP1POL protein / 0.662
2q55 MU0Protease / 0.661
3bgb LJGGag-Pol polyprotein 3.4.23.16 0.661
1d4h BEHGag-Pol polyprotein 3.4.23.16 0.660
1d4k PI8Gag-Pol polyprotein 3.4.23.16 0.660
1hpx KNIGag-Pol polyprotein / 0.660
3d1z 017Gag-Pol polyprotein 3.4.23.16 0.660
2xyf G40Gag-Pol polyprotein / 0.659
2psu MUUProtease / 0.658
2qi0 MZ3Gag-Pol polyprotein / 0.658
3sa4 F72Protease / 0.658
3ekx 1UNGag-Pol polyprotein 3.4.23.16 0.657
3lzu 017Gag-Pol polyprotein 3.4.23.16 0.657
3oy4 017Gag-Pol polyprotein 3.4.23.16 0.657
4kb9 G79Protease / 0.657
1b6l PI4Gag-Pol polyprotein 3.4.23.16 0.656
1ebw BEIGag-Pol polyprotein 3.4.23.16 0.656
1mrw K57Gag-Pol polyprotein 3.4.23.16 0.656
2pym 1UNGag-Pol polyprotein 3.4.23.16 0.656
2qhy MZ1Gag-Pol polyprotein / 0.656
3kfp 3TLGag-Pol polyprotein / 0.655
3o9g F53Gag-Pol polyprotein / 0.655
3o9i A61Gag-Pol polyprotein / 0.655
4q1y 017Gag-Pol polyprotein 3.4.23.16 0.655
1odx 0E8Gag-Pol polyprotein 3.4.23.16 0.654
1t7i 017Gag-Pol polyprotein 3.4.23.16 0.654
2qd6 065Gag-Pol polyprotein 3.4.23.16 0.654
3sm2 478Putative gag-pro-pol polyprotein / 0.654
3zpt M8YGag-Pol polyprotein 3.4.23.16 0.654
2hs1 017Protease / 0.653
2i4v DJRV-1 protease / 0.652
2qd7 065Gag-Pol polyprotein 3.4.23.16 0.652
3s56 ROCProtease / 0.652
4q1x 017Gag-Pol polyprotein 3.4.23.16 0.652
3a2o KNJGag-Pol polyprotein 3.4.23.16 0.651
2qi4 MZ6Gag-Pol polyprotein / 0.650
3nu4 478Gag-Pol polyprotein 3.4.23.16 0.650
3slz 3TLPutative gag-pro-pol polyprotein / 0.650
4djp M73Pol polyprotein / 0.650