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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
2cem 2AH Pol protein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity
Align
2cem 2AHPol protein / 1.560
2cen 4AHProtease / 1.319
2wkz 5AHGag-Pol polyprotein / 1.090
2cej 1AHPol protein / 1.025
2wl0 5AHGag-Pol polyprotein / 0.987
2bqv A1AProtease / 0.953
3oxx DR7Gag-Pol polyprotein 3.4.23.16 0.947
3eky DR7Gag-Pol polyprotein 3.4.23.16 0.940
1wbm BLLPol protein / 0.925
4a4q UX9Pol protein / 0.876
2aqu DR7Gag-Pol polyprotein 3.4.23.16 0.862
2avv MK1Gag-Pol polyprotein 3.4.23.16 0.862
2avs MK1Gag-Pol polyprotein 3.4.23.16 0.848
2uy0 HV1Gag-Pol polyprotein 3.4.23.16 0.842
3s85 LK0Gag-Pol polyprotein / 0.839
1ffi 2NCGag-Pol polyprotein 3.4.23.16 0.837
1sbg IM1Gag-Pol polyprotein / 0.833
1w5y BE6Gag-Pol polyprotein 3.4.23.16 0.830
3el9 DR7Gag-Pol polyprotein 3.4.23.16 0.830
3el1 DR7Gag-Pol polyprotein 3.4.23.16 0.829
1eby BEBGag-Pol polyprotein 3.4.23.16 0.823
1fgc 2NCGag-Pol polyprotein 3.4.23.16 0.819
2bb9 AKCGag-Pol polyprotein 3.4.23.16 0.818
1fg6 2NCGag-Pol polyprotein 3.4.23.16 0.815
1w5x BE5Gag-Pol polyprotein 3.4.23.16 0.815
3i2l 2NCProtease / 0.812
2fdd 385Pol protein / 0.811
1izh Q50Protease / 0.807
3ekw DR7Gag-Pol polyprotein 3.4.23.16 0.803
3em4 DR7Gag-Pol polyprotein 3.4.23.16 0.803
3dck KVIProtease / 0.802
4hdp G52Gag-Pol polyprotein 3.4.23.16 0.799
1w5w BE4Gag-Pol polyprotein 3.4.23.16 0.793
3hzc 2NCProtease / 0.791
4hdb G52Gag-Pol polyprotein 3.4.23.16 0.789
2fxd DR7Pol polyprotein / 0.788
1b6p PI7Gag-Pol polyprotein 3.4.23.16 0.787
1mtr PI6Gag-Pol polyprotein 3.4.23.16 0.787
1fej 2NCGag-Pol polyprotein 3.4.23.16 0.786
2a1e IPFGag-Pol polyprotein 3.4.23.16 0.785
3nyg 2NCGag-Pol polyprotein 3.4.23.16 0.785
3sab F78Protease / 0.782
1k2b 0Q4Gag-Pol polyprotein 3.4.23.16 0.779
3mws 017Pol protein / 0.778
1daz 0Q4Gag-Pol polyprotein 3.4.23.16 0.777
2xye CXGGag-Pol polyprotein / 0.776
3jvy 017Gag-Pol polyprotein 3.4.23.16 0.774
3ok9 G52Gag-Pol polyprotein 3.4.23.16 0.774
3o9h K2EGag-Pol polyprotein / 0.773
2hs2 017Protease / 0.772
2r5p MK1Gag-Pol polyprotein / 0.772
2fxe DR7Gag-Pol polyprotein 3.4.23.16 0.770
2i4u DJRProtease / 0.770
1sdv MK1Gag-Pol polyprotein 3.4.23.16 0.769
1jld 0PPGag-Pol polyprotein / 0.767
4kb9 G79Protease / 0.765
1b6k PI5Gag-Pol polyprotein 3.4.23.16 0.764
1hos PHPGag-Pol polyprotein / 0.764
1b6m PI6Gag-Pol polyprotein 3.4.23.16 0.763
1d4k PI8Gag-Pol polyprotein 3.4.23.16 0.763
3s43 478Protease / 0.763
4ye3 G04Gag-Pol polyprotein 3.4.23.16 0.763
3vfb 031Gag-Pol polyprotein 3.4.23.16 0.757
1sdt MK1Gag-Pol polyprotein 3.4.23.16 0.756
3nuo 478Gag-Pol polyprotein 3.4.23.16 0.756
3nxe 2NCProtease / 0.756
3bxr DRRGag-Pol polyprotein 3.4.23.16 0.755
3toh 079Gag-Pol polyprotein 2.7.7.49 0.755
2qi5 MZ7Gag-Pol polyprotein / 0.754
3kfs 3TLGag-Pol polyprotein / 0.754
4hdf G52Gag-Pol polyprotein 3.4.23.16 0.753
3s54 017Protease / 0.752
1dif A85Gag-Pol polyprotein / 0.751
1ida 0POGag-Pol polyprotein 3.4.23.47 0.751
2aoe 0Q4Gag-Pol polyprotein 3.4.23.16 0.751
1ec3 MS3Gag-Pol polyprotein 3.4.23.16 0.750
1tcx IM1Gag-Pol polyprotein 3.4.23.16 0.748
3nu5 478Gag-Pol polyprotein 3.4.23.16 0.748
1d4j MSCGag-Pol polyprotein 3.4.23.16 0.746
3tof 076Gag-Pol polyprotein 2.7.7.49 0.746
1z1r HBHGag-Pol polyprotein 3.4.23.16 0.745
2qd6 065Gag-Pol polyprotein 3.4.23.16 0.744
2xyf G40Gag-Pol polyprotein / 0.743
3bvb 017Gag-Pol polyprotein 3.4.23.16 0.743
4heg G52Gag-Pol polyprotein 3.4.23.16 0.743
1iiq 0ZRGag-Pol polyprotein 3.4.23.16 0.742
1k6c MK1Gag-Pol polyprotein 3.4.23.16 0.742
2pk6 O33V-1 protease / 0.742
3vf7 031Gag-Pol polyprotein 3.4.23.16 0.742
1d4l PI9Gag-Pol polyprotein 3.4.23.16 0.741
1ff0 2NCGag-Pol polyprotein 3.4.23.16 0.741
1z1h HBBGag-Pol polyprotein 3.4.23.16 0.741
2qci 065Gag-Pol polyprotein 3.4.23.16 0.740
3vfa 031Gag-Pol polyprotein 3.4.23.16 0.740
2fle AIProtease / 0.739
3kdb 006Gag-Pol polyprotein 3.4.23.16 0.739
4hla 017Gag-Pol polyprotein 3.4.23.16 0.739
1sdu MK1Gag-Pol polyprotein 3.4.23.16 0.738
3i6o GR6Gag-Pol polyprotein 3.4.23.16 0.738
3nwq 2NCGag-Pol polyprotein 3.4.23.16 0.738
1mrw K57Gag-Pol polyprotein 3.4.23.16 0.737
3sa5 A69Protease / 0.737
1ody LP1Gag-Pol polyprotein 3.4.23.16 0.735
3d20 017Gag-Pol polyprotein 3.4.23.16 0.735
3kfr 3TLGag-Pol polyprotein / 0.735
1k6t XN1Gag-Pol polyprotein 3.4.23.16 0.734
1izi Q50Gag-Pol polyprotein 3.4.23.16 0.732
2f8g 017Gag-Pol polyprotein 3.4.23.16 0.732
3jw2 017Gag-Pol polyprotein 3.4.23.16 0.731
1mrx K57Gag-Pol polyprotein 3.4.23.16 0.729
3bva 2NCGag-Pol polyprotein 3.4.23.16 0.729
1fff 0Q4Gag-Pol polyprotein 3.4.23.16 0.728
1hvr XK2Gag-Pol polyprotein / 0.728
3ecg 065Gag-Pol polyprotein 3.4.23.47 0.728
3zps EQMGag-Pol polyprotein 3.4.23.16 0.728
2avm 2NCGag-Pol polyprotein 3.4.23.16 0.726
2uxz HI1Gag-Pol polyprotein 3.4.23.16 0.726
3lzs 017Gag-Pol polyprotein 3.4.23.16 0.726
2i4w KGQProtease / 0.725
3ndw RITGag-Pol polyprotein 3.4.23.16 0.725
3sa9 A68Protease / 0.723
1ajv NMBGag-Pol polyprotein 3.4.23.16 0.722
1mui AB1Protease / 0.722
3qaa G04Gag-Pol polyprotein 3.4.23.16 0.722
4k4p 3TLGag-Pol polyprotein / 0.722
1d4i BEGGag-Pol polyprotein 3.4.23.16 0.721
3sa8 K83Protease / 0.719
4njt 017Protease / 0.719
2q5k AB1Protease / 0.718
3o9a K14Pol polyprotein / 0.717
3o9i A61Gag-Pol polyprotein / 0.717
2z4o 065Gag-Pol polyprotein 3.4.23.16 0.716
3liv E16Protease / 0.715
2qi0 MZ3Gag-Pol polyprotein / 0.714
4njs G08Protease / 0.714
3d1x ROCGag-Pol polyprotein 3.4.23.16 0.713
3gga GGWGag-Pol polyprotein / 0.713
1c6y MK1Protease / 0.712
3d1y ROCGag-Pol polyprotein 3.4.23.16 0.712
3zpu M8BGag-Pol polyprotein 3.4.23.16 0.712
1hii C20Gag-Pol polyprotein / 0.711
2q54 MU1Protease / 0.711
3nu3 478Gag-Pol polyprotein 3.4.23.16 0.711
3oxw 017Gag-Pol polyprotein 3.4.23.16 0.711
3nwx KVSGag-Pol polyprotein 3.4.23.16 0.710
3sa3 23XProtease / 0.710
3sa4 F72Protease / 0.710
2p3b 3TLV-1 PROTEASE protein / 0.709
2p3b 3TLV-1 protease / 0.709
1a8g 2Z4Gag-Pol polyprotein 3.4.23.16 0.708
1hvi A77Protease / 0.708
3ggu 017Gag-Pol polyprotein 3.4.23.16 0.708
4dqe 017Gag-Pol polyprotein / 0.708
1wbk 568Pol protein / 0.707
2qhc AB1Protease / 0.707
3em3 478Gag-Pol polyprotein 3.4.23.16 0.707
3sa7 55AProtease / 0.707
1fg8 0Q4Gag-Pol polyprotein 3.4.23.16 0.706
2az9 3TLGag-Pol polyprotein 3.4.23.16 0.706
2bbb HH1Gag-Pol polyprotein 3.4.23.16 0.706
2fde 385Gag-Pol polyprotein 3.4.23.16 0.706
3ndt ROCGag-Pol polyprotein 3.4.23.16 0.705
3ndx RITGag-Pol polyprotein 3.4.23.16 0.705
3wsj MK1Protease / 0.705
3fx5 KNIGag-Pol polyprotein 3.4.23.16 0.704
3k4v ROCGag-Pol polyprotein 3.4.23.16 0.704
3nu6 478Gag-Pol polyprotein 3.4.23.16 0.704
4rvj 478Protease / 0.704
1ebz BECGag-Pol polyprotein 3.4.23.16 0.703
1npv L27Gag-Pol polyprotein 3.4.23.16 0.703
2f81 017Gag-Pol polyprotein 3.4.23.16 0.703
3st5 G89Gag-Pol polyprotein 3.4.23.16 0.703
1ec0 BEDGag-Pol polyprotein 3.4.23.16 0.702
2hs1 017Protease / 0.702
3tog 079Gag-Pol polyprotein 2.7.7.49 0.702
3zpt M8YGag-Pol polyprotein 3.4.23.16 0.702
1ebk 0Q4Gag-Pol polyprotein 3.4.23.16 0.701
3ekt 017Gag-Pol polyprotein 3.4.23.16 0.700
3o9e A60Pol polyprotein / 0.700
1g35 AHFGag-Pol polyprotein 3.4.23.16 0.699
4njv RITProtease / 0.699
3o99 K13Pol polyprotein / 0.698
4j54 G52Gag-Pol polyprotein 3.4.23.16 0.698
2i4x KGQProtease / 0.697
3pwm 017Gag-Pol polyprotein 3.4.23.16 0.697
4q1w 017Gag-Pol polyprotein 3.4.23.16 0.697
2pk5 075Protease / 0.696
3i7e DJRGag-Pol polyprotein / 0.696
3ekq ROCGag-Pol polyprotein 3.4.23.16 0.695
3nu4 478Gag-Pol polyprotein 3.4.23.16 0.695
3saa 77FProtease / 0.695
2hb3 GRLProtease / 0.694
4dfg 0JVGag-Pol polyprotein 3.4.23.16 0.694
1hvk A79Gag-Pol polyprotein / 0.693
1rl8 RITGag-Pol polyprotein 3.4.23.16 0.693
1w5v BE3Gag-Pol polyprotein 3.4.23.16 0.693
3liq E14Protease / 0.693
3ndu ROCGag-Pol polyprotein 3.4.23.16 0.693
4j55 031Gag-Pol polyprotein 3.4.23.16 0.693
2qhy MZ1Gag-Pol polyprotein / 0.692
3vf5 031Gag-Pol polyprotein 3.4.23.16 0.692
1a94 0Q4Gag-Pol polyprotein 3.4.23.16 0.691
1k2c 0Q4Gag-Pol polyprotein 3.4.23.16 0.691
1k6p XN3Gag-Pol polyprotein 3.4.23.16 0.691
2rkf AB1Pol protein / 0.691
2b60 RITPol polyprotein / 0.689
2i0a MUIProtease / 0.688
3bxs DRSGag-Pol polyprotein 3.4.23.16 0.688
3ekv 478Gag-Pol polyprotein 3.4.23.16 0.688
3o9g F53Gag-Pol polyprotein / 0.688
2rkg AB1Pol protein / 0.685
3kf0 3TLGag-Pol polyprotein / 0.685
3nls 016Gag-Pol polyprotein 3.4.23.16 0.685
3o9f K2DGag-Pol polyprotein / 0.685
3lix E17Protease / 0.684
3pwr ROCGag-Pol polyprotein 3.4.23.16 0.684
4dqb 017Gag-Pol polyprotein / 0.683
2p3d 3TLProtease / 0.682
3slz 3TLPutative gag-pro-pol polyprotein / 0.682
4a6b QG8Gag-Pol polyprotein 3.4.23.16 0.682
4dqh 017Gag-Pol polyprotein / 0.682
1n49 RITGag-Pol polyprotein 3.4.23.16 0.681
3dcr KVSProtease / 0.681
3ec0 GRLGag-Pol polyprotein 3.4.23.47 0.681
1hpx KNIGag-Pol polyprotein / 0.680
1m0b 0ZQGag-Pol polyprotein 3.4.23.16 0.680
3kdc JZPGag-Pol polyprotein 3.4.23.16 0.680
3lit E15Protease / 0.680
1ivp 1ZKGag-Pol polyprotein / 0.679
1t3r 017Gag-Pol polyprotein 3.4.23.16 0.679
3cyw 017Gag-Pol polyprotein 3.4.23.16 0.679
4a6c QG9Gag-Pol polyprotein 3.4.23.16 0.679
1a9m U0EGag-Pol polyprotein / 0.678
3nuj 478Gag-Pol polyprotein 3.4.23.16 0.677
3s56 ROCProtease / 0.677
4djo MK5Pol polyprotein / 0.677
4djp M73Pol polyprotein / 0.677
1dw6 0Q4Gag-Pol polyprotein 3.4.23.16 0.676
3kdd JZQGag-Pol polyprotein 3.4.23.16 0.676
1b11 3TLPol polyprotein / 0.675
1c70 L75Protease / 0.675
1fmb HYBPol polyprotein / 0.675
1qbt 146Gag-Pol polyprotein 3.4.23.16 0.675
1hiv 1ZKGag-Pol polyprotein / 0.674
2qak 1UNGag-Pol polyprotein 3.4.23.16 0.674
3em6 017Gag-Pol polyprotein 3.4.23.16 0.674
3mxd K53Gag-Pol polyprotein 3.4.23.16 0.674
1pro A88Gag-Pol polyprotein / 0.673
3kfn 3TLGag-Pol polyprotein / 0.673
3sm2 478Putative gag-pro-pol polyprotein / 0.673
2ien 017Gag-Pol polyprotein 3.4.23.16 0.672
3oxv 478Gag-Pol polyprotein 3.4.23.16 0.671
1kzk JE2Gag-Pol polyprotein 3.4.23.16 0.670
3o9b K2APol polyprotein / 0.670
1hvj A78Gag-Pol polyprotein / 0.669
3d1z 017Gag-Pol polyprotein 3.4.23.16 0.669
3ufn ROCGag-Pol polyprotein / 0.669
4gb2 0LQGag-Pol polyprotein 2.7.7.49 0.669
1yt9 OISGag-Pol polyprotein / 0.668
2bpx MK1Gag-Pol polyprotein 3.4.23.16 0.668
3bgb LJGGag-Pol polyprotein 3.4.23.16 0.668
3o9c K20Pol polyprotein / 0.668
1zsr 0ZTGag-Pol polyprotein 3.4.23.16 0.667
2p3c 3TLProtease / 0.667
2i4d QFIProtease / 0.666
2pym 1UNGag-Pol polyprotein 3.4.23.16 0.666
3sac AF8Protease / 0.666
2psv MUVProtease / 0.665
2qi6 MZ8Gag-Pol polyprotein / 0.665
4q1y 017Gag-Pol polyprotein 3.4.23.16 0.665
3ekp 478Gag-Pol polyprotein 3.4.23.16 0.664
4q1x 017Gag-Pol polyprotein 3.4.23.16 0.664
1msm JE2Gag-Pol polyprotein 3.4.23.16 0.663
2f3k RO1Protease / 0.663
1bdr IM1Gag-Pol polyprotein 3.4.23.16 0.661
4dqf 017Gag-Pol polyprotein / 0.661
1hxw RITGag-Pol polyprotein / 0.660
3lzv 017Gag-Pol polyprotein 3.4.23.16 0.660
4djq M86Pol polyprotein / 0.660
2i4v DJRV-1 protease / 0.659
2nmy ROCProtease / 0.659
2q63 1UNGag-Pol polyprotein 3.4.23.16 0.658
2z54 AB1Gag-Pol polyprotein 3.4.23.16 0.658
4dqc 017Gag-Pol polyprotein / 0.657
9hvp 0E9Gag-Pol polyprotein / 0.657
3a2o KNJGag-Pol polyprotein 3.4.23.16 0.655
3dk1 G05Gag-Pol polyprotein 3.4.23.16 0.655
3sa6 F71Protease / 0.655
1hsh MK1Gag-Pol polyprotein / 0.654
3t3c 017Gag-Pol polyprotein 3.4.23.16 0.654
3uhl 2NCGag-Pol polyprotein 3.4.23.16 0.654
2idw 017Protease / 0.653
2psu MUUProtease / 0.653
1b6l PI4Gag-Pol polyprotein 3.4.23.16 0.652
2ieo 017Protease / 0.652
2qnq QN3Gag-Pol polyprotein 3.4.23.16 0.652
1t7k BH0Gag-Pol polyprotein 3.4.23.16 0.651
3nu9 478Gag-Pol polyprotein 3.4.23.16 0.651
4dgo 0JWCasein kinase II subunit alpha 2.7.11.1 0.650
4djr 0KJPol polyprotein / 0.650