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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
3el9 DR7 Gag-Pol polyprotein 3.4.23.16

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3el9 DR7Gag-Pol polyprotein 3.4.23.16 1.595
3eky DR7Gag-Pol polyprotein 3.4.23.16 1.366
3el1 DR7Gag-Pol polyprotein 3.4.23.16 1.301
3oxx DR7Gag-Pol polyprotein 3.4.23.16 1.228
3em4 DR7Gag-Pol polyprotein 3.4.23.16 1.172
2fxe DR7Gag-Pol polyprotein 3.4.23.16 1.130
3ekw DR7Gag-Pol polyprotein 3.4.23.16 1.119
2aqu DR7Gag-Pol polyprotein 3.4.23.16 1.068
2fxd DR7Pol polyprotein / 0.991
2qi5 MZ7Gag-Pol polyprotein / 0.950
3kfr 3TLGag-Pol polyprotein / 0.943
3gga GGWGag-Pol polyprotein / 0.942
3kfn 3TLGag-Pol polyprotein / 0.929
1hih C20Gag-Pol polyprotein / 0.914
3nwq 2NCGag-Pol polyprotein 3.4.23.16 0.901
3kf0 3TLGag-Pol polyprotein / 0.898
3sa9 A68Protease / 0.894
1hii C20Gag-Pol polyprotein / 0.892
3sa5 A69Protease / 0.891
3s85 LK0Gag-Pol polyprotein / 0.889
3slz 3TLPutative gag-pro-pol polyprotein / 0.887
4k4p 3TLGag-Pol polyprotein / 0.887
1hvj A78Gag-Pol polyprotein / 0.886
1z1h HBBGag-Pol polyprotein 3.4.23.16 0.886
2p3c 3TLProtease / 0.884
3dcr KVSProtease / 0.871
3sab F78Protease / 0.871
3vfa 031Gag-Pol polyprotein 3.4.23.16 0.867
1hvi A77Protease / 0.864
3o9b K2APol polyprotein / 0.864
1fgc 2NCGag-Pol polyprotein 3.4.23.16 0.861
3hzc 2NCProtease / 0.859
3st5 G89Gag-Pol polyprotein 3.4.23.16 0.859
2qi0 MZ3Gag-Pol polyprotein / 0.857
3nxe 2NCProtease / 0.856
3dck KVIProtease / 0.854
3o99 K13Pol polyprotein / 0.852
2q54 MU1Protease / 0.848
2z54 AB1Gag-Pol polyprotein 3.4.23.16 0.847
3o9c K20Pol polyprotein / 0.844
1a8g 2Z4Gag-Pol polyprotein 3.4.23.16 0.841
3lzv 017Gag-Pol polyprotein 3.4.23.16 0.841
4dfg 0JVGag-Pol polyprotein 3.4.23.16 0.839
3o9h K2EGag-Pol polyprotein / 0.837
4kb9 G79Protease / 0.836
4hdp G52Gag-Pol polyprotein 3.4.23.16 0.835
3vf7 031Gag-Pol polyprotein 3.4.23.16 0.834
1izh Q50Protease / 0.832
1hvs A77Gag-Pol polyprotein / 0.831
2f80 017Gag-Pol polyprotein 3.4.23.16 0.831
2cem 2AHPol protein / 0.830
3nyg 2NCGag-Pol polyprotein 3.4.23.16 0.829
2qci 065Gag-Pol polyprotein 3.4.23.16 0.828
3o9a K14Pol polyprotein / 0.825
2hb3 GRLProtease / 0.819
1ida 0POGag-Pol polyprotein 3.4.23.47 0.818
2a1e IPFGag-Pol polyprotein 3.4.23.16 0.817
4q1w 017Gag-Pol polyprotein 3.4.23.16 0.816
3i6o GR6Gag-Pol polyprotein 3.4.23.16 0.814
2nnp ROCProtease / 0.813
3d20 017Gag-Pol polyprotein 3.4.23.16 0.813
2qd7 065Gag-Pol polyprotein 3.4.23.16 0.812
3pwm 017Gag-Pol polyprotein 3.4.23.16 0.812
3vf5 031Gag-Pol polyprotein 3.4.23.16 0.811
3i2l 2NCProtease / 0.810
3oy4 017Gag-Pol polyprotein 3.4.23.16 0.810
3s56 ROCProtease / 0.810
4hdf G52Gag-Pol polyprotein 3.4.23.16 0.810
4dqb 017Gag-Pol polyprotein / 0.808
3zpt M8YGag-Pol polyprotein 3.4.23.16 0.807
4djr 0KJPol polyprotein / 0.807
3o9d K19Pol polyprotein / 0.806
4heg G52Gag-Pol polyprotein 3.4.23.16 0.805
2avm 2NCGag-Pol polyprotein 3.4.23.16 0.804
3r4b 74TGag-Pol polyprotein / 0.803
2idw 017Protease / 0.802
3kfs 3TLGag-Pol polyprotein / 0.802
3o9f K2DGag-Pol polyprotein / 0.802
2q5k AB1Protease / 0.801
2qd8 065Gag-Pol polyprotein 3.4.23.16 0.801
2ien 017Gag-Pol polyprotein 3.4.23.16 0.800
1hiv 1ZKGag-Pol polyprotein / 0.799
1fg6 2NCGag-Pol polyprotein 3.4.23.16 0.798
3sa4 F72Protease / 0.798
3sa8 K83Protease / 0.797
1hvk A79Gag-Pol polyprotein / 0.796
2aoe 0Q4Gag-Pol polyprotein 3.4.23.16 0.796
3bva 2NCGag-Pol polyprotein 3.4.23.16 0.796
4dqh 017Gag-Pol polyprotein / 0.795
3em6 017Gag-Pol polyprotein 3.4.23.16 0.794
3o9g F53Gag-Pol polyprotein / 0.794
3ufn ROCGag-Pol polyprotein / 0.794
4njt 017Protease / 0.794
2qi6 MZ8Gag-Pol polyprotein / 0.793
3toh 079Gag-Pol polyprotein 2.7.7.49 0.793
2f8g 017Gag-Pol polyprotein 3.4.23.16 0.792
1t3r 017Gag-Pol polyprotein 3.4.23.16 0.791
3sa6 F71Protease / 0.791
1izi Q50Gag-Pol polyprotein 3.4.23.16 0.790
2q63 1UNGag-Pol polyprotein 3.4.23.16 0.790
2qak 1UNGag-Pol polyprotein 3.4.23.16 0.790
4dqf 017Gag-Pol polyprotein / 0.789
1npa 3NHGag-Pol polyprotein 3.4.23.16 0.787
1npw LGZGag-Pol polyprotein 3.4.23.16 0.787
3cyx ROCGag-Pol polyprotein 3.4.23.16 0.787
3mxd K53Gag-Pol polyprotein 3.4.23.16 0.787
3tof 076Gag-Pol polyprotein 2.7.7.49 0.787
2f3k RO1Protease / 0.785
1daz 0Q4Gag-Pol polyprotein 3.4.23.16 0.784
1b6l PI4Gag-Pol polyprotein 3.4.23.16 0.783
1t7i 017Gag-Pol polyprotein 3.4.23.16 0.783
1d4l PI9Gag-Pol polyprotein 3.4.23.16 0.782
2b60 RITPol polyprotein / 0.782
3ggu 017Gag-Pol polyprotein 3.4.23.16 0.782
3t3c 017Gag-Pol polyprotein 3.4.23.16 0.782
4djo MK5Pol polyprotein / 0.782
2i4u DJRProtease / 0.781
2rkf AB1Pol protein / 0.781
3dk1 G05Gag-Pol polyprotein 3.4.23.16 0.781
3ecg 065Gag-Pol polyprotein 3.4.23.47 0.780
3oxw 017Gag-Pol polyprotein 3.4.23.16 0.780
2rkg AB1Pol protein / 0.779
1sbg IM1Gag-Pol polyprotein / 0.778
1siv PSIGag-Pol polyprotein / 0.778
2f81 017Gag-Pol polyprotein 3.4.23.16 0.778
1jld 0PPGag-Pol polyprotein / 0.776
4djp M73Pol polyprotein / 0.776
1dw6 0Q4Gag-Pol polyprotein 3.4.23.16 0.775
4dqc 017Gag-Pol polyprotein / 0.775
3ok9 G52Gag-Pol polyprotein 3.4.23.16 0.774
4njs G08Protease / 0.774
3el4 ROCGag-Pol polyprotein 3.4.23.16 0.773
3ekv 478Gag-Pol polyprotein 3.4.23.16 0.772
3lzu 017Gag-Pol polyprotein 3.4.23.16 0.772
2hs2 017Protease / 0.771
3sac AF8Protease / 0.771
2nmy ROCProtease / 0.770
3d1y ROCGag-Pol polyprotein 3.4.23.16 0.769
3saa 77FProtease / 0.769
4q1y 017Gag-Pol polyprotein 3.4.23.16 0.768
3ec0 GRLGag-Pol polyprotein 3.4.23.47 0.767
3em3 478Gag-Pol polyprotein 3.4.23.16 0.767
3tl9 ROCGag-Pol polyprotein 3.4.23.16 0.767
1k2b 0Q4Gag-Pol polyprotein 3.4.23.16 0.764
1ffi 2NCGag-Pol polyprotein 3.4.23.16 0.763
2qi4 MZ6Gag-Pol polyprotein / 0.763
2wkz 5AHGag-Pol polyprotein / 0.763
3d1z 017Gag-Pol polyprotein 3.4.23.16 0.763
3ndw RITGag-Pol polyprotein 3.4.23.16 0.763
4njv RITProtease / 0.763
2hs1 017Protease / 0.762
3vfb 031Gag-Pol polyprotein 3.4.23.16 0.762
9hvp 0E9Gag-Pol polyprotein / 0.761
2ieo 017Protease / 0.759
3k4v ROCGag-Pol polyprotein 3.4.23.16 0.759
3ucb 017Gag-Pol polyprotein / 0.759
3el5 1UNGag-Pol polyprotein / 0.758
1mrw K57Gag-Pol polyprotein 3.4.23.16 0.757
1ody LP1Gag-Pol polyprotein 3.4.23.16 0.757
2p3b 3TLV-1 PROTEASE protein / 0.757
2p3b 3TLV-1 protease / 0.757
3ekt 017Gag-Pol polyprotein 3.4.23.16 0.757
3i7e DJRGag-Pol polyprotein / 0.757
3s54 017Protease / 0.757
3d1x ROCGag-Pol polyprotein 3.4.23.16 0.756
3sa7 55AProtease / 0.756
2qhc AB1Protease / 0.755
3ggx GGXGag-Pol polyprotein / 0.755
3nu6 478Gag-Pol polyprotein 3.4.23.16 0.755
4j5j 478Gag-Pol polyprotein 3.4.23.16 0.754
1a94 0Q4Gag-Pol polyprotein 3.4.23.16 0.753
4hdb G52Gag-Pol polyprotein 3.4.23.16 0.753
2nnk ROCProtease / 0.752
3djk G55Gag-Pol polyprotein 3.4.23.16 0.751
2xye CXGGag-Pol polyprotein / 0.750
3nwx KVSGag-Pol polyprotein 3.4.23.16 0.750
3sm2 478Putative gag-pro-pol polyprotein / 0.747
2qd6 065Gag-Pol polyprotein 3.4.23.16 0.745
3ndx RITGag-Pol polyprotein 3.4.23.16 0.745
4qgi ROCGag-Pol polyprotein 3.4.23.16 0.745
1hpv 478Gag-Pol polyprotein / 0.744
2xyf G40Gag-Pol polyprotein / 0.744
3ekq ROCGag-Pol polyprotein 3.4.23.16 0.744
3qaa G04Gag-Pol polyprotein 3.4.23.16 0.743
3sa3 23XProtease / 0.742
3nu9 478Gag-Pol polyprotein 3.4.23.16 0.741
1z1r HBHGag-Pol polyprotein 3.4.23.16 0.740
2q55 MU0Protease / 0.740
2p3d 3TLProtease / 0.739
3o9e A60Pol polyprotein / 0.739
1k2c 0Q4Gag-Pol polyprotein 3.4.23.16 0.738
3bxr DRRGag-Pol polyprotein 3.4.23.16 0.738
3o9i A61Gag-Pol polyprotein / 0.738
1tcx IM1Gag-Pol polyprotein 3.4.23.16 0.737
2z4o 065Gag-Pol polyprotein 3.4.23.16 0.737
1fej 2NCGag-Pol polyprotein 3.4.23.16 0.736
2cen 4AHProtease / 0.735
1k6t XN1Gag-Pol polyprotein 3.4.23.16 0.734
1hxb ROCGag-Pol polyprotein 3.4.23.16 0.733
1pro A88Gag-Pol polyprotein / 0.731
3ndu ROCGag-Pol polyprotein 3.4.23.16 0.731
3nu3 478Gag-Pol polyprotein 3.4.23.16 0.731
3pwr ROCGag-Pol polyprotein 3.4.23.16 0.731
1vij BAYGag-Pol polyprotein / 0.730
4dqe 017Gag-Pol polyprotein / 0.730
2fdd 385Pol protein / 0.728
3mws 017Pol protein / 0.728
3s43 478Protease / 0.726
3oxv 478Gag-Pol polyprotein 3.4.23.16 0.725
3zps EQMGag-Pol polyprotein 3.4.23.16 0.724
3zpu M8BGag-Pol polyprotein 3.4.23.16 0.724
3jvy 017Gag-Pol polyprotein 3.4.23.16 0.721
3nuo 478Gag-Pol polyprotein 3.4.23.16 0.721
1hos PHPGag-Pol polyprotein / 0.720
3lzs 017Gag-Pol polyprotein 3.4.23.16 0.719
1fg8 0Q4Gag-Pol polyprotein 3.4.23.16 0.718
1npv L27Gag-Pol polyprotein 3.4.23.16 0.718
1hvl A76Gag-Pol polyprotein / 0.717
1ff0 2NCGag-Pol polyprotein 3.4.23.16 0.716
3liv E16Protease / 0.715
1bdr IM1Gag-Pol polyprotein 3.4.23.16 0.714
4i8z G08Gag-Pol polyprotein 3.4.23.16 0.714
3bxs DRSGag-Pol polyprotein 3.4.23.16 0.712
3lin E13Protease / 0.712
4j54 G52Gag-Pol polyprotein 3.4.23.16 0.711
2uxz HI1Gag-Pol polyprotein 3.4.23.16 0.710
3nu4 478Gag-Pol polyprotein 3.4.23.16 0.710
2bb9 AKCGag-Pol polyprotein 3.4.23.16 0.708
2fmb LP1Reverse transcriptase / 0.708
1mrx K57Gag-Pol polyprotein 3.4.23.16 0.707
2wl0 5AHGag-Pol polyprotein / 0.707
1g35 AHFGag-Pol polyprotein 3.4.23.16 0.706
2hc0 AB2Protease / 0.706
1b6k PI5Gag-Pol polyprotein 3.4.23.16 0.705
4hla 017Gag-Pol polyprotein 3.4.23.16 0.705
2pym 1UNGag-Pol polyprotein 3.4.23.16 0.704
2a4f AAUV-1 protease / 0.700
1b6p PI7Gag-Pol polyprotein 3.4.23.16 0.699
2qi1 MZ4Gag-Pol polyprotein / 0.697
4q1x 017Gag-Pol polyprotein 3.4.23.16 0.697
3gi6 D78Gag-Pol polyprotein / 0.694
2fde 385Gag-Pol polyprotein 3.4.23.16 0.693
2i4w KGQProtease / 0.693
2p3a 3TLPol protein / 0.693
2q64 1UNGag-Pol polyprotein 3.4.23.16 0.693
3el0 1UNGag-Pol polyprotein 3.4.23.16 0.693
1idb 0DOGag-Pol polyprotein / 0.692
1d4k PI8Gag-Pol polyprotein 3.4.23.16 0.689
1rl8 RITGag-Pol polyprotein 3.4.23.16 0.689
3nu5 478Gag-Pol polyprotein 3.4.23.16 0.689
1qbr XV6Gag-Pol polyprotein 3.4.23.16 0.688
2pyn 1UNGag-Pol polyprotein 3.4.23.16 0.687
4a6c QG9Gag-Pol polyprotein 3.4.23.16 0.687
1ohr 1UNV-1 PROTEASE protein / 0.686
1fmb HYBPol polyprotein / 0.685
1ivq 0PXGag-Pol polyprotein / 0.685
1hpx KNIGag-Pol polyprotein / 0.684
3jw2 017Gag-Pol polyprotein 3.4.23.16 0.684
1iiq 0ZRGag-Pol polyprotein 3.4.23.16 0.682
4ye3 G04Gag-Pol polyprotein 3.4.23.16 0.682
1m0b 0ZQGag-Pol polyprotein 3.4.23.16 0.681
1ec0 BEDGag-Pol polyprotein 3.4.23.16 0.675
1a8k 0Q4Gag-Pol polyprotein 3.4.23.16 0.674
1ec1 BEEGag-Pol polyprotein 3.4.23.16 0.673
1mtr PI6Gag-Pol polyprotein 3.4.23.16 0.673
3ttp 017Gag-Pol polyprotein 3.4.23.16 0.673
1ebk 0Q4Gag-Pol polyprotein 3.4.23.16 0.671
1zsf 0ZSGag-Pol polyprotein 3.4.23.16 0.669
2r5q 1UNGag-Pol polyprotein / 0.669
1sh9 RITGag-Pol polyprotein 3.4.23.16 0.667
2jji 0QSEndothiapepsin 3.4.23.22 0.667
3lix E17Protease / 0.666
2bpz 3INGag-Pol polyprotein 3.4.23.16 0.665
3ndt ROCGag-Pol polyprotein 3.4.23.16 0.665
2fle AIProtease / 0.664
2i0a MUIProtease / 0.664
4a4q UX9Pol protein / 0.664
1d4i BEGGag-Pol polyprotein 3.4.23.16 0.663
3nuj 478Gag-Pol polyprotein 3.4.23.16 0.663
2bpy 3INGag-Pol polyprotein 3.4.23.16 0.662
4djq M86Pol polyprotein / 0.662
1qbt 146Gag-Pol polyprotein 3.4.23.16 0.660
1ec3 MS3Gag-Pol polyprotein 3.4.23.16 0.659
2az8 3TLGag-Pol polyprotein 3.4.23.16 0.659
2az9 3TLGag-Pol polyprotein 3.4.23.16 0.658
2pk5 075Protease / 0.658
3kfp 3TLGag-Pol polyprotein / 0.658
2i4d QFIProtease / 0.656
3cyw 017Gag-Pol polyprotein 3.4.23.16 0.656
3ekx 1UNGag-Pol polyprotein 3.4.23.16 0.656
3gi5 K62Gag-Pol polyprotein / 0.655
1ppk IVVPenicillopepsin-1 3.4.23.20 0.654
1e82 M90Endothiapepsin 3.4.23.22 0.653
1yt9 OISGag-Pol polyprotein / 0.653
1ec2 BEJGag-Pol polyprotein 3.4.23.16 0.652
1k6v XN2Gag-Pol polyprotein 3.4.23.16 0.651
1bwa XV6Gag-Pol polyprotein 3.4.23.16 0.650
3so9 017Pol protein / 0.650