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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
3vfa 031 Gag-Pol polyprotein 3.4.23.16

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity
Align
3vfa 031Gag-Pol polyprotein 3.4.23.16 1.454
3vf7 031Gag-Pol polyprotein 3.4.23.16 1.307
3st5 G89Gag-Pol polyprotein 3.4.23.16 1.284
3dk1 G05Gag-Pol polyprotein 3.4.23.16 1.223
2hb3 GRLProtease / 1.220
3vfb 031Gag-Pol polyprotein 3.4.23.16 1.208
3vf5 031Gag-Pol polyprotein 3.4.23.16 1.186
4dfg 0JVGag-Pol polyprotein 3.4.23.16 1.185
3pwm 017Gag-Pol polyprotein 3.4.23.16 1.166
3djk G55Gag-Pol polyprotein 3.4.23.16 1.165
4j55 031Gag-Pol polyprotein 3.4.23.16 1.140
2qci 065Gag-Pol polyprotein 3.4.23.16 1.136
2z4o 065Gag-Pol polyprotein 3.4.23.16 1.118
3o9a K14Pol polyprotein / 1.117
4hdb G52Gag-Pol polyprotein 3.4.23.16 1.114
2qd7 065Gag-Pol polyprotein 3.4.23.16 1.110
4heg G52Gag-Pol polyprotein 3.4.23.16 1.106
4kb9 G79Protease / 1.095
2qd8 065Gag-Pol polyprotein 3.4.23.16 1.090
3o9b K2APol polyprotein / 1.089
4dqh 017Gag-Pol polyprotein / 1.084
3ok9 G52Gag-Pol polyprotein 3.4.23.16 1.083
3o9c K20Pol polyprotein / 1.080
3oy4 017Gag-Pol polyprotein 3.4.23.16 1.080
2i4w KGQProtease / 1.076
4djo MK5Pol polyprotein / 1.073
2i4d QFIProtease / 1.072
3qaa G04Gag-Pol polyprotein 3.4.23.16 1.072
2f80 017Gag-Pol polyprotein 3.4.23.16 1.071
4njs G08Protease / 1.070
2i4u DJRProtease / 1.069
3sa8 K83Protease / 1.069
3o9h K2EGag-Pol polyprotein / 1.065
4dqe 017Gag-Pol polyprotein / 1.062
4dqf 017Gag-Pol polyprotein / 1.060
3o9d K19Pol polyprotein / 1.057
3ecg 065Gag-Pol polyprotein 3.4.23.47 1.049
3saa 77FProtease / 1.047
4dqb 017Gag-Pol polyprotein / 1.047
4hdf G52Gag-Pol polyprotein 3.4.23.16 1.046
2idw 017Protease / 1.042
3o9f K2DGag-Pol polyprotein / 1.041
3o9g F53Gag-Pol polyprotein / 1.041
4hdp G52Gag-Pol polyprotein 3.4.23.16 1.039
2qd6 065Gag-Pol polyprotein 3.4.23.16 1.037
3d20 017Gag-Pol polyprotein 3.4.23.16 1.036
4dqc 017Gag-Pol polyprotein / 1.036
3ec0 GRLGag-Pol polyprotein 3.4.23.47 1.030
2f81 017Gag-Pol polyprotein 3.4.23.16 1.029
1t3r 017Gag-Pol polyprotein 3.4.23.16 1.028
3sab F78Protease / 1.027
3o9e A60Pol polyprotein / 1.023
3mws 017Pol protein / 1.021
3r4b 74TGag-Pol polyprotein / 1.021
4q1w 017Gag-Pol polyprotein 3.4.23.16 1.012
3mxd K53Gag-Pol polyprotein 3.4.23.16 1.009
2qi4 MZ6Gag-Pol polyprotein / 1.008
4djq M86Pol polyprotein / 1.006
1t7i 017Gag-Pol polyprotein 3.4.23.16 1.005
4q1y 017Gag-Pol polyprotein 3.4.23.16 1.002
3i6o GR6Gag-Pol polyprotein 3.4.23.16 1.001
3mxe K54Gag-Pol polyprotein 3.4.23.16 0.999
3gi4 K60Gag-Pol polyprotein / 0.998
3jvy 017Gag-Pol polyprotein 3.4.23.16 0.993
4i8z G08Gag-Pol polyprotein 3.4.23.16 0.992
2i0a MUIProtease / 0.984
3oxw 017Gag-Pol polyprotein 3.4.23.16 0.984
2fdd 385Pol protein / 0.979
3t3c 017Gag-Pol polyprotein 3.4.23.16 0.978
3lzs 017Gag-Pol polyprotein 3.4.23.16 0.972
3lzv 017Gag-Pol polyprotein 3.4.23.16 0.971
4njt 017Protease / 0.970
2i4x KGQProtease / 0.967
3jw2 017Gag-Pol polyprotein 3.4.23.16 0.967
3sa4 F72Protease / 0.967
1z1h HBBGag-Pol polyprotein 3.4.23.16 0.965
3o9i A61Gag-Pol polyprotein / 0.965
3gi6 D78Gag-Pol polyprotein / 0.964
3lzu 017Gag-Pol polyprotein 3.4.23.16 0.959
2ien 017Gag-Pol polyprotein 3.4.23.16 0.956
2qi6 MZ8Gag-Pol polyprotein / 0.956
2psu MUUProtease / 0.953
3ekv 478Gag-Pol polyprotein 3.4.23.16 0.952
3em6 017Gag-Pol polyprotein 3.4.23.16 0.952
2ieo 017Protease / 0.946
2qi7 MZ9Gag-Pol polyprotein / 0.946
3sa9 A68Protease / 0.945
3o99 K13Pol polyprotein / 0.942
4j54 G52Gag-Pol polyprotein 3.4.23.16 0.942
2qi0 MZ3Gag-Pol polyprotein / 0.936
3nu6 478Gag-Pol polyprotein 3.4.23.16 0.935
3sac AF8Protease / 0.927
3cyw 017Gag-Pol polyprotein 3.4.23.16 0.924
3ucb 017Gag-Pol polyprotein / 0.923
1z1r HBHGag-Pol polyprotein 3.4.23.16 0.922
3ekt 017Gag-Pol polyprotein 3.4.23.16 0.922
2i0d MUTProtease / 0.920
2qhy MZ1Gag-Pol polyprotein / 0.920
3gi5 K62Gag-Pol polyprotein / 0.918
4djp M73Pol polyprotein / 0.918
4ye3 G04Gag-Pol polyprotein 3.4.23.16 0.918
2hs1 017Protease / 0.916
3em3 478Gag-Pol polyprotein 3.4.23.16 0.911
4djr 0KJPol polyprotein / 0.911
3i7e DJRGag-Pol polyprotein / 0.909
3d1z 017Gag-Pol polyprotein 3.4.23.16 0.907
2qi5 MZ7Gag-Pol polyprotein / 0.901
3s54 017Protease / 0.898
2qhz MZ2Gag-Pol polyprotein / 0.892
3sa5 A69Protease / 0.892
2f8g 017Gag-Pol polyprotein 3.4.23.16 0.888
3nuo 478Gag-Pol polyprotein 3.4.23.16 0.887
3eky DR7Gag-Pol polyprotein 3.4.23.16 0.882
2hs2 017Protease / 0.881
3oxx DR7Gag-Pol polyprotein 3.4.23.16 0.880
4hla 017Gag-Pol polyprotein 3.4.23.16 0.878
4q1x 017Gag-Pol polyprotein 3.4.23.16 0.877
3nu3 478Gag-Pol polyprotein 3.4.23.16 0.873
2qi3 MZ5Gag-Pol polyprotein / 0.871
1d4l PI9Gag-Pol polyprotein 3.4.23.16 0.868
3el9 DR7Gag-Pol polyprotein 3.4.23.16 0.867
3sa3 23XProtease / 0.867
4rvj 478Protease / 0.867
3sa7 55AProtease / 0.866
3oxv 478Gag-Pol polyprotein 3.4.23.16 0.864
2fde 385Gag-Pol polyprotein 3.4.23.16 0.860
3nu4 478Gag-Pol polyprotein 3.4.23.16 0.860
3nu9 478Gag-Pol polyprotein 3.4.23.16 0.858
4j5j 478Gag-Pol polyprotein 3.4.23.16 0.842
3sa6 F71Protease / 0.841
3sm2 478Putative gag-pro-pol polyprotein / 0.834
3el1 DR7Gag-Pol polyprotein 3.4.23.16 0.832
3nuj 478Gag-Pol polyprotein 3.4.23.16 0.824
2q63 1UNGag-Pol polyprotein 3.4.23.16 0.816
2psv MUVProtease / 0.814
1npv L27Gag-Pol polyprotein 3.4.23.16 0.807
3nu5 478Gag-Pol polyprotein 3.4.23.16 0.805
2aqu DR7Gag-Pol polyprotein 3.4.23.16 0.799
2fxe DR7Gag-Pol polyprotein 3.4.23.16 0.799
2pym 1UNGag-Pol polyprotein 3.4.23.16 0.789
1izh Q50Protease / 0.784
1sdt MK1Gag-Pol polyprotein 3.4.23.16 0.779
1mrw K57Gag-Pol polyprotein 3.4.23.16 0.778
2nmy ROCProtease / 0.775
3ggu 017Gag-Pol polyprotein 3.4.23.16 0.775
1yt9 OISGag-Pol polyprotein / 0.774
3tl9 ROCGag-Pol polyprotein 3.4.23.16 0.773
1b6k PI5Gag-Pol polyprotein 3.4.23.16 0.769
3em4 DR7Gag-Pol polyprotein 3.4.23.16 0.769
3k4v ROCGag-Pol polyprotein 3.4.23.16 0.769
4k4p 3TLGag-Pol polyprotein / 0.767
3s43 478Protease / 0.766
2p3a 3TLPol protein / 0.765
3s56 ROCProtease / 0.764
3bvb 017Gag-Pol polyprotein 3.4.23.16 0.763
3s85 LK0Gag-Pol polyprotein / 0.761
1izi Q50Gag-Pol polyprotein 3.4.23.16 0.760
3slz 3TLPutative gag-pro-pol polyprotein / 0.754
3kfs 3TLGag-Pol polyprotein / 0.750
1k6t XN1Gag-Pol polyprotein 3.4.23.16 0.748
1d4i BEGGag-Pol polyprotein 3.4.23.16 0.747
3el0 1UNGag-Pol polyprotein 3.4.23.16 0.746
1k2b 0Q4Gag-Pol polyprotein 3.4.23.16 0.743
2nnk ROCProtease / 0.742
1a8g 2Z4Gag-Pol polyprotein 3.4.23.16 0.741
2bpw 1INGag-Pol polyprotein 3.4.23.16 0.741
2nnp ROCProtease / 0.741
1fej 2NCGag-Pol polyprotein 3.4.23.16 0.738
1tcx IM1Gag-Pol polyprotein 3.4.23.16 0.737
1ohr 1UNV-1 PROTEASE protein / 0.732
3cyx ROCGag-Pol polyprotein 3.4.23.16 0.731
1sdv MK1Gag-Pol polyprotein 3.4.23.16 0.730
2fle AIProtease / 0.730
1hih C20Gag-Pol polyprotein / 0.729
2hc0 AB2Protease / 0.729
3ufn ROCGag-Pol polyprotein / 0.726
1b6l PI4Gag-Pol polyprotein 3.4.23.16 0.725
1fff 0Q4Gag-Pol polyprotein 3.4.23.16 0.725
1ida 0POGag-Pol polyprotein 3.4.23.47 0.725
2cem 2AHPol protein / 0.725
2q64 1UNGag-Pol polyprotein 3.4.23.16 0.725
2a1e IPFGag-Pol polyprotein 3.4.23.16 0.722
2cen 4AHProtease / 0.722
1msm JE2Gag-Pol polyprotein 3.4.23.16 0.721
2avs MK1Gag-Pol polyprotein 3.4.23.16 0.721
2p3d 3TLProtease / 0.720
1fg6 2NCGag-Pol polyprotein 3.4.23.16 0.719
3ekq ROCGag-Pol polyprotein 3.4.23.16 0.719
1ec1 BEEGag-Pol polyprotein 3.4.23.16 0.718
1npa 3NHGag-Pol polyprotein 3.4.23.16 0.717
1npw LGZGag-Pol polyprotein 3.4.23.16 0.717
4qgi ROCGag-Pol polyprotein 3.4.23.16 0.717
3gga GGWGag-Pol polyprotein / 0.716
1siv PSIGag-Pol polyprotein / 0.715
3kfr 3TLGag-Pol polyprotein / 0.715
1b6m PI6Gag-Pol polyprotein 3.4.23.16 0.713
1hxw RITGag-Pol polyprotein / 0.713
3pwr ROCGag-Pol polyprotein 3.4.23.16 0.712
1ebz BECGag-Pol polyprotein 3.4.23.16 0.710
2f3k RO1Protease / 0.710
3ekp 478Gag-Pol polyprotein 3.4.23.16 0.710
3d1y ROCGag-Pol polyprotein 3.4.23.16 0.708
3bxr DRRGag-Pol polyprotein 3.4.23.16 0.707
3d1x ROCGag-Pol polyprotein 3.4.23.16 0.707
3kf0 3TLGag-Pol polyprotein / 0.706
3ttp 017Gag-Pol polyprotein 3.4.23.16 0.705
1hvi A77Protease / 0.704
1iiq 0ZRGag-Pol polyprotein 3.4.23.16 0.704
1fgc 2NCGag-Pol polyprotein 3.4.23.16 0.703
1ivq 0PXGag-Pol polyprotein / 0.703
2bb9 AKCGag-Pol polyprotein 3.4.23.16 0.703
2qak 1UNGag-Pol polyprotein 3.4.23.16 0.703
1w5x BE5Gag-Pol polyprotein 3.4.23.16 0.702
1ec0 BEDGag-Pol polyprotein 3.4.23.16 0.701
2pk5 075Protease / 0.700
1k2c 0Q4Gag-Pol polyprotein 3.4.23.16 0.697
1qbr XV6Gag-Pol polyprotein 3.4.23.16 0.697
2fxd DR7Pol polyprotein / 0.697
1hvr XK2Gag-Pol polyprotein / 0.696
2i4v DJRV-1 protease / 0.696
3el4 ROCGag-Pol polyprotein 3.4.23.16 0.696
3nyg 2NCGag-Pol polyprotein 3.4.23.16 0.696
3kdc JZPGag-Pol polyprotein 3.4.23.16 0.690
1bdr IM1Gag-Pol polyprotein 3.4.23.16 0.687
1dmp DMQGag-Pol polyprotein 3.4.23.16 0.687
1ec3 MS3Gag-Pol polyprotein 3.4.23.16 0.687
1d4h BEHGag-Pol polyprotein 3.4.23.16 0.686
1qbu 846Gag-Pol polyprotein 3.4.23.16 0.686
1w5y BE6Gag-Pol polyprotein 3.4.23.16 0.686
1ec2 BEJGag-Pol polyprotein 3.4.23.16 0.685
1hvj A78Gag-Pol polyprotein / 0.685
1g35 AHFGag-Pol polyprotein 3.4.23.16 0.684
1mtr PI6Gag-Pol polyprotein 3.4.23.16 0.683
1pro A88Gag-Pol polyprotein / 0.683
2pk6 O33V-1 protease / 0.682
1hiv 1ZKGag-Pol polyprotein / 0.681
1hvs A77Gag-Pol polyprotein / 0.679
3kdd JZQGag-Pol polyprotein 3.4.23.16 0.679
3a2o KNJGag-Pol polyprotein 3.4.23.16 0.677
3hzc 2NCProtease / 0.675
2p4j 23IBeta-secretase 1 3.4.23.46 0.674
1a94 0Q4Gag-Pol polyprotein 3.4.23.16 0.673
2aoe 0Q4Gag-Pol polyprotein 3.4.23.16 0.672
1hsh MK1Gag-Pol polyprotein / 0.671
2q54 MU1Protease / 0.671
1eag A70Candidapepsin-2 3.4.23.24 0.670
3kfn 3TLGag-Pol polyprotein / 0.670
1wbm BLLPol protein / 0.668
2wl0 5AHGag-Pol polyprotein / 0.667
3dck KVIProtease / 0.667
1sbg IM1Gag-Pol polyprotein / 0.665
2q55 MU0Protease / 0.665
1mrx K57Gag-Pol polyprotein 3.4.23.16 0.664
1hvl A76Gag-Pol polyprotein / 0.661
1b6p PI7Gag-Pol polyprotein 3.4.23.16 0.659
1dw6 0Q4Gag-Pol polyprotein 3.4.23.16 0.658
1ff0 2NCGag-Pol polyprotein 3.4.23.16 0.658
3dcr KVSProtease / 0.658
2cej 1AHPol protein / 0.657
3jvw DMPGag-Pol polyprotein 3.4.23.16 0.656
1hos PHPGag-Pol polyprotein / 0.655
3nwq 2NCGag-Pol polyprotein 3.4.23.16 0.655
1ffi 2NCGag-Pol polyprotein 3.4.23.16 0.654
1jld 0PPGag-Pol polyprotein / 0.653
1od1 0QSEndothiapepsin 3.4.23.22 0.653
1eby BEBGag-Pol polyprotein 3.4.23.16 0.652
2avm 2NCGag-Pol polyprotein 3.4.23.16 0.652
3ekw DR7Gag-Pol polyprotein 3.4.23.16 0.652
3el5 1UNGag-Pol polyprotein / 0.652
3ndx RITGag-Pol polyprotein 3.4.23.16 0.652
3so9 017Pol protein / 0.652
3uhl 2NCGag-Pol polyprotein 3.4.23.16 0.650