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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
3sa9 A68 Protease

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity
Align
3sa9 A68Protease / 1.388
4djp M73Pol polyprotein / 1.167
3sa8 K83Protease / 1.158
3sa7 55AProtease / 1.150
3sa3 23XProtease / 1.141
2i0a MUIProtease / 1.140
2qi5 MZ7Gag-Pol polyprotein / 1.138
3gi4 K60Gag-Pol polyprotein / 1.128
3o9c K20Pol polyprotein / 1.102
3gi6 D78Gag-Pol polyprotein / 1.101
3o9f K2DGag-Pol polyprotein / 1.093
4hdp G52Gag-Pol polyprotein 3.4.23.16 1.093
3sab F78Protease / 1.091
2qi7 MZ9Gag-Pol polyprotein / 1.089
3o9h K2EGag-Pol polyprotein / 1.087
4kb9 G79Protease / 1.087
2i0d MUTProtease / 1.083
4djo MK5Pol polyprotein / 1.083
3mxd K53Gag-Pol polyprotein 3.4.23.16 1.081
4djq M86Pol polyprotein / 1.078
3gi5 K62Gag-Pol polyprotein / 1.074
4heg G52Gag-Pol polyprotein 3.4.23.16 1.060
3o9a K14Pol polyprotein / 1.053
3ekv 478Gag-Pol polyprotein 3.4.23.16 1.040
3oy4 017Gag-Pol polyprotein 3.4.23.16 1.040
2qi0 MZ3Gag-Pol polyprotein / 1.030
3st5 G89Gag-Pol polyprotein 3.4.23.16 1.030
3saa 77FProtease / 1.027
4hdf G52Gag-Pol polyprotein 3.4.23.16 1.020
3o9d K19Pol polyprotein / 1.013
2psu MUUProtease / 1.005
3o9g F53Gag-Pol polyprotein / 1.003
2qi4 MZ6Gag-Pol polyprotein / 1.000
2qhy MZ1Gag-Pol polyprotein / 0.999
2hb3 GRLProtease / 0.998
3dk1 G05Gag-Pol polyprotein 3.4.23.16 0.998
2qci 065Gag-Pol polyprotein 3.4.23.16 0.997
4j54 G52Gag-Pol polyprotein 3.4.23.16 0.992
1t3r 017Gag-Pol polyprotein 3.4.23.16 0.990
4djr 0KJPol polyprotein / 0.988
1z1h HBBGag-Pol polyprotein 3.4.23.16 0.987
3qaa G04Gag-Pol polyprotein 3.4.23.16 0.987
2qi6 MZ8Gag-Pol polyprotein / 0.985
3djk G55Gag-Pol polyprotein 3.4.23.16 0.982
3pwm 017Gag-Pol polyprotein 3.4.23.16 0.981
3vf7 031Gag-Pol polyprotein 3.4.23.16 0.980
2qd7 065Gag-Pol polyprotein 3.4.23.16 0.979
3vf5 031Gag-Pol polyprotein 3.4.23.16 0.978
3mxe K54Gag-Pol polyprotein 3.4.23.16 0.977
4hdb G52Gag-Pol polyprotein 3.4.23.16 0.974
2i4d QFIProtease / 0.973
4dfg 0JVGag-Pol polyprotein 3.4.23.16 0.969
3o99 K13Pol polyprotein / 0.966
2i4u DJRProtease / 0.965
2qd6 065Gag-Pol polyprotein 3.4.23.16 0.963
3o9i A61Gag-Pol polyprotein / 0.962
3o9e A60Pol polyprotein / 0.960
2qd8 065Gag-Pol polyprotein 3.4.23.16 0.959
3eky DR7Gag-Pol polyprotein 3.4.23.16 0.957
3sa5 A69Protease / 0.955
2i4x KGQProtease / 0.954
3r4b 74TGag-Pol polyprotein / 0.954
3sa4 F72Protease / 0.954
3nu4 478Gag-Pol polyprotein 3.4.23.16 0.953
2f80 017Gag-Pol polyprotein 3.4.23.16 0.951
2z4o 065Gag-Pol polyprotein 3.4.23.16 0.951
4dqh 017Gag-Pol polyprotein / 0.950
2i4v DJRV-1 protease / 0.946
3o9b K2APol polyprotein / 0.945
3vfa 031Gag-Pol polyprotein 3.4.23.16 0.945
4dqb 017Gag-Pol polyprotein / 0.945
4q1w 017Gag-Pol polyprotein 3.4.23.16 0.942
4dqc 017Gag-Pol polyprotein / 0.938
2fdd 385Pol protein / 0.933
4j55 031Gag-Pol polyprotein 3.4.23.16 0.926
3lzv 017Gag-Pol polyprotein 3.4.23.16 0.925
4dqe 017Gag-Pol polyprotein / 0.925
3oxv 478Gag-Pol polyprotein 3.4.23.16 0.920
3ecg 065Gag-Pol polyprotein 3.4.23.47 0.919
3el1 DR7Gag-Pol polyprotein 3.4.23.16 0.918
3em3 478Gag-Pol polyprotein 3.4.23.16 0.915
3ok9 G52Gag-Pol polyprotein 3.4.23.16 0.912
4njs G08Protease / 0.911
3d1z 017Gag-Pol polyprotein 3.4.23.16 0.910
3d20 017Gag-Pol polyprotein 3.4.23.16 0.910
3vfb 031Gag-Pol polyprotein 3.4.23.16 0.907
4q1x 017Gag-Pol polyprotein 3.4.23.16 0.905
1t7i 017Gag-Pol polyprotein 3.4.23.16 0.902
3nuj 478Gag-Pol polyprotein 3.4.23.16 0.902
3nuo 478Gag-Pol polyprotein 3.4.23.16 0.902
3mws 017Pol protein / 0.901
4dqf 017Gag-Pol polyprotein / 0.897
2hs1 017Protease / 0.894
2qi3 MZ5Gag-Pol polyprotein / 0.894
3ec0 GRLGag-Pol polyprotein 3.4.23.47 0.894
3el9 DR7Gag-Pol polyprotein 3.4.23.16 0.894
2idw 017Protease / 0.892
3nu6 478Gag-Pol polyprotein 3.4.23.16 0.886
3em6 017Gag-Pol polyprotein 3.4.23.16 0.885
3oxw 017Gag-Pol polyprotein 3.4.23.16 0.884
3s43 478Protease / 0.882
4q1y 017Gag-Pol polyprotein 3.4.23.16 0.882
3i6o GR6Gag-Pol polyprotein 3.4.23.16 0.879
3cyw 017Gag-Pol polyprotein 3.4.23.16 0.878
2psv MUVProtease / 0.875
3nu3 478Gag-Pol polyprotein 3.4.23.16 0.875
3sa6 F71Protease / 0.871
1z1r HBHGag-Pol polyprotein 3.4.23.16 0.868
3nu9 478Gag-Pol polyprotein 3.4.23.16 0.867
3t3c 017Gag-Pol polyprotein 3.4.23.16 0.866
3nu5 478Gag-Pol polyprotein 3.4.23.16 0.865
3oxx DR7Gag-Pol polyprotein 3.4.23.16 0.864
4j5j 478Gag-Pol polyprotein 3.4.23.16 0.861
3sac AF8Protease / 0.860
2f81 017Gag-Pol polyprotein 3.4.23.16 0.856
4rvj 478Protease / 0.850
2hs2 017Protease / 0.847
3s54 017Protease / 0.847
1d4l PI9Gag-Pol polyprotein 3.4.23.16 0.843
3em4 DR7Gag-Pol polyprotein 3.4.23.16 0.840
2aqu DR7Gag-Pol polyprotein 3.4.23.16 0.837
3jvy 017Gag-Pol polyprotein 3.4.23.16 0.834
3bvb 017Gag-Pol polyprotein 3.4.23.16 0.831
3ucb 017Gag-Pol polyprotein / 0.827
3kfr 3TLGag-Pol polyprotein / 0.826
2fxe DR7Gag-Pol polyprotein 3.4.23.16 0.821
2a1e IPFGag-Pol polyprotein 3.4.23.16 0.819
4i8z G08Gag-Pol polyprotein 3.4.23.16 0.819
3jw2 017Gag-Pol polyprotein 3.4.23.16 0.815
4ye3 G04Gag-Pol polyprotein 3.4.23.16 0.815
3sm2 478Putative gag-pro-pol polyprotein / 0.813
2qhz MZ2Gag-Pol polyprotein / 0.811
1ida 0POGag-Pol polyprotein 3.4.23.47 0.810
2ien 017Gag-Pol polyprotein 3.4.23.16 0.809
1hpv 478Gag-Pol polyprotein / 0.806
3ekt 017Gag-Pol polyprotein 3.4.23.16 0.793
2ieo 017Protease / 0.792
3s85 LK0Gag-Pol polyprotein / 0.788
2fde 385Gag-Pol polyprotein 3.4.23.16 0.783
3lzs 017Gag-Pol polyprotein 3.4.23.16 0.782
1hih C20Gag-Pol polyprotein / 0.776
2qak 1UNGag-Pol polyprotein 3.4.23.16 0.774
1jld 0PPGag-Pol polyprotein / 0.772
2nmy ROCProtease / 0.771
3i7e DJRGag-Pol polyprotein / 0.771
3ekw DR7Gag-Pol polyprotein 3.4.23.16 0.770
1b6l PI4Gag-Pol polyprotein 3.4.23.16 0.769
1izh Q50Protease / 0.769
2fxd DR7Pol polyprotein / 0.768
2avs MK1Gag-Pol polyprotein 3.4.23.16 0.767
1npa 3NHGag-Pol polyprotein 3.4.23.16 0.766
1npw LGZGag-Pol polyprotein 3.4.23.16 0.766
2hc0 AB2Protease / 0.764
2f8g 017Gag-Pol polyprotein 3.4.23.16 0.763
3el4 ROCGag-Pol polyprotein 3.4.23.16 0.763
3k4v ROCGag-Pol polyprotein 3.4.23.16 0.762
3lzu 017Gag-Pol polyprotein 3.4.23.16 0.762
3i2l 2NCProtease / 0.761
1ffi 2NCGag-Pol polyprotein 3.4.23.16 0.758
1tcx IM1Gag-Pol polyprotein 3.4.23.16 0.758
3kfn 3TLGag-Pol polyprotein / 0.757
3tl9 ROCGag-Pol polyprotein 3.4.23.16 0.757
3ufn ROCGag-Pol polyprotein / 0.757
3d1x ROCGag-Pol polyprotein 3.4.23.16 0.755
1fg6 2NCGag-Pol polyprotein 3.4.23.16 0.752
2p3c 3TLProtease / 0.752
1fgc 2NCGag-Pol polyprotein 3.4.23.16 0.750
2fle AIProtease / 0.749
3s56 ROCProtease / 0.749
2pym 1UNGag-Pol polyprotein 3.4.23.16 0.748
3ggu 017Gag-Pol polyprotein 3.4.23.16 0.747
3kf0 3TLGag-Pol polyprotein / 0.745
2nnp ROCProtease / 0.744
3dck KVIProtease / 0.744
3slz 3TLPutative gag-pro-pol polyprotein / 0.744
1daz 0Q4Gag-Pol polyprotein 3.4.23.16 0.742
3cyx ROCGag-Pol polyprotein 3.4.23.16 0.742
1yt9 OISGag-Pol polyprotein / 0.740
2nnk ROCProtease / 0.740
9hvp 0E9Gag-Pol polyprotein / 0.738
4njt 017Protease / 0.736
4hla 017Gag-Pol polyprotein 3.4.23.16 0.734
1hvl A76Gag-Pol polyprotein / 0.733
1fej 2NCGag-Pol polyprotein 3.4.23.16 0.732
1fff 0Q4Gag-Pol polyprotein 3.4.23.16 0.732
1k6t XN1Gag-Pol polyprotein 3.4.23.16 0.732
1pro A88Gag-Pol polyprotein / 0.732
2p3d 3TLProtease / 0.731
3bxs DRSGag-Pol polyprotein 3.4.23.16 0.731
2qnp QN2Gag-Pol polyprotein 3.4.23.16 0.729
1sdv MK1Gag-Pol polyprotein 3.4.23.16 0.728
2f3k RO1Protease / 0.728
2q63 1UNGag-Pol polyprotein 3.4.23.16 0.728
2q64 1UNGag-Pol polyprotein 3.4.23.16 0.727
3kfs 3TLGag-Pol polyprotein / 0.727
2bb9 AKCGag-Pol polyprotein 3.4.23.16 0.726
2wkz 5AHGag-Pol polyprotein / 0.724
1sdt MK1Gag-Pol polyprotein 3.4.23.16 0.723
2cem 2AHPol protein / 0.723
1b6k PI5Gag-Pol polyprotein 3.4.23.16 0.722
1ff0 2NCGag-Pol polyprotein 3.4.23.16 0.721
1fg8 0Q4Gag-Pol polyprotein 3.4.23.16 0.717
3gga GGWGag-Pol polyprotein / 0.717
1bv7 XV6Gag-Pol polyprotein 3.4.23.16 0.716
1qbr XV6Gag-Pol polyprotein 3.4.23.16 0.714
1wbk 568Pol protein / 0.714
4qgi ROCGag-Pol polyprotein 3.4.23.16 0.714
1ohr 1UNV-1 PROTEASE protein / 0.713
1ajv NMBGag-Pol polyprotein 3.4.23.16 0.711
1a8g 2Z4Gag-Pol polyprotein 3.4.23.16 0.710
3ekq ROCGag-Pol polyprotein 3.4.23.16 0.710
2q54 MU1Protease / 0.709
3tof 076Gag-Pol polyprotein 2.7.7.49 0.708
1b6m PI6Gag-Pol polyprotein 3.4.23.16 0.707
2p3b 3TLV-1 PROTEASE protein / 0.706
2p3b 3TLV-1 protease / 0.706
2qi1 MZ4Gag-Pol polyprotein / 0.706
1siv PSIGag-Pol polyprotein / 0.702
3nyg 2NCGag-Pol polyprotein 3.4.23.16 0.702
2rkf AB1Pol protein / 0.701
1mrw K57Gag-Pol polyprotein 3.4.23.16 0.700
3jvw DMPGag-Pol polyprotein 3.4.23.16 0.700
2z54 AB1Gag-Pol polyprotein 3.4.23.16 0.697
1qbt 146Gag-Pol polyprotein 3.4.23.16 0.696
1sdu MK1Gag-Pol polyprotein 3.4.23.16 0.696
3bxr DRRGag-Pol polyprotein 3.4.23.16 0.695
1ec3 MS3Gag-Pol polyprotein 3.4.23.16 0.694
1d4j MSCGag-Pol polyprotein 3.4.23.16 0.691
2cen 4AHProtease / 0.690
3ggx GGXGag-Pol polyprotein / 0.688
1hos PHPGag-Pol polyprotein / 0.685
3pwr ROCGag-Pol polyprotein 3.4.23.16 0.685
1npv L27Gag-Pol polyprotein 3.4.23.16 0.683
3d1y ROCGag-Pol polyprotein 3.4.23.16 0.683
3ndt ROCGag-Pol polyprotein 3.4.23.16 0.683
1bdr IM1Gag-Pol polyprotein 3.4.23.16 0.682
1a94 0Q4Gag-Pol polyprotein 3.4.23.16 0.681
1k2c 0Q4Gag-Pol polyprotein 3.4.23.16 0.681
1b6p PI7Gag-Pol polyprotein 3.4.23.16 0.680
2pwr G4GGag-Pol polyprotein 3.4.23.16 0.678
2pyn 1UNGag-Pol polyprotein 3.4.23.16 0.678
1m0b 0ZQGag-Pol polyprotein 3.4.23.16 0.676
1meu DMPGag-Pol polyprotein 3.4.23.16 0.675
2bpy 3INGag-Pol polyprotein 3.4.23.16 0.675
2fmb LP1Reverse transcriptase / 0.675
1mrx K57Gag-Pol polyprotein 3.4.23.16 0.673
1hvk A79Gag-Pol polyprotein / 0.671
1ebz BECGag-Pol polyprotein 3.4.23.16 0.670
1msm JE2Gag-Pol polyprotein 3.4.23.16 0.670
1ivq 0PXGag-Pol polyprotein / 0.669
3uhl 2NCGag-Pol polyprotein 3.4.23.16 0.669
1d4i BEGGag-Pol polyprotein 3.4.23.16 0.668
1zsf 0ZSGag-Pol polyprotein 3.4.23.16 0.667
2bbb HH1Gag-Pol polyprotein 3.4.23.16 0.667
4k4p 3TLGag-Pol polyprotein / 0.667
1idb 0DOGag-Pol polyprotein / 0.665
1mtr PI6Gag-Pol polyprotein 3.4.23.16 0.665
2i4w KGQProtease / 0.664
3el0 1UNGag-Pol polyprotein 3.4.23.16 0.664
1bwa XV6Gag-Pol polyprotein 3.4.23.16 0.663
1hxb ROCGag-Pol polyprotein 3.4.23.16 0.663
2p3a 3TLPol protein / 0.663
2q55 MU0Protease / 0.660
3ekp 478Gag-Pol polyprotein 3.4.23.16 0.660
1w5w BE4Gag-Pol polyprotein 3.4.23.16 0.659
2cej 1AHPol protein / 0.659
1ec1 BEEGag-Pol polyprotein 3.4.23.16 0.658
1wbm BLLPol protein / 0.658
2pk5 075Protease / 0.658
2r5p MK1Gag-Pol polyprotein / 0.658
1rl8 RITGag-Pol polyprotein 3.4.23.16 0.657
1sbg IM1Gag-Pol polyprotein / 0.657
1ec0 BEDGag-Pol polyprotein 3.4.23.16 0.655
1ec2 BEJGag-Pol polyprotein 3.4.23.16 0.655
3nwx KVSGag-Pol polyprotein 3.4.23.16 0.655
1dw6 0Q4Gag-Pol polyprotein 3.4.23.16 0.654
3bva 2NCGag-Pol polyprotein 3.4.23.16 0.654
1c6x 3INProtease / 0.653
2avm 2NCGag-Pol polyprotein 3.4.23.16 0.651