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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
3st5 G89 Gag-Pol polyprotein 3.4.23.16

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity
Align
3st5 G89Gag-Pol polyprotein 3.4.23.16 1.424
3vfa 031Gag-Pol polyprotein 3.4.23.16 1.284
4dfg 0JVGag-Pol polyprotein 3.4.23.16 1.278
2hb3 GRLProtease / 1.262
3dk1 G05Gag-Pol polyprotein 3.4.23.16 1.259
2qci 065Gag-Pol polyprotein 3.4.23.16 1.257
3pwm 017Gag-Pol polyprotein 3.4.23.16 1.254
3vf7 031Gag-Pol polyprotein 3.4.23.16 1.234
2z4o 065Gag-Pol polyprotein 3.4.23.16 1.233
4kb9 G79Protease / 1.228
3qaa G04Gag-Pol polyprotein 3.4.23.16 1.205
3ok9 G52Gag-Pol polyprotein 3.4.23.16 1.202
2qd8 065Gag-Pol polyprotein 3.4.23.16 1.191
3djk G55Gag-Pol polyprotein 3.4.23.16 1.176
4heg G52Gag-Pol polyprotein 3.4.23.16 1.166
2qd6 065Gag-Pol polyprotein 3.4.23.16 1.162
3d20 017Gag-Pol polyprotein 3.4.23.16 1.154
2i4u DJRProtease / 1.151
3o9h K2EGag-Pol polyprotein / 1.127
4njs G08Protease / 1.127
3r4b 74TGag-Pol polyprotein / 1.125
2f80 017Gag-Pol polyprotein 3.4.23.16 1.124
3sa8 K83Protease / 1.124
4hdf G52Gag-Pol polyprotein 3.4.23.16 1.123
3oy4 017Gag-Pol polyprotein 3.4.23.16 1.112
3o9a K14Pol polyprotein / 1.111
4dqc 017Gag-Pol polyprotein / 1.107
3ecg 065Gag-Pol polyprotein 3.4.23.47 1.100
2f81 017Gag-Pol polyprotein 3.4.23.16 1.098
3o9b K2APol polyprotein / 1.091
4i8z G08Gag-Pol polyprotein 3.4.23.16 1.089
3o9g F53Gag-Pol polyprotein / 1.086
2i4x KGQProtease / 1.085
4dqe 017Gag-Pol polyprotein / 1.085
2i4v DJRV-1 protease / 1.082
3vfb 031Gag-Pol polyprotein 3.4.23.16 1.079
3vf5 031Gag-Pol polyprotein 3.4.23.16 1.077
4j55 031Gag-Pol polyprotein 3.4.23.16 1.074
3o9f K2DGag-Pol polyprotein / 1.073
4dqb 017Gag-Pol polyprotein / 1.073
3sab F78Protease / 1.072
4hdp G52Gag-Pol polyprotein 3.4.23.16 1.072
3o9c K20Pol polyprotein / 1.068
2qd7 065Gag-Pol polyprotein 3.4.23.16 1.065
3o9d K19Pol polyprotein / 1.062
4q1w 017Gag-Pol polyprotein 3.4.23.16 1.062
3lzu 017Gag-Pol polyprotein 3.4.23.16 1.060
2ien 017Gag-Pol polyprotein 3.4.23.16 1.057
2fdd 385Pol protein / 1.056
3ec0 GRLGag-Pol polyprotein 3.4.23.47 1.054
4djo MK5Pol polyprotein / 1.054
3mxd K53Gag-Pol polyprotein 3.4.23.16 1.053
4dqh 017Gag-Pol polyprotein / 1.050
2i4d QFIProtease / 1.049
2i4w KGQProtease / 1.049
3mws 017Pol protein / 1.049
4hdb G52Gag-Pol polyprotein 3.4.23.16 1.046
3o9i A61Gag-Pol polyprotein / 1.045
4j54 G52Gag-Pol polyprotein 3.4.23.16 1.041
1t3r 017Gag-Pol polyprotein 3.4.23.16 1.040
3i6o GR6Gag-Pol polyprotein 3.4.23.16 1.040
3jvy 017Gag-Pol polyprotein 3.4.23.16 1.040
4djq M86Pol polyprotein / 1.040
4dqf 017Gag-Pol polyprotein / 1.040
3em6 017Gag-Pol polyprotein 3.4.23.16 1.036
2idw 017Protease / 1.031
3saa 77FProtease / 1.031
3cyw 017Gag-Pol polyprotein 3.4.23.16 1.030
3sa9 A68Protease / 1.030
1t7i 017Gag-Pol polyprotein 3.4.23.16 1.028
3jw2 017Gag-Pol polyprotein 3.4.23.16 1.024
2ieo 017Protease / 1.017
3lzs 017Gag-Pol polyprotein 3.4.23.16 1.016
2qi7 MZ9Gag-Pol polyprotein / 1.012
3gi4 K60Gag-Pol polyprotein / 1.010
3t3c 017Gag-Pol polyprotein 3.4.23.16 1.010
3oxw 017Gag-Pol polyprotein 3.4.23.16 1.006
3lzv 017Gag-Pol polyprotein 3.4.23.16 1.005
3ucb 017Gag-Pol polyprotein / 1.003
2qi4 MZ6Gag-Pol polyprotein / 1.000
2hs1 017Protease / 0.999
2i0a MUIProtease / 0.998
4djp M73Pol polyprotein / 0.997
4q1y 017Gag-Pol polyprotein 3.4.23.16 0.994
3gi6 D78Gag-Pol polyprotein / 0.991
3o99 K13Pol polyprotein / 0.991
2qhy MZ1Gag-Pol polyprotein / 0.989
3o9e A60Pol polyprotein / 0.988
2qi0 MZ3Gag-Pol polyprotein / 0.981
3nu6 478Gag-Pol polyprotein 3.4.23.16 0.974
3ekv 478Gag-Pol polyprotein 3.4.23.16 0.972
1z1h HBBGag-Pol polyprotein 3.4.23.16 0.970
2qi6 MZ8Gag-Pol polyprotein / 0.968
3mxe K54Gag-Pol polyprotein 3.4.23.16 0.966
2psu MUUProtease / 0.963
3sa4 F72Protease / 0.962
3d1z 017Gag-Pol polyprotein 3.4.23.16 0.961
3em3 478Gag-Pol polyprotein 3.4.23.16 0.955
3ekt 017Gag-Pol polyprotein 3.4.23.16 0.953
4njt 017Protease / 0.944
3gi5 K62Gag-Pol polyprotein / 0.940
3sa7 55AProtease / 0.940
4djr 0KJPol polyprotein / 0.938
2i0d MUTProtease / 0.934
3nuo 478Gag-Pol polyprotein 3.4.23.16 0.921
4j5j 478Gag-Pol polyprotein 3.4.23.16 0.921
2f8g 017Gag-Pol polyprotein 3.4.23.16 0.919
2qhz MZ2Gag-Pol polyprotein / 0.919
3nu3 478Gag-Pol polyprotein 3.4.23.16 0.911
3nu9 478Gag-Pol polyprotein 3.4.23.16 0.911
2hs2 017Protease / 0.910
3s54 017Protease / 0.908
4q1x 017Gag-Pol polyprotein 3.4.23.16 0.908
3sac AF8Protease / 0.907
3sa5 A69Protease / 0.903
4ye3 G04Gag-Pol polyprotein 3.4.23.16 0.901
1z1r HBHGag-Pol polyprotein 3.4.23.16 0.896
3oxv 478Gag-Pol polyprotein 3.4.23.16 0.896
3nu4 478Gag-Pol polyprotein 3.4.23.16 0.895
3oxx DR7Gag-Pol polyprotein 3.4.23.16 0.894
3sa3 23XProtease / 0.893
1d4l PI9Gag-Pol polyprotein 3.4.23.16 0.892
3sa6 F71Protease / 0.885
3i7e DJRGag-Pol polyprotein / 0.871
2qi3 MZ5Gag-Pol polyprotein / 0.870
4hla 017Gag-Pol polyprotein 3.4.23.16 0.869
2fde 385Gag-Pol polyprotein 3.4.23.16 0.865
2qi5 MZ7Gag-Pol polyprotein / 0.864
3nuj 478Gag-Pol polyprotein 3.4.23.16 0.864
3nu5 478Gag-Pol polyprotein 3.4.23.16 0.861
3el9 DR7Gag-Pol polyprotein 3.4.23.16 0.859
2fxe DR7Gag-Pol polyprotein 3.4.23.16 0.858
2hc0 AB2Protease / 0.845
2psv MUVProtease / 0.842
3ggu 017Gag-Pol polyprotein 3.4.23.16 0.840
3el1 DR7Gag-Pol polyprotein 3.4.23.16 0.827
4rvj 478Protease / 0.825
1pro A88Gag-Pol polyprotein / 0.817
3em4 DR7Gag-Pol polyprotein 3.4.23.16 0.808
2nmy ROCProtease / 0.802
3s43 478Protease / 0.798
2a1e IPFGag-Pol polyprotein 3.4.23.16 0.788
1b6k PI5Gag-Pol polyprotein 3.4.23.16 0.784
1mrw K57Gag-Pol polyprotein 3.4.23.16 0.782
3bvb 017Gag-Pol polyprotein 3.4.23.16 0.782
3d1y ROCGag-Pol polyprotein 3.4.23.16 0.778
1npa 3NHGag-Pol polyprotein 3.4.23.16 0.772
1npw LGZGag-Pol polyprotein 3.4.23.16 0.772
3tl9 ROCGag-Pol polyprotein 3.4.23.16 0.772
2aqu DR7Gag-Pol polyprotein 3.4.23.16 0.771
1k6t XN1Gag-Pol polyprotein 3.4.23.16 0.761
3s85 LK0Gag-Pol polyprotein / 0.761
1izh Q50Protease / 0.759
2nnp ROCProtease / 0.759
1mrx K57Gag-Pol polyprotein 3.4.23.16 0.758
2bb9 AKCGag-Pol polyprotein 3.4.23.16 0.758
3kfn 3TLGag-Pol polyprotein / 0.756
1sdt MK1Gag-Pol polyprotein 3.4.23.16 0.755
1yt9 OISGag-Pol polyprotein / 0.755
3el4 ROCGag-Pol polyprotein 3.4.23.16 0.753
3k4v ROCGag-Pol polyprotein 3.4.23.16 0.751
4k4p 3TLGag-Pol polyprotein / 0.751
1ebz BECGag-Pol polyprotein 3.4.23.16 0.750
1b6l PI4Gag-Pol polyprotein 3.4.23.16 0.747
2q63 1UNGag-Pol polyprotein 3.4.23.16 0.744
1hvr XK2Gag-Pol polyprotein / 0.742
3eky DR7Gag-Pol polyprotein 3.4.23.16 0.742
2wkz 5AHGag-Pol polyprotein / 0.741
1a8g 2Z4Gag-Pol polyprotein 3.4.23.16 0.739
1siv PSIGag-Pol polyprotein / 0.736
4qgi ROCGag-Pol polyprotein 3.4.23.16 0.736
3cyx ROCGag-Pol polyprotein 3.4.23.16 0.735
1fff 0Q4Gag-Pol polyprotein 3.4.23.16 0.734
3kfs 3TLGag-Pol polyprotein / 0.732
1jld 0PPGag-Pol polyprotein / 0.729
2p3a 3TLPol protein / 0.729
1fej 2NCGag-Pol polyprotein 3.4.23.16 0.727
2nnk ROCProtease / 0.727
3s56 ROCProtease / 0.727
3ufn ROCGag-Pol polyprotein / 0.725
1bdr IM1Gag-Pol polyprotein 3.4.23.16 0.724
3ekp 478Gag-Pol polyprotein 3.4.23.16 0.724
1ida 0POGag-Pol polyprotein 3.4.23.47 0.723
2fle AIProtease / 0.723
3kfr 3TLGag-Pol polyprotein / 0.723
3el0 1UNGag-Pol polyprotein 3.4.23.16 0.722
1hiv 1ZKGag-Pol polyprotein / 0.721
3d1x ROCGag-Pol polyprotein 3.4.23.16 0.720
3i2l 2NCProtease / 0.718
1sdu MK1Gag-Pol polyprotein 3.4.23.16 0.717
2qak 1UNGag-Pol polyprotein 3.4.23.16 0.717
3slz 3TLPutative gag-pro-pol polyprotein / 0.717
3toh 079Gag-Pol polyprotein 2.7.7.49 0.717
3a2o KNJGag-Pol polyprotein 3.4.23.16 0.716
3pwr ROCGag-Pol polyprotein 3.4.23.16 0.714
1ffi 2NCGag-Pol polyprotein 3.4.23.16 0.712
1fgc 2NCGag-Pol polyprotein 3.4.23.16 0.711
1ec1 BEEGag-Pol polyprotein 3.4.23.16 0.710
1ivq 0PXGag-Pol polyprotein / 0.710
2f3k RO1Protease / 0.710
1ec3 MS3Gag-Pol polyprotein 3.4.23.16 0.707
1npv L27Gag-Pol polyprotein 3.4.23.16 0.706
1tcx IM1Gag-Pol polyprotein 3.4.23.16 0.706
3gga GGWGag-Pol polyprotein / 0.706
1g35 AHFGag-Pol polyprotein 3.4.23.16 0.705
1hih C20Gag-Pol polyprotein / 0.705
2pym 1UNGag-Pol polyprotein 3.4.23.16 0.704
4njv RITProtease / 0.704
2cem 2AHPol protein / 0.703
1c6y MK1Protease / 0.702
1ec0 BEDGag-Pol polyprotein 3.4.23.16 0.702
1sdv MK1Gag-Pol polyprotein 3.4.23.16 0.702
1hii C20Gag-Pol polyprotein / 0.701
1hvj A78Gag-Pol polyprotein / 0.701
1m0b 0ZQGag-Pol polyprotein 3.4.23.16 0.701
1b6m PI6Gag-Pol polyprotein 3.4.23.16 0.699
1w5x BE5Gag-Pol polyprotein 3.4.23.16 0.698
2q5k AB1Protease / 0.698
2cej 1AHPol protein / 0.695
1qbt 146Gag-Pol polyprotein 3.4.23.16 0.694
2r5p MK1Gag-Pol polyprotein / 0.694
1c6x 3INProtease / 0.693
3nyg 2NCGag-Pol polyprotein 3.4.23.16 0.693
1hvk A79Gag-Pol polyprotein / 0.690
2p3d 3TLProtease / 0.690
2q54 MU1Protease / 0.690
1rl8 RITGag-Pol polyprotein 3.4.23.16 0.689
3jvw DMPGag-Pol polyprotein 3.4.23.16 0.688
1qbu 846Gag-Pol polyprotein 3.4.23.16 0.685
3wsj MK1Protease / 0.684
2q64 1UNGag-Pol polyprotein 3.4.23.16 0.683
3bva 2NCGag-Pol polyprotein 3.4.23.16 0.683
2q55 MU0Protease / 0.681
3el5 1UNGag-Pol polyprotein / 0.678
1ec2 BEJGag-Pol polyprotein 3.4.23.16 0.676
1d4h BEHGag-Pol polyprotein 3.4.23.16 0.675
2b60 RITPol polyprotein / 0.671
2fxd DR7Pol polyprotein / 0.671
2wl0 5AHGag-Pol polyprotein / 0.671
3qp0 NI8Gag-Pol polyprotein 3.4.23.16 0.671
1dmp DMQGag-Pol polyprotein 3.4.23.16 0.670
3nwx KVSGag-Pol polyprotein 3.4.23.16 0.670
3qn8 NI7Gag-Pol polyprotein 3.4.23.16 0.669
1daz 0Q4Gag-Pol polyprotein 3.4.23.16 0.668
1bv7 XV6Gag-Pol polyprotein 3.4.23.16 0.667
2bqv A1AProtease / 0.665
3ekx 1UNGag-Pol polyprotein 3.4.23.16 0.665
1ohr 1UNV-1 PROTEASE protein / 0.664
2uy0 HV1Gag-Pol polyprotein 3.4.23.16 0.664
1eag A70Candidapepsin-2 3.4.23.24 0.662
1eby BEBGag-Pol polyprotein 3.4.23.16 0.661
2avv MK1Gag-Pol polyprotein 3.4.23.16 0.661
2bbb HH1Gag-Pol polyprotein 3.4.23.16 0.659
1d4i BEGGag-Pol polyprotein 3.4.23.16 0.658
3ekw DR7Gag-Pol polyprotein 3.4.23.16 0.658
3hzc 2NCProtease / 0.657
3qih NI7Gag-Pol polyprotein 3.4.23.16 0.657
1ajx AH1Gag-Pol polyprotein 3.4.23.16 0.656
1g2k NM1Gag-Pol polyprotein 3.4.23.16 0.656
2cen 4AHProtease / 0.656
2qnp QN2Gag-Pol polyprotein 3.4.23.16 0.656
3bgb LJGGag-Pol polyprotein 3.4.23.16 0.656
1od1 0QSEndothiapepsin 3.4.23.22 0.655
3bxr DRRGag-Pol polyprotein 3.4.23.16 0.655
3tof 076Gag-Pol polyprotein 2.7.7.49 0.655
1fg6 2NCGag-Pol polyprotein 3.4.23.16 0.652
1hpv 478Gag-Pol polyprotein / 0.652
1qbs DMPGag-Pol polyprotein 3.4.23.16 0.652
1hxw RITGag-Pol polyprotein / 0.651
2pwr G4GGag-Pol polyprotein 3.4.23.16 0.651
2uxz HI1Gag-Pol polyprotein 3.4.23.16 0.650