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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
4dqh 017 Gag-Pol polyprotein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4dqh 017Gag-Pol polyprotein / 1.303
4dqe 017Gag-Pol polyprotein / 1.260
4dqb 017Gag-Pol polyprotein / 1.241
1t3r 017Gag-Pol polyprotein 3.4.23.16 1.240
2qd7 065Gag-Pol polyprotein 3.4.23.16 1.233
3o9a K14Pol polyprotein / 1.231
3oy4 017Gag-Pol polyprotein 3.4.23.16 1.224
3o9b K2APol polyprotein / 1.218
4q1w 017Gag-Pol polyprotein 3.4.23.16 1.214
3o9e A60Pol polyprotein / 1.206
4dqc 017Gag-Pol polyprotein / 1.200
3o9c K20Pol polyprotein / 1.187
3o9g F53Gag-Pol polyprotein / 1.187
2idw 017Protease / 1.184
3o9h K2EGag-Pol polyprotein / 1.183
3o9d K19Pol polyprotein / 1.182
4dqf 017Gag-Pol polyprotein / 1.181
3o9f K2DGag-Pol polyprotein / 1.175
3pwm 017Gag-Pol polyprotein 3.4.23.16 1.173
3lzv 017Gag-Pol polyprotein 3.4.23.16 1.171
3d20 017Gag-Pol polyprotein 3.4.23.16 1.167
3o99 K13Pol polyprotein / 1.166
1t7i 017Gag-Pol polyprotein 3.4.23.16 1.160
2qci 065Gag-Pol polyprotein 3.4.23.16 1.144
3ecg 065Gag-Pol polyprotein 3.4.23.47 1.138
3o9i A61Gag-Pol polyprotein / 1.137
4njs G08Protease / 1.132
2hb3 GRLProtease / 1.128
3em6 017Gag-Pol polyprotein 3.4.23.16 1.127
4heg G52Gag-Pol polyprotein 3.4.23.16 1.124
4q1y 017Gag-Pol polyprotein 3.4.23.16 1.105
3lzu 017Gag-Pol polyprotein 3.4.23.16 1.104
2ien 017Gag-Pol polyprotein 3.4.23.16 1.100
3dk1 G05Gag-Pol polyprotein 3.4.23.16 1.093
4q1x 017Gag-Pol polyprotein 3.4.23.16 1.089
3ekt 017Gag-Pol polyprotein 3.4.23.16 1.086
3r4b 74TGag-Pol polyprotein / 1.085
3vfa 031Gag-Pol polyprotein 3.4.23.16 1.084
2f81 017Gag-Pol polyprotein 3.4.23.16 1.082
3t3c 017Gag-Pol polyprotein 3.4.23.16 1.080
3oxw 017Gag-Pol polyprotein 3.4.23.16 1.079
3mws 017Pol protein / 1.074
3vf7 031Gag-Pol polyprotein 3.4.23.16 1.072
2f80 017Gag-Pol polyprotein 3.4.23.16 1.071
2ieo 017Protease / 1.067
3sa8 K83Protease / 1.067
3mxd K53Gag-Pol polyprotein 3.4.23.16 1.066
4djo MK5Pol polyprotein / 1.061
3ekv 478Gag-Pol polyprotein 3.4.23.16 1.059
4njt 017Protease / 1.056
3djk G55Gag-Pol polyprotein 3.4.23.16 1.055
3gi4 K60Gag-Pol polyprotein / 1.050
3st5 G89Gag-Pol polyprotein 3.4.23.16 1.050
2i4u DJRProtease / 1.049
2qd8 065Gag-Pol polyprotein 3.4.23.16 1.046
3ucb 017Gag-Pol polyprotein / 1.044
2i0a MUIProtease / 1.043
3s54 017Protease / 1.042
4hdp G52Gag-Pol polyprotein 3.4.23.16 1.039
3cyw 017Gag-Pol polyprotein 3.4.23.16 1.037
2hs1 017Protease / 1.036
3vf5 031Gag-Pol polyprotein 3.4.23.16 1.036
2qd6 065Gag-Pol polyprotein 3.4.23.16 1.033
2z4o 065Gag-Pol polyprotein 3.4.23.16 1.033
2qi4 MZ6Gag-Pol polyprotein / 1.031
2hs2 017Protease / 1.030
3jvy 017Gag-Pol polyprotein 3.4.23.16 1.029
4hdf G52Gag-Pol polyprotein 3.4.23.16 1.029
3em3 478Gag-Pol polyprotein 3.4.23.16 1.028
3bvb 017Gag-Pol polyprotein 3.4.23.16 1.021
3lzs 017Gag-Pol polyprotein 3.4.23.16 1.019
2i4d QFIProtease / 1.016
3ggu 017Gag-Pol polyprotein 3.4.23.16 1.007
3gi5 K62Gag-Pol polyprotein / 1.003
2f8g 017Gag-Pol polyprotein 3.4.23.16 1.000
2qi6 MZ8Gag-Pol polyprotein / 0.999
3i6o GR6Gag-Pol polyprotein 3.4.23.16 0.998
4kb9 G79Protease / 0.997
3ec0 GRLGag-Pol polyprotein 3.4.23.47 0.996
3d1z 017Gag-Pol polyprotein 3.4.23.16 0.991
2psu MUUProtease / 0.990
2qi7 MZ9Gag-Pol polyprotein / 0.985
3gi6 D78Gag-Pol polyprotein / 0.984
2i4v DJRV-1 protease / 0.982
3sa4 F72Protease / 0.981
4djq M86Pol polyprotein / 0.975
2fdd 385Pol protein / 0.974
2qhy MZ1Gag-Pol polyprotein / 0.973
2qi0 MZ3Gag-Pol polyprotein / 0.972
4dfg 0JVGag-Pol polyprotein 3.4.23.16 0.972
3sab F78Protease / 0.968
3mxe K54Gag-Pol polyprotein 3.4.23.16 0.966
4djp M73Pol polyprotein / 0.964
3saa 77FProtease / 0.957
3sac AF8Protease / 0.953
4hla 017Gag-Pol polyprotein 3.4.23.16 0.953
4j55 031Gag-Pol polyprotein 3.4.23.16 0.953
2i4x KGQProtease / 0.950
3sa9 A68Protease / 0.950
4djr 0KJPol polyprotein / 0.945
2i0d MUTProtease / 0.940
3oxv 478Gag-Pol polyprotein 3.4.23.16 0.936
3qaa G04Gag-Pol polyprotein 3.4.23.16 0.935
3ok9 G52Gag-Pol polyprotein 3.4.23.16 0.933
3nuo 478Gag-Pol polyprotein 3.4.23.16 0.932
3jw2 017Gag-Pol polyprotein 3.4.23.16 0.930
1z1r HBHGag-Pol polyprotein 3.4.23.16 0.929
3nu9 478Gag-Pol polyprotein 3.4.23.16 0.928
3sa7 55AProtease / 0.924
3sa6 F71Protease / 0.922
2qi5 MZ7Gag-Pol polyprotein / 0.921
4j54 G52Gag-Pol polyprotein 3.4.23.16 0.914
4i8z G08Gag-Pol polyprotein 3.4.23.16 0.913
3nuj 478Gag-Pol polyprotein 3.4.23.16 0.910
1hpv 478Gag-Pol polyprotein / 0.907
4ye3 G04Gag-Pol polyprotein 3.4.23.16 0.905
3sa3 23XProtease / 0.902
4rvj 478Protease / 0.902
3nu4 478Gag-Pol polyprotein 3.4.23.16 0.900
3nu5 478Gag-Pol polyprotein 3.4.23.16 0.899
3nu3 478Gag-Pol polyprotein 3.4.23.16 0.896
3ttp 017Gag-Pol polyprotein 3.4.23.16 0.895
3vfb 031Gag-Pol polyprotein 3.4.23.16 0.893
3nu6 478Gag-Pol polyprotein 3.4.23.16 0.891
4hdb G52Gag-Pol polyprotein 3.4.23.16 0.891
2qhz MZ2Gag-Pol polyprotein / 0.871
4j5j 478Gag-Pol polyprotein 3.4.23.16 0.868
2qi3 MZ5Gag-Pol polyprotein / 0.861
1z1h HBBGag-Pol polyprotein 3.4.23.16 0.860
3eky DR7Gag-Pol polyprotein 3.4.23.16 0.854
3sa5 A69Protease / 0.854
3sm2 478Putative gag-pro-pol polyprotein / 0.852
1d4l PI9Gag-Pol polyprotein 3.4.23.16 0.850
3s43 478Protease / 0.845
1t7j 478Gag-Pol polyprotein 3.4.23.16 0.844
2psv MUVProtease / 0.833
3i7e DJRGag-Pol polyprotein / 0.825
3oxx DR7Gag-Pol polyprotein 3.4.23.16 0.815
3el1 DR7Gag-Pol polyprotein 3.4.23.16 0.802
2fde 385Gag-Pol polyprotein 3.4.23.16 0.801
3el9 DR7Gag-Pol polyprotein 3.4.23.16 0.795
1b6l PI4Gag-Pol polyprotein 3.4.23.16 0.793
2nmy ROCProtease / 0.786
1bdr IM1Gag-Pol polyprotein 3.4.23.16 0.778
2qak 1UNGag-Pol polyprotein 3.4.23.16 0.775
3s56 ROCProtease / 0.775
1npv L27Gag-Pol polyprotein 3.4.23.16 0.773
3em4 DR7Gag-Pol polyprotein 3.4.23.16 0.772
1iiq 0ZRGag-Pol polyprotein 3.4.23.16 0.770
2hc0 AB2Protease / 0.767
2pym 1UNGag-Pol polyprotein 3.4.23.16 0.763
1izi Q50Gag-Pol polyprotein 3.4.23.16 0.760
1ohr 1UNV-1 PROTEASE protein / 0.760
1sdt MK1Gag-Pol polyprotein 3.4.23.16 0.758
2aqu DR7Gag-Pol polyprotein 3.4.23.16 0.757
1ida 0POGag-Pol polyprotein 3.4.23.47 0.755
2fxe DR7Gag-Pol polyprotein 3.4.23.16 0.754
1mrw K57Gag-Pol polyprotein 3.4.23.16 0.753
1siv PSIGag-Pol polyprotein / 0.753
2bb9 AKCGag-Pol polyprotein 3.4.23.16 0.753
1npa 3NHGag-Pol polyprotein 3.4.23.16 0.748
1npw LGZGag-Pol polyprotein 3.4.23.16 0.748
3ufn ROCGag-Pol polyprotein / 0.747
3k4v ROCGag-Pol polyprotein 3.4.23.16 0.746
2p3b 3TLV-1 PROTEASE protein / 0.744
2p3b 3TLV-1 protease / 0.744
2q63 1UNGag-Pol polyprotein 3.4.23.16 0.744
3tl9 ROCGag-Pol polyprotein 3.4.23.16 0.741
3el4 ROCGag-Pol polyprotein 3.4.23.16 0.738
3d1y ROCGag-Pol polyprotein 3.4.23.16 0.737
4qgi ROCGag-Pol polyprotein 3.4.23.16 0.737
1izh Q50Protease / 0.736
2avv MK1Gag-Pol polyprotein 3.4.23.16 0.736
1hvi A77Protease / 0.734
2nnp ROCProtease / 0.734
1sdv MK1Gag-Pol polyprotein 3.4.23.16 0.732
2p3a 3TLPol protein / 0.732
3kfs 3TLGag-Pol polyprotein / 0.731
2i4w KGQProtease / 0.730
3so9 017Pol protein / 0.730
1mtr PI6Gag-Pol polyprotein 3.4.23.16 0.729
3ekw DR7Gag-Pol polyprotein 3.4.23.16 0.729
3el0 1UNGag-Pol polyprotein 3.4.23.16 0.728
2pk5 075Protease / 0.726
2nnk ROCProtease / 0.724
3ekq ROCGag-Pol polyprotein 3.4.23.16 0.724
1k6t XN1Gag-Pol polyprotein 3.4.23.16 0.723
3kfr 3TLGag-Pol polyprotein / 0.723
1yt9 OISGag-Pol polyprotein / 0.722
2rkg AB1Pol protein / 0.722
3slz 3TLPutative gag-pro-pol polyprotein / 0.722
2b60 RITPol polyprotein / 0.721
2avm 2NCGag-Pol polyprotein 3.4.23.16 0.720
2avs MK1Gag-Pol polyprotein 3.4.23.16 0.720
1hvr XK2Gag-Pol polyprotein / 0.717
1a8g 2Z4Gag-Pol polyprotein 3.4.23.16 0.716
1bv7 XV6Gag-Pol polyprotein 3.4.23.16 0.715
3d1x ROCGag-Pol polyprotein 3.4.23.16 0.713
2wkz 5AHGag-Pol polyprotein / 0.711
2q54 MU1Protease / 0.710
3kdb 006Gag-Pol polyprotein 3.4.23.16 0.710
3tof 076Gag-Pol polyprotein 2.7.7.49 0.709
1m0b 0ZQGag-Pol polyprotein 3.4.23.16 0.708
4gb2 0LQGag-Pol polyprotein 2.7.7.49 0.708
1tcx IM1Gag-Pol polyprotein 3.4.23.16 0.705
2a1e IPFGag-Pol polyprotein 3.4.23.16 0.705
3pwr ROCGag-Pol polyprotein 3.4.23.16 0.703
1hvj A78Gag-Pol polyprotein / 0.702
1sdu MK1Gag-Pol polyprotein 3.4.23.16 0.701
3gga GGWGag-Pol polyprotein / 0.699
3cyx ROCGag-Pol polyprotein 3.4.23.16 0.698
2f3k RO1Protease / 0.694
3dcr KVSProtease / 0.694
1fgc 2NCGag-Pol polyprotein 3.4.23.16 0.692
1ivq 0PXGag-Pol polyprotein / 0.692
3fx5 KNIGag-Pol polyprotein 3.4.23.16 0.692
1vij BAYGag-Pol polyprotein / 0.691
3kf0 3TLGag-Pol polyprotein / 0.691
1qbr XV6Gag-Pol polyprotein 3.4.23.16 0.690
2p3c 3TLProtease / 0.690
1hpx KNIGag-Pol polyprotein / 0.689
2uy0 HV1Gag-Pol polyprotein 3.4.23.16 0.689
1ody LP1Gag-Pol polyprotein 3.4.23.16 0.688
2rkf AB1Pol protein / 0.687
1g2k NM1Gag-Pol polyprotein 3.4.23.16 0.686
1wbk 568Pol protein / 0.686
1hvk A79Gag-Pol polyprotein / 0.685
1daz 0Q4Gag-Pol polyprotein 3.4.23.16 0.682
4fe6 0TQGag-Pol polyprotein 3.4.23.16 0.681
1b6m PI6Gag-Pol polyprotein 3.4.23.16 0.678
1k6c MK1Gag-Pol polyprotein 3.4.23.16 0.677
2q64 1UNGag-Pol polyprotein 3.4.23.16 0.677
1hih C20Gag-Pol polyprotein / 0.676
3i2l 2NCProtease / 0.676
1a9m U0EGag-Pol polyprotein / 0.675
1zsf 0ZSGag-Pol polyprotein 3.4.23.16 0.674
2bqv A1AProtease / 0.674
3aid ARQGag-Pol polyprotein 3.4.23.16 0.674
2fxd DR7Pol polyprotein / 0.673
1a94 0Q4Gag-Pol polyprotein 3.4.23.16 0.672
1meu DMPGag-Pol polyprotein 3.4.23.16 0.672
1w5v BE3Gag-Pol polyprotein 3.4.23.16 0.672
3dm6 757Beta-secretase 1 3.4.23.46 0.672
1fej 2NCGag-Pol polyprotein 3.4.23.16 0.671
1hii C20Gag-Pol polyprotein / 0.669
1hsg MK1Gag-Pol polyprotein / 0.669
2xye CXGGag-Pol polyprotein / 0.669
3nwx KVSGag-Pol polyprotein 3.4.23.16 0.669
2wl0 5AHGag-Pol polyprotein / 0.668
1hwr 216Gag-Pol polyprotein 3.4.23.16 0.667
1k1u 0Q4Gag-Pol polyprotein 3.4.23.16 0.667
2q5k AB1Protease / 0.667
2p3d 3TLProtease / 0.666
1hsh MK1Gag-Pol polyprotein / 0.665
2cem 2AHPol protein / 0.665
1b6k PI5Gag-Pol polyprotein 3.4.23.16 0.663
1hvs A77Gag-Pol polyprotein / 0.663
3el5 1UNGag-Pol polyprotein / 0.663
3ixj 586Beta-secretase 1 3.4.23.46 0.663
1ec1 BEEGag-Pol polyprotein 3.4.23.16 0.662
1fg6 2NCGag-Pol polyprotein 3.4.23.16 0.662
2qnp QN2Gag-Pol polyprotein 3.4.23.16 0.662
3lit E15Protease / 0.662
3liq E14Protease / 0.661
1b6p PI7Gag-Pol polyprotein 3.4.23.16 0.659
1k2c 0Q4Gag-Pol polyprotein 3.4.23.16 0.659
1eag A70Candidapepsin-2 3.4.23.24 0.658
3jvw DMPGag-Pol polyprotein 3.4.23.16 0.658
2upj U02Gag-Pol polyprotein 3.4.23.16 0.656
1hiv 1ZKGag-Pol polyprotein / 0.655
3s85 LK0Gag-Pol polyprotein / 0.654
1hos PHPGag-Pol polyprotein / 0.653
3bxr DRRGag-Pol polyprotein 3.4.23.16 0.653
1hxw RITGag-Pol polyprotein / 0.652
2aoe 0Q4Gag-Pol polyprotein 3.4.23.16 0.652
1idb 0DOGag-Pol polyprotein / 0.651
1odw 0E8Gag-Pol polyprotein 3.4.23.16 0.650