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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
4dqc 017 Gag-Pol polyprotein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity
Align
4dqc 017Gag-Pol polyprotein / 1.328
4dqb 017Gag-Pol polyprotein / 1.252
3oy4 017Gag-Pol polyprotein 3.4.23.16 1.235
4dqe 017Gag-Pol polyprotein / 1.202
3o9e A60Pol polyprotein / 1.201
4dqh 017Gag-Pol polyprotein / 1.200
1t3r 017Gag-Pol polyprotein 3.4.23.16 1.199
4q1w 017Gag-Pol polyprotein 3.4.23.16 1.199
3pwm 017Gag-Pol polyprotein 3.4.23.16 1.197
3o9a K14Pol polyprotein / 1.194
4dqf 017Gag-Pol polyprotein / 1.194
3o9b K2APol polyprotein / 1.191
3o9c K20Pol polyprotein / 1.173
3lzv 017Gag-Pol polyprotein 3.4.23.16 1.163
2f80 017Gag-Pol polyprotein 3.4.23.16 1.162
3o9h K2EGag-Pol polyprotein / 1.162
2qci 065Gag-Pol polyprotein 3.4.23.16 1.144
3d20 017Gag-Pol polyprotein 3.4.23.16 1.143
2f81 017Gag-Pol polyprotein 3.4.23.16 1.139
2hb3 GRLProtease / 1.137
4heg G52Gag-Pol polyprotein 3.4.23.16 1.137
3o99 K13Pol polyprotein / 1.132
3o9f K2DGag-Pol polyprotein / 1.131
3lzu 017Gag-Pol polyprotein 3.4.23.16 1.130
2z4o 065Gag-Pol polyprotein 3.4.23.16 1.121
3r4b 74TGag-Pol polyprotein / 1.118
3ok9 G52Gag-Pol polyprotein 3.4.23.16 1.117
3o9d K19Pol polyprotein / 1.115
3o9g F53Gag-Pol polyprotein / 1.115
3em6 017Gag-Pol polyprotein 3.4.23.16 1.111
2qd7 065Gag-Pol polyprotein 3.4.23.16 1.110
3st5 G89Gag-Pol polyprotein 3.4.23.16 1.107
3oxw 017Gag-Pol polyprotein 3.4.23.16 1.105
4hdp G52Gag-Pol polyprotein 3.4.23.16 1.102
4njs G08Protease / 1.102
2ien 017Gag-Pol polyprotein 3.4.23.16 1.100
3djk G55Gag-Pol polyprotein 3.4.23.16 1.099
3ecg 065Gag-Pol polyprotein 3.4.23.47 1.094
2hs1 017Protease / 1.089
3bvb 017Gag-Pol polyprotein 3.4.23.16 1.088
3ucb 017Gag-Pol polyprotein / 1.083
2idw 017Protease / 1.081
3d1z 017Gag-Pol polyprotein 3.4.23.16 1.080
3jvy 017Gag-Pol polyprotein 3.4.23.16 1.078
3ekt 017Gag-Pol polyprotein 3.4.23.16 1.077
3ekv 478Gag-Pol polyprotein 3.4.23.16 1.075
3t3c 017Gag-Pol polyprotein 3.4.23.16 1.075
3o9i A61Gag-Pol polyprotein / 1.071
1t7i 017Gag-Pol polyprotein 3.4.23.16 1.067
3mws 017Pol protein / 1.064
2qd6 065Gag-Pol polyprotein 3.4.23.16 1.063
4q1y 017Gag-Pol polyprotein 3.4.23.16 1.061
3lzs 017Gag-Pol polyprotein 3.4.23.16 1.060
4hdf G52Gag-Pol polyprotein 3.4.23.16 1.055
4kb9 G79Protease / 1.055
3dk1 G05Gag-Pol polyprotein 3.4.23.16 1.054
4njt 017Protease / 1.052
2i4u DJRProtease / 1.048
2qd8 065Gag-Pol polyprotein 3.4.23.16 1.047
3qaa G04Gag-Pol polyprotein 3.4.23.16 1.044
3vfa 031Gag-Pol polyprotein 3.4.23.16 1.036
3sa8 K83Protease / 1.035
3cyw 017Gag-Pol polyprotein 3.4.23.16 1.034
2hs2 017Protease / 1.029
4djo MK5Pol polyprotein / 1.026
4q1x 017Gag-Pol polyprotein 3.4.23.16 1.024
3em3 478Gag-Pol polyprotein 3.4.23.16 1.023
2ieo 017Protease / 1.021
4dfg 0JVGag-Pol polyprotein 3.4.23.16 1.021
3nuo 478Gag-Pol polyprotein 3.4.23.16 1.014
2i0a MUIProtease / 1.011
3vf7 031Gag-Pol polyprotein 3.4.23.16 1.007
3gi4 K60Gag-Pol polyprotein / 1.001
2qi0 MZ3Gag-Pol polyprotein / 0.999
3jw2 017Gag-Pol polyprotein 3.4.23.16 0.998
3i6o GR6Gag-Pol polyprotein 3.4.23.16 0.997
3s54 017Protease / 0.996
3nu9 478Gag-Pol polyprotein 3.4.23.16 0.993
3ec0 GRLGag-Pol polyprotein 3.4.23.47 0.987
2i4d QFIProtease / 0.982
2psu MUUProtease / 0.982
3mxd K53Gag-Pol polyprotein 3.4.23.16 0.981
2qi4 MZ6Gag-Pol polyprotein / 0.980
3nu6 478Gag-Pol polyprotein 3.4.23.16 0.976
4hdb G52Gag-Pol polyprotein 3.4.23.16 0.968
3vf5 031Gag-Pol polyprotein 3.4.23.16 0.964
4hla 017Gag-Pol polyprotein 3.4.23.16 0.961
3ggu 017Gag-Pol polyprotein 3.4.23.16 0.960
3oxv 478Gag-Pol polyprotein 3.4.23.16 0.960
3mxe K54Gag-Pol polyprotein 3.4.23.16 0.955
3nuj 478Gag-Pol polyprotein 3.4.23.16 0.953
2i4v DJRV-1 protease / 0.952
2qi7 MZ9Gag-Pol polyprotein / 0.952
4j5j 478Gag-Pol polyprotein 3.4.23.16 0.952
2f8g 017Gag-Pol polyprotein 3.4.23.16 0.951
4djp M73Pol polyprotein / 0.951
3sa7 55AProtease / 0.950
4djr 0KJPol polyprotein / 0.948
2qi6 MZ8Gag-Pol polyprotein / 0.946
3gi6 D78Gag-Pol polyprotein / 0.944
2i4x KGQProtease / 0.943
4i8z G08Gag-Pol polyprotein 3.4.23.16 0.940
3sac AF8Protease / 0.939
3sa9 A68Protease / 0.938
3sab F78Protease / 0.938
3vfb 031Gag-Pol polyprotein 3.4.23.16 0.938
3gi5 K62Gag-Pol polyprotein / 0.935
3nu3 478Gag-Pol polyprotein 3.4.23.16 0.930
2i0d MUTProtease / 0.929
1hpv 478Gag-Pol polyprotein / 0.927
4ye3 G04Gag-Pol polyprotein 3.4.23.16 0.921
3nu4 478Gag-Pol polyprotein 3.4.23.16 0.919
3sa6 F71Protease / 0.916
1z1r HBHGag-Pol polyprotein 3.4.23.16 0.908
3nu5 478Gag-Pol polyprotein 3.4.23.16 0.904
4rvj 478Protease / 0.903
3sa4 F72Protease / 0.901
2qhy MZ1Gag-Pol polyprotein / 0.900
3saa 77FProtease / 0.895
4j54 G52Gag-Pol polyprotein 3.4.23.16 0.893
1d4l PI9Gag-Pol polyprotein 3.4.23.16 0.890
4djq M86Pol polyprotein / 0.884
2qi3 MZ5Gag-Pol polyprotein / 0.875
2qi5 MZ7Gag-Pol polyprotein / 0.873
3sa3 23XProtease / 0.873
1z1h HBBGag-Pol polyprotein 3.4.23.16 0.871
3i7e DJRGag-Pol polyprotein / 0.865
3sm2 478Putative gag-pro-pol polyprotein / 0.863
4j55 031Gag-Pol polyprotein 3.4.23.16 0.863
2fdd 385Pol protein / 0.857
2fxe DR7Gag-Pol polyprotein 3.4.23.16 0.855
3sa5 A69Protease / 0.854
3oxx DR7Gag-Pol polyprotein 3.4.23.16 0.849
3s43 478Protease / 0.845
3eky DR7Gag-Pol polyprotein 3.4.23.16 0.841
1npv L27Gag-Pol polyprotein 3.4.23.16 0.840
2i4w KGQProtease / 0.838
2psv MUVProtease / 0.835
2qhz MZ2Gag-Pol polyprotein / 0.832
3el1 DR7Gag-Pol polyprotein 3.4.23.16 0.823
1siv PSIGag-Pol polyprotein / 0.796
3em4 DR7Gag-Pol polyprotein 3.4.23.16 0.791
2fde 385Gag-Pol polyprotein 3.4.23.16 0.788
2q63 1UNGag-Pol polyprotein 3.4.23.16 0.786
3s56 ROCProtease / 0.784
3d1y ROCGag-Pol polyprotein 3.4.23.16 0.782
1hih C20Gag-Pol polyprotein / 0.780
3s85 LK0Gag-Pol polyprotein / 0.776
3el9 DR7Gag-Pol polyprotein 3.4.23.16 0.775
3tl9 ROCGag-Pol polyprotein 3.4.23.16 0.775
1yt9 OISGag-Pol polyprotein / 0.773
3el4 ROCGag-Pol polyprotein 3.4.23.16 0.773
1hvr XK2Gag-Pol polyprotein / 0.772
1pro A88Gag-Pol polyprotein / 0.770
1ida 0POGag-Pol polyprotein 3.4.23.47 0.766
2pym 1UNGag-Pol polyprotein 3.4.23.16 0.762
3kfr 3TLGag-Pol polyprotein / 0.762
2p3c 3TLProtease / 0.761
3pwr ROCGag-Pol polyprotein 3.4.23.16 0.761
3ufn ROCGag-Pol polyprotein / 0.761
3nxe 2NCProtease / 0.748
3ttp 017Gag-Pol polyprotein 3.4.23.16 0.748
1a8g 2Z4Gag-Pol polyprotein 3.4.23.16 0.746
1mrw K57Gag-Pol polyprotein 3.4.23.16 0.743
1sdt MK1Gag-Pol polyprotein 3.4.23.16 0.743
1sdv MK1Gag-Pol polyprotein 3.4.23.16 0.743
1izi Q50Gag-Pol polyprotein 3.4.23.16 0.741
1k6t XN1Gag-Pol polyprotein 3.4.23.16 0.738
2avm 2NCGag-Pol polyprotein 3.4.23.16 0.738
2nmy ROCProtease / 0.737
3i2l 2NCProtease / 0.737
2q54 MU1Protease / 0.735
2bb9 AKCGag-Pol polyprotein 3.4.23.16 0.732
2p3b 3TLV-1 PROTEASE protein / 0.732
2p3b 3TLV-1 protease / 0.732
3kfs 3TLGag-Pol polyprotein / 0.728
3cyx ROCGag-Pol polyprotein 3.4.23.16 0.727
3nwq 2NCGag-Pol polyprotein 3.4.23.16 0.727
1m0b 0ZQGag-Pol polyprotein 3.4.23.16 0.726
1npa 3NHGag-Pol polyprotein 3.4.23.16 0.726
1npw LGZGag-Pol polyprotein 3.4.23.16 0.726
1fgc 2NCGag-Pol polyprotein 3.4.23.16 0.725
1bdr IM1Gag-Pol polyprotein 3.4.23.16 0.723
2nnp ROCProtease / 0.723
1ffi 2NCGag-Pol polyprotein 3.4.23.16 0.718
1hvs A77Gag-Pol polyprotein / 0.718
1d4i BEGGag-Pol polyprotein 3.4.23.16 0.717
1ec1 BEEGag-Pol polyprotein 3.4.23.16 0.715
3ekq ROCGag-Pol polyprotein 3.4.23.16 0.715
2nnk ROCProtease / 0.714
2qak 1UNGag-Pol polyprotein 3.4.23.16 0.714
4qgi ROCGag-Pol polyprotein 3.4.23.16 0.713
3d1x ROCGag-Pol polyprotein 3.4.23.16 0.712
1ivq 0PXGag-Pol polyprotein / 0.711
2avv MK1Gag-Pol polyprotein 3.4.23.16 0.711
2fle AIProtease / 0.711
2hc0 AB2Protease / 0.711
3k4v ROCGag-Pol polyprotein 3.4.23.16 0.709
3nyg 2NCGag-Pol polyprotein 3.4.23.16 0.708
1izh Q50Protease / 0.706
1tcx IM1Gag-Pol polyprotein 3.4.23.16 0.706
1qbt 146Gag-Pol polyprotein 3.4.23.16 0.705
1sdu MK1Gag-Pol polyprotein 3.4.23.16 0.705
3bgc LJHGag-Pol polyprotein 3.4.23.16 0.705
3gga GGWGag-Pol polyprotein / 0.705
1b6l PI4Gag-Pol polyprotein 3.4.23.16 0.701
1iiq 0ZRGag-Pol polyprotein 3.4.23.16 0.699
2pk6 O33V-1 protease / 0.699
1hiv 1ZKGag-Pol polyprotein / 0.698
3ekw DR7Gag-Pol polyprotein 3.4.23.16 0.696
1hii C20Gag-Pol polyprotein / 0.695
3slz 3TLPutative gag-pro-pol polyprotein / 0.692
3ndu ROCGag-Pol polyprotein 3.4.23.16 0.691
2avs MK1Gag-Pol polyprotein 3.4.23.16 0.690
3jvw DMPGag-Pol polyprotein 3.4.23.16 0.689
3el0 1UNGag-Pol polyprotein 3.4.23.16 0.688
3so9 017Pol protein / 0.688
1bwa XV6Gag-Pol polyprotein 3.4.23.16 0.687
1jld 0PPGag-Pol polyprotein / 0.686
2bpw 1INGag-Pol polyprotein 3.4.23.16 0.685
2uxz HI1Gag-Pol polyprotein 3.4.23.16 0.685
2f3k RO1Protease / 0.680
3qp0 NI8Gag-Pol polyprotein 3.4.23.16 0.679
1ec3 MS3Gag-Pol polyprotein 3.4.23.16 0.678
1rl8 RITGag-Pol polyprotein 3.4.23.16 0.678
2a1e IPFGag-Pol polyprotein 3.4.23.16 0.678
1ohr 1UNV-1 PROTEASE protein / 0.676
1ff0 2NCGag-Pol polyprotein 3.4.23.16 0.674
2q64 1UNGag-Pol polyprotein 3.4.23.16 0.674
2pqz G0GGag-Pol polyprotein 3.4.23.16 0.673
1ajv NMBGag-Pol polyprotein 3.4.23.16 0.672
1b6p PI7Gag-Pol polyprotein 3.4.23.16 0.672
1ebz BECGag-Pol polyprotein 3.4.23.16 0.672
1hvj A78Gag-Pol polyprotein / 0.672
1zsf 0ZSGag-Pol polyprotein 3.4.23.16 0.672
1fg6 2NCGag-Pol polyprotein 3.4.23.16 0.671
2qnq QN3Gag-Pol polyprotein 3.4.23.16 0.670
2p3d 3TLProtease / 0.669
4k4p 3TLGag-Pol polyprotein / 0.669
1fg8 0Q4Gag-Pol polyprotein 3.4.23.16 0.668
1fej 2NCGag-Pol polyprotein 3.4.23.16 0.667
1hxw RITGag-Pol polyprotein / 0.667
2pwr G4GGag-Pol polyprotein 3.4.23.16 0.666
2p3a 3TLPol protein / 0.665
1mtr PI6Gag-Pol polyprotein 3.4.23.16 0.663
1a94 0Q4Gag-Pol polyprotein 3.4.23.16 0.662
1k1u 0Q4Gag-Pol polyprotein 3.4.23.16 0.662
2qnp QN2Gag-Pol polyprotein 3.4.23.16 0.662
2q55 MU0Protease / 0.661
1bwb 146Gag-Pol polyprotein 3.4.23.16 0.659
3kdb 006Gag-Pol polyprotein 3.4.23.16 0.659
1hsh MK1Gag-Pol polyprotein / 0.658
1sbg IM1Gag-Pol polyprotein / 0.658
2cem 2AHPol protein / 0.657
3ggx GGXGag-Pol polyprotein / 0.655
3qn8 NI7Gag-Pol polyprotein 3.4.23.16 0.655
1dmp DMQGag-Pol polyprotein 3.4.23.16 0.654
1ec2 BEJGag-Pol polyprotein 3.4.23.16 0.654
1k6p XN3Gag-Pol polyprotein 3.4.23.16 0.654
2r38 G4GGag-Pol polyprotein 3.4.23.16 0.652
1k2c 0Q4Gag-Pol polyprotein 3.4.23.16 0.651
1w5y BE6Gag-Pol polyprotein 3.4.23.16 0.651
3a2o KNJGag-Pol polyprotein 3.4.23.16 0.651
1bv7 XV6Gag-Pol polyprotein 3.4.23.16 0.650
1w5w BE4Gag-Pol polyprotein 3.4.23.16 0.650
1zsr 0ZTGag-Pol polyprotein 3.4.23.16 0.650
2aqu DR7Gag-Pol polyprotein 3.4.23.16 0.650
3nwx KVSGag-Pol polyprotein 3.4.23.16 0.650