Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
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
4hdf G52 Gag-Pol polyprotein 3.4.23.16

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4hdf G52Gag-Pol polyprotein 3.4.23.16 1.400
4heg G52Gag-Pol polyprotein 3.4.23.16 1.232
3qaa G04Gag-Pol polyprotein 3.4.23.16 1.208
4hdp G52Gag-Pol polyprotein 3.4.23.16 1.200
2qd8 065Gag-Pol polyprotein 3.4.23.16 1.174
4kb9 G79Protease / 1.162
4dfg 0JVGag-Pol polyprotein 3.4.23.16 1.161
3mws 017Pol protein / 1.137
3st5 G89Gag-Pol polyprotein 3.4.23.16 1.123
3o9f K2DGag-Pol polyprotein / 1.119
3o9h K2EGag-Pol polyprotein / 1.116
3o9a K14Pol polyprotein / 1.110
3ecg 065Gag-Pol polyprotein 3.4.23.47 1.109
3ok9 G52Gag-Pol polyprotein 3.4.23.16 1.099
3pwm 017Gag-Pol polyprotein 3.4.23.16 1.098
2z4o 065Gag-Pol polyprotein 3.4.23.16 1.092
2qci 065Gag-Pol polyprotein 3.4.23.16 1.089
4hdb G52Gag-Pol polyprotein 3.4.23.16 1.088
2ien 017Gag-Pol polyprotein 3.4.23.16 1.085
2f8g 017Gag-Pol polyprotein 3.4.23.16 1.078
1t7i 017Gag-Pol polyprotein 3.4.23.16 1.062
4i8z G08Gag-Pol polyprotein 3.4.23.16 1.062
4dqc 017Gag-Pol polyprotein / 1.055
2f81 017Gag-Pol polyprotein 3.4.23.16 1.054
4djp M73Pol polyprotein / 1.054
3d20 017Gag-Pol polyprotein 3.4.23.16 1.048
3vfa 031Gag-Pol polyprotein 3.4.23.16 1.046
2hb3 GRLProtease / 1.045
4j54 G52Gag-Pol polyprotein 3.4.23.16 1.042
3lzu 017Gag-Pol polyprotein 3.4.23.16 1.039
2fdd 385Pol protein / 1.038
3t3c 017Gag-Pol polyprotein 3.4.23.16 1.034
3sab F78Protease / 1.032
2f80 017Gag-Pol polyprotein 3.4.23.16 1.030
4dqh 017Gag-Pol polyprotein / 1.029
2ieo 017Protease / 1.027
3dk1 G05Gag-Pol polyprotein 3.4.23.16 1.027
3r4b 74TGag-Pol polyprotein / 1.025
3jvy 017Gag-Pol polyprotein 3.4.23.16 1.022
4dqb 017Gag-Pol polyprotein / 1.022
2i4v DJRV-1 protease / 1.021
3em6 017Gag-Pol polyprotein 3.4.23.16 1.021
3i6o GR6Gag-Pol polyprotein 3.4.23.16 1.020
3oy4 017Gag-Pol polyprotein 3.4.23.16 1.020
3sa9 A68Protease / 1.020
2i4u DJRProtease / 1.019
1t3r 017Gag-Pol polyprotein 3.4.23.16 1.017
2qd6 065Gag-Pol polyprotein 3.4.23.16 1.017
4njs G08Protease / 1.016
3o9c K20Pol polyprotein / 1.014
4ye3 G04Gag-Pol polyprotein 3.4.23.16 1.014
4dqf 017Gag-Pol polyprotein / 1.011
3cyw 017Gag-Pol polyprotein 3.4.23.16 1.010
3sa8 K83Protease / 1.009
3ggu 017Gag-Pol polyprotein 3.4.23.16 1.007
3o9b K2APol polyprotein / 1.007
2i4x KGQProtease / 1.006
3o9g F53Gag-Pol polyprotein / 1.002
3vf7 031Gag-Pol polyprotein 3.4.23.16 1.001
3ec0 GRLGag-Pol polyprotein 3.4.23.47 0.996
3gi4 K60Gag-Pol polyprotein / 0.995
2qd7 065Gag-Pol polyprotein 3.4.23.16 0.991
2i0a MUIProtease / 0.983
3o9e A60Pol polyprotein / 0.982
3d1z 017Gag-Pol polyprotein 3.4.23.16 0.980
3lzs 017Gag-Pol polyprotein 3.4.23.16 0.980
3ucb 017Gag-Pol polyprotein / 0.979
2i4d QFIProtease / 0.976
2idw 017Protease / 0.975
3o9d K19Pol polyprotein / 0.968
3jw2 017Gag-Pol polyprotein 3.4.23.16 0.965
4dqe 017Gag-Pol polyprotein / 0.963
4q1y 017Gag-Pol polyprotein 3.4.23.16 0.963
3djk G55Gag-Pol polyprotein 3.4.23.16 0.962
3o9i A61Gag-Pol polyprotein / 0.956
2qi4 MZ6Gag-Pol polyprotein / 0.955
4q1w 017Gag-Pol polyprotein 3.4.23.16 0.954
2qi0 MZ3Gag-Pol polyprotein / 0.952
2qi5 MZ7Gag-Pol polyprotein / 0.950
3saa 77FProtease / 0.950
3gi6 D78Gag-Pol polyprotein / 0.947
3ekt 017Gag-Pol polyprotein 3.4.23.16 0.944
3mxd K53Gag-Pol polyprotein 3.4.23.16 0.944
4djo MK5Pol polyprotein / 0.941
3mxe K54Gag-Pol polyprotein 3.4.23.16 0.940
3oxw 017Gag-Pol polyprotein 3.4.23.16 0.939
3sa7 55AProtease / 0.935
2hs1 017Protease / 0.934
4j55 031Gag-Pol polyprotein 3.4.23.16 0.933
3lzv 017Gag-Pol polyprotein 3.4.23.16 0.931
2hs2 017Protease / 0.928
3sa4 F72Protease / 0.927
4djq M86Pol polyprotein / 0.925
3gi5 K62Gag-Pol polyprotein / 0.922
2qhy MZ1Gag-Pol polyprotein / 0.921
3o99 K13Pol polyprotein / 0.915
3vf5 031Gag-Pol polyprotein 3.4.23.16 0.913
1z1r HBHGag-Pol polyprotein 3.4.23.16 0.912
2qi7 MZ9Gag-Pol polyprotein / 0.909
3nu3 478Gag-Pol polyprotein 3.4.23.16 0.908
3nu9 478Gag-Pol polyprotein 3.4.23.16 0.908
3sa3 23XProtease / 0.903
4q1x 017Gag-Pol polyprotein 3.4.23.16 0.899
3nuo 478Gag-Pol polyprotein 3.4.23.16 0.898
3s54 017Protease / 0.895
2qi6 MZ8Gag-Pol polyprotein / 0.894
3sa5 A69Protease / 0.894
2i0d MUTProtease / 0.893
4njt 017Protease / 0.886
2psu MUUProtease / 0.883
3nu6 478Gag-Pol polyprotein 3.4.23.16 0.882
1d4l PI9Gag-Pol polyprotein 3.4.23.16 0.880
3sa6 F71Protease / 0.879
2qi3 MZ5Gag-Pol polyprotein / 0.876
3oxv 478Gag-Pol polyprotein 3.4.23.16 0.875
3nu4 478Gag-Pol polyprotein 3.4.23.16 0.871
3ekv 478Gag-Pol polyprotein 3.4.23.16 0.868
3vfb 031Gag-Pol polyprotein 3.4.23.16 0.868
3sac AF8Protease / 0.867
1z1h HBBGag-Pol polyprotein 3.4.23.16 0.865
4djr 0KJPol polyprotein / 0.865
4j5j 478Gag-Pol polyprotein 3.4.23.16 0.859
2fde 385Gag-Pol polyprotein 3.4.23.16 0.855
3eky DR7Gag-Pol polyprotein 3.4.23.16 0.852
3nu5 478Gag-Pol polyprotein 3.4.23.16 0.842
3sm2 478Putative gag-pro-pol polyprotein / 0.840
3el1 DR7Gag-Pol polyprotein 3.4.23.16 0.832
3nuj 478Gag-Pol polyprotein 3.4.23.16 0.831
3oxx DR7Gag-Pol polyprotein 3.4.23.16 0.821
2fxe DR7Gag-Pol polyprotein 3.4.23.16 0.820
1hpv 478Gag-Pol polyprotein / 0.818
2qhz MZ2Gag-Pol polyprotein / 0.817
3el9 DR7Gag-Pol polyprotein 3.4.23.16 0.810
2hc0 AB2Protease / 0.809
3s43 478Protease / 0.807
3em3 478Gag-Pol polyprotein 3.4.23.16 0.804
3kfn 3TLGag-Pol polyprotein / 0.799
3tl9 ROCGag-Pol polyprotein 3.4.23.16 0.798
2nmy ROCProtease / 0.796
2qak 1UNGag-Pol polyprotein 3.4.23.16 0.795
1d4i BEGGag-Pol polyprotein 3.4.23.16 0.789
1mrw K57Gag-Pol polyprotein 3.4.23.16 0.789
3kfr 3TLGag-Pol polyprotein / 0.788
3ekq ROCGag-Pol polyprotein 3.4.23.16 0.778
1fej 2NCGag-Pol polyprotein 3.4.23.16 0.773
1fg6 2NCGag-Pol polyprotein 3.4.23.16 0.770
1fff 0Q4Gag-Pol polyprotein 3.4.23.16 0.769
3el4 ROCGag-Pol polyprotein 3.4.23.16 0.769
1ffi 2NCGag-Pol polyprotein 3.4.23.16 0.767
1hvj A78Gag-Pol polyprotein / 0.762
2fle AIProtease / 0.762
2i4w KGQProtease / 0.762
1sdt MK1Gag-Pol polyprotein 3.4.23.16 0.759
2nnp ROCProtease / 0.759
3k4v ROCGag-Pol polyprotein 3.4.23.16 0.758
3s56 ROCProtease / 0.758
1npa 3NHGag-Pol polyprotein 3.4.23.16 0.757
1npw LGZGag-Pol polyprotein 3.4.23.16 0.757
3s85 LK0Gag-Pol polyprotein / 0.757
2p3c 3TLProtease / 0.756
3dcr KVSProtease / 0.754
2cem 2AHPol protein / 0.753
1k6t XN1Gag-Pol polyprotein 3.4.23.16 0.749
2avm 2NCGag-Pol polyprotein 3.4.23.16 0.748
1izi Q50Gag-Pol polyprotein 3.4.23.16 0.747
2psv MUVProtease / 0.747
1pro A88Gag-Pol polyprotein / 0.745
1sdu MK1Gag-Pol polyprotein 3.4.23.16 0.745
3ufn ROCGag-Pol polyprotein / 0.745
1ff0 2NCGag-Pol polyprotein 3.4.23.16 0.740
2q64 1UNGag-Pol polyprotein 3.4.23.16 0.739
1hvs A77Gag-Pol polyprotein / 0.736
3nwx KVSGag-Pol polyprotein 3.4.23.16 0.735
2bb9 AKCGag-Pol polyprotein 3.4.23.16 0.733
1hih C20Gag-Pol polyprotein / 0.732
1ohr 1UNV-1 PROTEASE protein / 0.732
1yt9 OISGag-Pol polyprotein / 0.732
3d1y ROCGag-Pol polyprotein 3.4.23.16 0.732
1ida 0POGag-Pol polyprotein 3.4.23.47 0.731
1jld 0PPGag-Pol polyprotein / 0.731
2avs MK1Gag-Pol polyprotein 3.4.23.16 0.731
1k2b 0Q4Gag-Pol polyprotein 3.4.23.16 0.730
2nnk ROCProtease / 0.730
3ndu ROCGag-Pol polyprotein 3.4.23.16 0.730
2q63 1UNGag-Pol polyprotein 3.4.23.16 0.729
1hvl A76Gag-Pol polyprotein / 0.728
2aqu DR7Gag-Pol polyprotein 3.4.23.16 0.727
3ekp 478Gag-Pol polyprotein 3.4.23.16 0.726
3cyx ROCGag-Pol polyprotein 3.4.23.16 0.725
1hiv 1ZKGag-Pol polyprotein / 0.722
3jvw DMPGag-Pol polyprotein 3.4.23.16 0.721
4qgi ROCGag-Pol polyprotein 3.4.23.16 0.721
3ggx GGXGag-Pol polyprotein / 0.720
1npv L27Gag-Pol polyprotein 3.4.23.16 0.719
3wsj MK1Protease / 0.719
4hla 017Gag-Pol polyprotein 3.4.23.16 0.719
1b6l PI4Gag-Pol polyprotein 3.4.23.16 0.718
1d4j MSCGag-Pol polyprotein 3.4.23.16 0.716
2avv MK1Gag-Pol polyprotein 3.4.23.16 0.715
2z54 AB1Gag-Pol polyprotein 3.4.23.16 0.715
1mrx K57Gag-Pol polyprotein 3.4.23.16 0.714
1sdv MK1Gag-Pol polyprotein 3.4.23.16 0.714
2wkz 5AHGag-Pol polyprotein / 0.713
3pwr ROCGag-Pol polyprotein 3.4.23.16 0.712
1k2c 0Q4Gag-Pol polyprotein 3.4.23.16 0.711
1fgc 2NCGag-Pol polyprotein 3.4.23.16 0.710
3d1x ROCGag-Pol polyprotein 3.4.23.16 0.710
2f3k RO1Protease / 0.706
2pym 1UNGag-Pol polyprotein 3.4.23.16 0.706
3i7e DJRGag-Pol polyprotein / 0.706
3i2l 2NCProtease / 0.704
1rl8 RITGag-Pol polyprotein 3.4.23.16 0.703
3slz 3TLPutative gag-pro-pol polyprotein / 0.701
1c6x 3INProtease / 0.700
3gga GGWGag-Pol polyprotein / 0.700
1fg8 0Q4Gag-Pol polyprotein 3.4.23.16 0.698
1d4h BEHGag-Pol polyprotein 3.4.23.16 0.696
3qrm NK7Gag-Pol polyprotein 3.4.23.16 0.695
2bpw 1INGag-Pol polyprotein 3.4.23.16 0.694
3hzc 2NCProtease / 0.694
1zsr 0ZTGag-Pol polyprotein 3.4.23.16 0.693
1dw6 0Q4Gag-Pol polyprotein 3.4.23.16 0.691
3kfs 3TLGag-Pol polyprotein / 0.690
1wbm BLLPol protein / 0.689
1zsf 0ZSGag-Pol polyprotein 3.4.23.16 0.689
3ttp 017Gag-Pol polyprotein 3.4.23.16 0.689
1daz 0Q4Gag-Pol polyprotein 3.4.23.16 0.688
2q5k AB1Protease / 0.687
3bxr DRRGag-Pol polyprotein 3.4.23.16 0.687
1bdr IM1Gag-Pol polyprotein 3.4.23.16 0.686
1w5w BE4Gag-Pol polyprotein 3.4.23.16 0.686
2q54 MU1Protease / 0.686
2b60 RITPol polyprotein / 0.682
2cen 4AHProtease / 0.682
1hsg MK1Gag-Pol polyprotein / 0.681
4njv RITProtease / 0.681
3qp0 NI8Gag-Pol polyprotein 3.4.23.16 0.680
1a94 0Q4Gag-Pol polyprotein 3.4.23.16 0.679
2p3d 3TLProtease / 0.678
4fe6 0TQGag-Pol polyprotein 3.4.23.16 0.678
1izh Q50Protease / 0.677
3ekw DR7Gag-Pol polyprotein 3.4.23.16 0.677
1a9m U0EGag-Pol polyprotein / 0.676
3tog 079Gag-Pol polyprotein 2.7.7.49 0.676
1hii C20Gag-Pol polyprotein / 0.675
1hvi A77Protease / 0.675
1a8g 2Z4Gag-Pol polyprotein 3.4.23.16 0.674
1ec2 BEJGag-Pol polyprotein 3.4.23.16 0.674
4rvj 478Protease / 0.674
1ec1 BEEGag-Pol polyprotein 3.4.23.16 0.673
1m0b 0ZQGag-Pol polyprotein 3.4.23.16 0.673
1iiq 0ZRGag-Pol polyprotein 3.4.23.16 0.671
1meu DMPGag-Pol polyprotein 3.4.23.16 0.671
2wl0 5AHGag-Pol polyprotein / 0.670
3dck KVIProtease / 0.670
3bvb 017Gag-Pol polyprotein 3.4.23.16 0.667
1hxw RITGag-Pol polyprotein / 0.666
2a1e IPFGag-Pol polyprotein 3.4.23.16 0.666
3kdc JZPGag-Pol polyprotein 3.4.23.16 0.665
2fxd DR7Pol polyprotein / 0.663
1c70 L75Protease / 0.662
2b7z MK1Gag-Pol polyprotein / 0.662
2uxz HI1Gag-Pol polyprotein 3.4.23.16 0.661
3zpt M8YGag-Pol polyprotein 3.4.23.16 0.661
1ec3 MS3Gag-Pol polyprotein 3.4.23.16 0.660
1hos PHPGag-Pol polyprotein / 0.660
2qnp QN2Gag-Pol polyprotein 3.4.23.16 0.659
2xyf G40Gag-Pol polyprotein / 0.659
3el0 1UNGag-Pol polyprotein 3.4.23.16 0.659
1k6c MK1Gag-Pol polyprotein 3.4.23.16 0.658
1siv PSIGag-Pol polyprotein / 0.658
1ajv NMBGag-Pol polyprotein 3.4.23.16 0.657
1ec0 BEDGag-Pol polyprotein 3.4.23.16 0.657
3qn8 NI7Gag-Pol polyprotein 3.4.23.16 0.657
1d4k PI8Gag-Pol polyprotein 3.4.23.16 0.655
1ebz BECGag-Pol polyprotein 3.4.23.16 0.655
2pqz G0GGag-Pol polyprotein 3.4.23.16 0.655
1hsh MK1Gag-Pol polyprotein / 0.654
1ebw BEIGag-Pol polyprotein 3.4.23.16 0.653
1k6v XN2Gag-Pol polyprotein 3.4.23.16 0.653
1c6y MK1Protease / 0.652
2xye CXGGag-Pol polyprotein / 0.652
3dm6 757Beta-secretase 1 3.4.23.46 0.652
3ndw RITGag-Pol polyprotein 3.4.23.16 0.652
3ndx RITGag-Pol polyprotein 3.4.23.16 0.652
1bai 0Q4Gag-Pro polyprotein / 0.651
1ivp 1ZKGag-Pol polyprotein / 0.651
1qbt 146Gag-Pol polyprotein 3.4.23.16 0.651
1odw 0E8Gag-Pol polyprotein 3.4.23.16 0.650
3ogq AB1Pol polyprotein / 0.650