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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
3jvw DMP Gag-Pol polyprotein 3.4.23.16

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3jvw DMPGag-Pol polyprotein 3.4.23.16 1.312
1t7k BH0Gag-Pol polyprotein 3.4.23.16 0.780
3nuo 478Gag-Pol polyprotein 3.4.23.16 0.755
2a4f AAUV-1 protease / 0.750
3kfr 3TLGag-Pol polyprotein / 0.746
1mes DMPGag-Pol polyprotein 3.4.23.16 0.745
1bwa XV6Gag-Pol polyprotein 3.4.23.16 0.735
3nu3 478Gag-Pol polyprotein 3.4.23.16 0.733
1z1h HBBGag-Pol polyprotein 3.4.23.16 0.730
1ajx AH1Gag-Pol polyprotein 3.4.23.16 0.729
2psu MUUProtease / 0.724
4kb9 G79Protease / 0.724
4hdf G52Gag-Pol polyprotein 3.4.23.16 0.721
1bve DMPGag-Pol polyprotein 3.4.23.16 0.720
3i6o GR6Gag-Pol polyprotein 3.4.23.16 0.718
4hdp G52Gag-Pol polyprotein 3.4.23.16 0.718
3ndx RITGag-Pol polyprotein 3.4.23.16 0.712
3sa8 K83Protease / 0.711
3o9h K2EGag-Pol polyprotein / 0.710
1ida 0POGag-Pol polyprotein 3.4.23.47 0.708
4heg G52Gag-Pol polyprotein 3.4.23.16 0.708
2z4o 065Gag-Pol polyprotein 3.4.23.16 0.707
1qbt 146Gag-Pol polyprotein 3.4.23.16 0.706
3eky DR7Gag-Pol polyprotein 3.4.23.16 0.706
3oy4 017Gag-Pol polyprotein 3.4.23.16 0.704
2q5k AB1Protease / 0.703
3nu4 478Gag-Pol polyprotein 3.4.23.16 0.702
2qi0 MZ3Gag-Pol polyprotein / 0.701
3el1 DR7Gag-Pol polyprotein 3.4.23.16 0.701
3jvy 017Gag-Pol polyprotein 3.4.23.16 0.701
1npa 3NHGag-Pol polyprotein 3.4.23.16 0.700
1npw LGZGag-Pol polyprotein 3.4.23.16 0.700
2nmy ROCProtease / 0.700
3o9c K20Pol polyprotein / 0.700
3sa9 A68Protease / 0.700
1met DMPGag-Pol polyprotein 3.4.23.16 0.699
4dqb 017Gag-Pol polyprotein / 0.699
3lzv 017Gag-Pol polyprotein 3.4.23.16 0.698
1hvi A77Protease / 0.697
1pro A88Gag-Pol polyprotein / 0.697
1hvs A77Gag-Pol polyprotein / 0.694
4dqf 017Gag-Pol polyprotein / 0.694
4njs G08Protease / 0.694
2rkg AB1Pol protein / 0.690
1ec3 MS3Gag-Pol polyprotein 3.4.23.16 0.689
4dqc 017Gag-Pol polyprotein / 0.689
1hxw RITGag-Pol polyprotein / 0.688
2i0a MUIProtease / 0.688
3st5 G89Gag-Pol polyprotein 3.4.23.16 0.688
3vfb 031Gag-Pol polyprotein 3.4.23.16 0.687
3sa7 55AProtease / 0.686
2qci 065Gag-Pol polyprotein 3.4.23.16 0.685
3saa 77FProtease / 0.685
2fxe DR7Gag-Pol polyprotein 3.4.23.16 0.683
2qi4 MZ6Gag-Pol polyprotein / 0.682
3mws 017Pol protein / 0.680
1npv L27Gag-Pol polyprotein 3.4.23.16 0.679
3d1y ROCGag-Pol polyprotein 3.4.23.16 0.679
3sa6 F71Protease / 0.679
1bvg DMPGag-Pol polyprotein 3.4.23.16 0.678
1jld 0PPGag-Pol polyprotein / 0.677
2qi6 MZ8Gag-Pol polyprotein / 0.676
3tl9 ROCGag-Pol polyprotein 3.4.23.16 0.675
1hii C20Gag-Pol polyprotein / 0.674
3o9d K19Pol polyprotein / 0.674
3k4v ROCGag-Pol polyprotein 3.4.23.16 0.673
3oxv 478Gag-Pol polyprotein 3.4.23.16 0.673
2rkf AB1Pol protein / 0.672
3el4 ROCGag-Pol polyprotein 3.4.23.16 0.672
3gi4 K60Gag-Pol polyprotein / 0.672
3nu9 478Gag-Pol polyprotein 3.4.23.16 0.672
3r4b 74TGag-Pol polyprotein / 0.672
3mxd K53Gag-Pol polyprotein 3.4.23.16 0.671
4dqe 017Gag-Pol polyprotein / 0.671
1hvk A79Gag-Pol polyprotein / 0.670
3sac AF8Protease / 0.670
1izh Q50Protease / 0.669
3s85 LK0Gag-Pol polyprotein / 0.669
1bv7 XV6Gag-Pol polyprotein 3.4.23.16 0.668
1izi Q50Gag-Pol polyprotein 3.4.23.16 0.668
1qbr XV6Gag-Pol polyprotein 3.4.23.16 0.668
3cyw 017Gag-Pol polyprotein 3.4.23.16 0.668
4k4p 3TLGag-Pol polyprotein / 0.668
1hvj A78Gag-Pol polyprotein / 0.667
2q55 MU0Protease / 0.666
2r5p MK1Gag-Pol polyprotein / 0.665
2aqu DR7Gag-Pol polyprotein 3.4.23.16 0.663
4j54 G52Gag-Pol polyprotein 3.4.23.16 0.663
3gi5 K62Gag-Pol polyprotein / 0.661
1idb 0DOGag-Pol polyprotein / 0.660
1t7i 017Gag-Pol polyprotein 3.4.23.16 0.660
1b6k PI5Gag-Pol polyprotein 3.4.23.16 0.659
3cyx ROCGag-Pol polyprotein 3.4.23.16 0.659
3kfn 3TLGag-Pol polyprotein / 0.659
3pwm 017Gag-Pol polyprotein 3.4.23.16 0.659
1mrw K57Gag-Pol polyprotein 3.4.23.16 0.658
3djk G55Gag-Pol polyprotein 3.4.23.16 0.658
3em4 DR7Gag-Pol polyprotein 3.4.23.16 0.658
4dqh 017Gag-Pol polyprotein / 0.658
3ekq ROCGag-Pol polyprotein 3.4.23.16 0.657
4dfg 0JVGag-Pol polyprotein 3.4.23.16 0.657
2f81 017Gag-Pol polyprotein 3.4.23.16 0.656
3o99 K13Pol polyprotein / 0.656
3o9i A61Gag-Pol polyprotein / 0.656
3vfa 031Gag-Pol polyprotein 3.4.23.16 0.656
1msm JE2Gag-Pol polyprotein 3.4.23.16 0.655
1t3r 017Gag-Pol polyprotein 3.4.23.16 0.655
1z1r HBHGag-Pol polyprotein 3.4.23.16 0.655
3dk1 G05Gag-Pol polyprotein 3.4.23.16 0.655
3nu6 478Gag-Pol polyprotein 3.4.23.16 0.655
2fdd 385Pol protein / 0.654
1tcx IM1Gag-Pol polyprotein 3.4.23.16 0.653
2b7z MK1Gag-Pol polyprotein / 0.653
2bb9 AKCGag-Pol polyprotein 3.4.23.16 0.653
2hb3 GRLProtease / 0.653
2pym 1UNGag-Pol polyprotein 3.4.23.16 0.653
1ec0 BEDGag-Pol polyprotein 3.4.23.16 0.652
2i4v DJRV-1 protease / 0.652
2aoe 0Q4Gag-Pol polyprotein 3.4.23.16 0.651
2qhz MZ2Gag-Pol polyprotein / 0.650