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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
2rkg AB1 Pol protein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2rkg AB1Pol protein / 1.321
2rkf AB1Pol protein / 1.065
2q5k AB1Protease / 1.015
2qhc AB1Protease / 0.986
2z54 AB1Gag-Pol polyprotein 3.4.23.16 0.893
3eky DR7Gag-Pol polyprotein 3.4.23.16 0.859
3ndx RITGag-Pol polyprotein 3.4.23.16 0.840
3ndw RITGag-Pol polyprotein 3.4.23.16 0.831
4njv RITProtease / 0.819
3el1 DR7Gag-Pol polyprotein 3.4.23.16 0.799
2bqv A1AProtease / 0.797
3kfr 3TLGag-Pol polyprotein / 0.794
1rl8 RITGag-Pol polyprotein 3.4.23.16 0.792
2fxe DR7Gag-Pol polyprotein 3.4.23.16 0.791
3oxx DR7Gag-Pol polyprotein 3.4.23.16 0.784
3el9 DR7Gag-Pol polyprotein 3.4.23.16 0.779
1b6k PI5Gag-Pol polyprotein 3.4.23.16 0.776
1b6m PI6Gag-Pol polyprotein 3.4.23.16 0.770
1npv L27Gag-Pol polyprotein 3.4.23.16 0.749
3em4 DR7Gag-Pol polyprotein 3.4.23.16 0.749
1hvj A78Gag-Pol polyprotein / 0.743
3kfn 3TLGag-Pol polyprotein / 0.742
1odw 0E8Gag-Pol polyprotein 3.4.23.16 0.741
1hii C20Gag-Pol polyprotein / 0.739
1t3r 017Gag-Pol polyprotein 3.4.23.16 0.734
1hvi A77Protease / 0.732
3kf0 3TLGag-Pol polyprotein / 0.732
2aoe 0Q4Gag-Pol polyprotein 3.4.23.16 0.731
1zsf 0ZSGag-Pol polyprotein 3.4.23.16 0.729
3ggx GGXGag-Pol polyprotein / 0.729
1jld 0PPGag-Pol polyprotein / 0.725
1hpx KNIGag-Pol polyprotein / 0.724
2fxd DR7Pol polyprotein / 0.724
4k4p 3TLGag-Pol polyprotein / 0.724
2p3d 3TLProtease / 0.723
4dqh 017Gag-Pol polyprotein / 0.722
3a2o KNJGag-Pol polyprotein 3.4.23.16 0.721
1iiq 0ZRGag-Pol polyprotein 3.4.23.16 0.720
2a1e IPFGag-Pol polyprotein 3.4.23.16 0.715
3ggu 017Gag-Pol polyprotein 3.4.23.16 0.715
1zsr 0ZTGag-Pol polyprotein 3.4.23.16 0.713
1hih C20Gag-Pol polyprotein / 0.712
2nmy ROCProtease / 0.712
1hxw RITGag-Pol polyprotein / 0.711
1hvs A77Gag-Pol polyprotein / 0.708
1ec0 BEDGag-Pol polyprotein 3.4.23.16 0.707
1hvl A76Gag-Pol polyprotein / 0.707
2b60 RITPol polyprotein / 0.707
3kfs 3TLGag-Pol polyprotein / 0.707
1d4k PI8Gag-Pol polyprotein 3.4.23.16 0.706
1kzk JE2Gag-Pol polyprotein 3.4.23.16 0.705
3bvb 017Gag-Pol polyprotein 3.4.23.16 0.703
3o9e A60Pol polyprotein / 0.703
1w5w BE4Gag-Pol polyprotein 3.4.23.16 0.701
2wkz 5AHGag-Pol polyprotein / 0.700
1t7i 017Gag-Pol polyprotein 3.4.23.16 0.699
2bb9 AKCGag-Pol polyprotein 3.4.23.16 0.699
3kdb 006Gag-Pol polyprotein 3.4.23.16 0.699
1a8g 2Z4Gag-Pol polyprotein 3.4.23.16 0.697
3o9b K2APol polyprotein / 0.697
4q1x 017Gag-Pol polyprotein 3.4.23.16 0.697
1b6p PI7Gag-Pol polyprotein 3.4.23.16 0.696
1hpv 478Gag-Pol polyprotein / 0.694
3o9f K2DGag-Pol polyprotein / 0.694
3i2l 2NCProtease / 0.691
2q55 MU0Protease / 0.690
3jvw DMPGag-Pol polyprotein 3.4.23.16 0.690
1siv PSIGag-Pol polyprotein / 0.689
2bbb HH1Gag-Pol polyprotein 3.4.23.16 0.689
1odx 0E8Gag-Pol polyprotein 3.4.23.16 0.687
1ec1 BEEGag-Pol polyprotein 3.4.23.16 0.686
3s54 017Protease / 0.686
2bpz 3INGag-Pol polyprotein 3.4.23.16 0.685
2cem 2AHPol protein / 0.685
4hdb G52Gag-Pol polyprotein 3.4.23.16 0.685
1hxb ROCGag-Pol polyprotein 3.4.23.16 0.684
2bpy 3INGag-Pol polyprotein 3.4.23.16 0.684
2q64 1UNGag-Pol polyprotein 3.4.23.16 0.684
2bpx MK1Gag-Pol polyprotein 3.4.23.16 0.683
2aqu DR7Gag-Pol polyprotein 3.4.23.16 0.682
3o9g F53Gag-Pol polyprotein / 0.682
1ec2 BEJGag-Pol polyprotein 3.4.23.16 0.679
1izi Q50Gag-Pol polyprotein 3.4.23.16 0.679
3o9d K19Pol polyprotein / 0.679
3s85 LK0Gag-Pol polyprotein / 0.679
3d20 017Gag-Pol polyprotein 3.4.23.16 0.678
3nyg 2NCGag-Pol polyprotein 3.4.23.16 0.678
2p3c 3TLProtease / 0.677
2hb3 GRLProtease / 0.676
2qci 065Gag-Pol polyprotein 3.4.23.16 0.676
3liv E16Protease / 0.675
3el5 1UNGag-Pol polyprotein / 0.674
3lin E13Protease / 0.674
3lix E17Protease / 0.674
1bdr IM1Gag-Pol polyprotein 3.4.23.16 0.672
4rvj 478Protease / 0.672
1t7j 478Gag-Pol polyprotein 3.4.23.16 0.671
2qi6 MZ8Gag-Pol polyprotein / 0.671
3t3c 017Gag-Pol polyprotein 3.4.23.16 0.671
3tog 079Gag-Pol polyprotein 2.7.7.49 0.671
1npa 3NHGag-Pol polyprotein 3.4.23.16 0.670
1npw LGZGag-Pol polyprotein 3.4.23.16 0.670
2qi4 MZ6Gag-Pol polyprotein / 0.670
3ekw DR7Gag-Pol polyprotein 3.4.23.16 0.670
3jvy 017Gag-Pol polyprotein 3.4.23.16 0.670
3mws 017Pol protein / 0.670
4djo MK5Pol polyprotein / 0.669
2b7z MK1Gag-Pol polyprotein / 0.668
1hsh MK1Gag-Pol polyprotein / 0.667
3bxr DRRGag-Pol polyprotein 3.4.23.16 0.667
4ye3 G04Gag-Pol polyprotein 3.4.23.16 0.667
1d4j MSCGag-Pol polyprotein 3.4.23.16 0.666
3liq E14Protease / 0.666
1daz 0Q4Gag-Pol polyprotein 3.4.23.16 0.665
1ida 0POGag-Pol polyprotein 3.4.23.47 0.665
2pk6 O33V-1 protease / 0.665
2uy0 HV1Gag-Pol polyprotein 3.4.23.16 0.665
2z4o 065Gag-Pol polyprotein 3.4.23.16 0.663
3ec0 GRLGag-Pol polyprotein 3.4.23.47 0.663
3nuo 478Gag-Pol polyprotein 3.4.23.16 0.662
3q70 RITCandidapepsin-2 3.4.23.24 0.661
4djq M86Pol polyprotein / 0.661
2idw 017Protease / 0.660
1d4l PI9Gag-Pol polyprotein 3.4.23.16 0.659
1eby BEBGag-Pol polyprotein 3.4.23.16 0.659
3o9i A61Gag-Pol polyprotein / 0.659
2f3k RO1Protease / 0.658
3bva 2NCGag-Pol polyprotein 3.4.23.16 0.658
3toh 079Gag-Pol polyprotein 2.7.7.49 0.658
4dqb 017Gag-Pol polyprotein / 0.658
1a8k 0Q4Gag-Pol polyprotein 3.4.23.16 0.657
1w5v BE3Gag-Pol polyprotein 3.4.23.16 0.657
3fx5 KNIGag-Pol polyprotein 3.4.23.16 0.657
3kdc JZPGag-Pol polyprotein 3.4.23.16 0.657
1d4h BEHGag-Pol polyprotein 3.4.23.16 0.656
1fg8 0Q4Gag-Pol polyprotein 3.4.23.16 0.656
3dcr KVSProtease / 0.656
4q1w 017Gag-Pol polyprotein 3.4.23.16 0.656
3nwq 2NCGag-Pol polyprotein 3.4.23.16 0.655
3o9c K20Pol polyprotein / 0.655
3ekx 1UNGag-Pol polyprotein 3.4.23.16 0.654
1k2b 0Q4Gag-Pol polyprotein 3.4.23.16 0.653
2hs2 017Protease / 0.653
3ecg 065Gag-Pol polyprotein 3.4.23.47 0.652
3ttp 017Gag-Pol polyprotein 3.4.23.16 0.652
3vf7 031Gag-Pol polyprotein 3.4.23.16 0.652
1a94 0Q4Gag-Pol polyprotein 3.4.23.16 0.650
1fej 2NCGag-Pol polyprotein 3.4.23.16 0.650
1w5y BE6Gag-Pol polyprotein 3.4.23.16 0.650
2cen 4AHProtease / 0.650
2qhy MZ1Gag-Pol polyprotein / 0.650
3nu4 478Gag-Pol polyprotein 3.4.23.16 0.650
4heg G52Gag-Pol polyprotein 3.4.23.16 0.650
4q1y 017Gag-Pol polyprotein 3.4.23.16 0.650