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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
3toh 079 Gag-Pol polyprotein 2.7.7.49

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3toh 079Gag-Pol polyprotein 2.7.7.49 1.262
3tof 076Gag-Pol polyprotein 2.7.7.49 1.122
3tog 079Gag-Pol polyprotein 2.7.7.49 0.954
3gga GGWGag-Pol polyprotein / 0.878
2qi5 MZ7Gag-Pol polyprotein / 0.864
3dcr KVSProtease / 0.864
2fxe DR7Gag-Pol polyprotein 3.4.23.16 0.856
3ekw DR7Gag-Pol polyprotein 3.4.23.16 0.856
3eky DR7Gag-Pol polyprotein 3.4.23.16 0.830
3sa3 23XProtease / 0.825
3kf0 3TLGag-Pol polyprotein / 0.811
1hvk A79Gag-Pol polyprotein / 0.807
2wkz 5AHGag-Pol polyprotein / 0.797
3em4 DR7Gag-Pol polyprotein 3.4.23.16 0.797
3ndu ROCGag-Pol polyprotein 3.4.23.16 0.794
3el9 DR7Gag-Pol polyprotein 3.4.23.16 0.793
1ida 0POGag-Pol polyprotein 3.4.23.47 0.792
3sab F78Protease / 0.792
3kfr 3TLGag-Pol polyprotein / 0.791
3slz 3TLPutative gag-pro-pol polyprotein / 0.790
3kfn 3TLGag-Pol polyprotein / 0.787
1fg6 2NCGag-Pol polyprotein 3.4.23.16 0.786
3el1 DR7Gag-Pol polyprotein 3.4.23.16 0.781
1hih C20Gag-Pol polyprotein / 0.777
1hvj A78Gag-Pol polyprotein / 0.776
1fff 0Q4Gag-Pol polyprotein 3.4.23.16 0.775
2a1e IPFGag-Pol polyprotein 3.4.23.16 0.775
1ffi 2NCGag-Pol polyprotein 3.4.23.16 0.771
3sa5 A69Protease / 0.771
1hvs A77Gag-Pol polyprotein / 0.768
1hxw RITGag-Pol polyprotein / 0.765
1n49 RITGag-Pol polyprotein 3.4.23.16 0.763
2q54 MU1Protease / 0.763
3nwx KVSGag-Pol polyprotein 3.4.23.16 0.761
2p3b 3TLV-1 PROTEASE protein / 0.757
2p3b 3TLV-1 protease / 0.757
2cem 2AHPol protein / 0.755
3s85 LK0Gag-Pol polyprotein / 0.753
2aqu DR7Gag-Pol polyprotein 3.4.23.16 0.752
4k4p 3TLGag-Pol polyprotein / 0.750
3kfs 3TLGag-Pol polyprotein / 0.749
4a4q UX9Pol protein / 0.747
1dif A85Gag-Pol polyprotein / 0.737
1vik BAYGag-Pol polyprotein / 0.735
3oxx DR7Gag-Pol polyprotein 3.4.23.16 0.735
1ec3 MS3Gag-Pol polyprotein 3.4.23.16 0.734
3ttp 017Gag-Pol polyprotein 3.4.23.16 0.733
1a8g 2Z4Gag-Pol polyprotein 3.4.23.16 0.732
3i2l 2NCProtease / 0.732
2b60 RITPol polyprotein / 0.731
2fxd DR7Pol polyprotein / 0.730
1sbg IM1Gag-Pol polyprotein / 0.726
2bqv A1AProtease / 0.726
3bxs DRSGag-Pol polyprotein 3.4.23.16 0.726
3sa7 55AProtease / 0.725
1iiq 0ZRGag-Pol polyprotein 3.4.23.16 0.723
2z4o 065Gag-Pol polyprotein 3.4.23.16 0.721
1mtr PI6Gag-Pol polyprotein 3.4.23.16 0.719
1rl8 RITGag-Pol polyprotein 3.4.23.16 0.718
3ndw RITGag-Pol polyprotein 3.4.23.16 0.717
3st5 G89Gag-Pol polyprotein 3.4.23.16 0.717
1izh Q50Protease / 0.716
2aoe 0Q4Gag-Pol polyprotein 3.4.23.16 0.716
2p3c 3TLProtease / 0.716
1ff0 2NCGag-Pol polyprotein 3.4.23.16 0.714
2pk6 O33V-1 protease / 0.714
3ndx RITGag-Pol polyprotein 3.4.23.16 0.712
1hxb ROCGag-Pol polyprotein 3.4.23.16 0.711
1jld 0PPGag-Pol polyprotein / 0.711
3fx5 KNIGag-Pol polyprotein 3.4.23.16 0.711
1fgc 2NCGag-Pol polyprotein 3.4.23.16 0.709
1ody LP1Gag-Pol polyprotein 3.4.23.16 0.708
3ggx GGXGag-Pol polyprotein / 0.707
2qd6 065Gag-Pol polyprotein 3.4.23.16 0.706
1b6p PI7Gag-Pol polyprotein 3.4.23.16 0.704
1hos PHPGag-Pol polyprotein / 0.704
2az8 3TLGag-Pol polyprotein 3.4.23.16 0.704
1fg8 0Q4Gag-Pol polyprotein 3.4.23.16 0.702
1fej 2NCGag-Pol polyprotein 3.4.23.16 0.701
4a6c QG9Gag-Pol polyprotein 3.4.23.16 0.701
1hpx KNIGag-Pol polyprotein / 0.699
1tcx IM1Gag-Pol polyprotein 3.4.23.16 0.698
2z54 AB1Gag-Pol polyprotein 3.4.23.16 0.696
1siv PSIGag-Pol polyprotein / 0.695
2p3d 3TLProtease / 0.694
3ekx 1UNGag-Pol polyprotein 3.4.23.16 0.693
3liq E14Protease / 0.693
2fmb LP1Reverse transcriptase / 0.690
2wl0 5AHGag-Pol polyprotein / 0.690
1hii C20Gag-Pol polyprotein / 0.688
3el5 1UNGag-Pol polyprotein / 0.688
1izi Q50Gag-Pol polyprotein 3.4.23.16 0.687
1z1r HBHGag-Pol polyprotein 3.4.23.16 0.687
1sh9 RITGag-Pol polyprotein 3.4.23.16 0.683
4njv RITProtease / 0.683
1hvi A77Protease / 0.682
3tlh 3TLGag-Pol polyprotein 3.4.23.16 0.682
1a94 0Q4Gag-Pol polyprotein 3.4.23.16 0.679
3pwr ROCGag-Pol polyprotein 3.4.23.16 0.679
3zps EQMGag-Pol polyprotein 3.4.23.16 0.679
1hvl A76Gag-Pol polyprotein / 0.678
1k2c 0Q4Gag-Pol polyprotein 3.4.23.16 0.678
2fde 385Gag-Pol polyprotein 3.4.23.16 0.677
3pwm 017Gag-Pol polyprotein 3.4.23.16 0.677
1xe5 5FEPlasmepsin-2 3.4.23.39 0.676
2fle AIProtease / 0.676
3lzs 017Gag-Pol polyprotein 3.4.23.16 0.676
3sac AF8Protease / 0.676
1d4i BEGGag-Pol polyprotein 3.4.23.16 0.675
2pk5 075Protease / 0.675
2psv MUVProtease / 0.674
4i8z G08Gag-Pol polyprotein 3.4.23.16 0.673
9hvp 0E9Gag-Pol polyprotein / 0.672
4kb9 G79Protease / 0.671
1w5v BE3Gag-Pol polyprotein 3.4.23.16 0.670
1b11 3TLPol polyprotein / 0.669
1m0b 0ZQGag-Pol polyprotein 3.4.23.16 0.669
3ndt ROCGag-Pol polyprotein 3.4.23.16 0.669
3nwq 2NCGag-Pol polyprotein 3.4.23.16 0.669
3ekv 478Gag-Pol polyprotein 3.4.23.16 0.668
2qi4 MZ6Gag-Pol polyprotein / 0.667
2az9 3TLGag-Pol polyprotein 3.4.23.16 0.666
2qhc AB1Protease / 0.666
4a6b QG8Gag-Pol polyprotein 3.4.23.16 0.666
1b6m PI6Gag-Pol polyprotein 3.4.23.16 0.665
1mui AB1Protease / 0.665
2q5k AB1Protease / 0.665
2rkf AB1Pol protein / 0.665
3kfp 3TLGag-Pol polyprotein / 0.665
1vij BAYGag-Pol polyprotein / 0.664
2q55 MU0Protease / 0.664
3ekp 478Gag-Pol polyprotein 3.4.23.16 0.664
3nuo 478Gag-Pol polyprotein 3.4.23.16 0.664
3zpt M8YGag-Pol polyprotein 3.4.23.16 0.664
2q63 1UNGag-Pol polyprotein 3.4.23.16 0.663
1ivp 1ZKGag-Pol polyprotein / 0.661
1hiv 1ZKGag-Pol polyprotein / 0.660
2a4f AAUV-1 protease / 0.660
1ec1 BEEGag-Pol polyprotein 3.4.23.16 0.658
2qd8 065Gag-Pol polyprotein 3.4.23.16 0.658
2rkg AB1Pol protein / 0.658
1c6z ROCProtease / 0.657
1od1 0QSEndothiapepsin 3.4.23.22 0.656
2azb 3TLGag-Pol polyprotein 3.4.23.16 0.655
1zj7 0ZTGag-Pol polyprotein 3.4.23.16 0.654
2p3a 3TLPol protein / 0.654
3ok9 G52Gag-Pol polyprotein 3.4.23.16 0.654
2cen 4AHProtease / 0.652
2uy0 HV1Gag-Pol polyprotein 3.4.23.16 0.652
3k5d XLIBeta-secretase 1 3.4.23.46 0.652
3nyg 2NCGag-Pol polyprotein 3.4.23.16 0.652
3sa4 F72Protease / 0.652
3d1x ROCGag-Pol polyprotein 3.4.23.16 0.651
1t7j 478Gag-Pol polyprotein 3.4.23.16 0.650
4djr 0KJPol polyprotein / 0.650