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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
3nls 016 Gag-Pol polyprotein 3.4.23.16

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3nls 016Gag-Pol polyprotein 3.4.23.16 1.535
3kdd JZQGag-Pol polyprotein 3.4.23.16 1.053
2pk6 O33V-1 protease / 1.034
2pk5 075Protease / 1.033
3kdc JZPGag-Pol polyprotein 3.4.23.16 0.976
3a2o KNJGag-Pol polyprotein 3.4.23.16 0.954
3kdb 006Gag-Pol polyprotein 3.4.23.16 0.892
1kzk JE2Gag-Pol polyprotein 3.4.23.16 0.862
1msm JE2Gag-Pol polyprotein 3.4.23.16 0.846
1w5x BE5Gag-Pol polyprotein 3.4.23.16 0.841
1xl5 190Gag-Pol polyprotein 3.4.23.16 0.820
1w5w BE4Gag-Pol polyprotein 3.4.23.16 0.819
1ebz BECGag-Pol polyprotein 3.4.23.16 0.807
1wbm BLLPol protein / 0.780
1ec0 BEDGag-Pol polyprotein 3.4.23.16 0.775
3wsj MK1Protease / 0.770
2avm 2NCGag-Pol polyprotein 3.4.23.16 0.764
2qd6 065Gag-Pol polyprotein 3.4.23.16 0.753
2z4o 065Gag-Pol polyprotein 3.4.23.16 0.753
3gi4 K60Gag-Pol polyprotein / 0.753
2avs MK1Gag-Pol polyprotein 3.4.23.16 0.750
3gi6 D78Gag-Pol polyprotein / 0.746
1hpx KNIGag-Pol polyprotein / 0.745
3nu5 478Gag-Pol polyprotein 3.4.23.16 0.745
3s43 478Protease / 0.744
2r5p MK1Gag-Pol polyprotein / 0.741
1msn JE2Gag-Pol polyprotein 3.4.23.16 0.740
3hzc 2NCProtease / 0.738
1mrw K57Gag-Pol polyprotein 3.4.23.16 0.734
3fx5 KNIGag-Pol polyprotein 3.4.23.16 0.734
4djp M73Pol polyprotein / 0.734
1mrx K57Gag-Pol polyprotein 3.4.23.16 0.726
3o9h K2EGag-Pol polyprotein / 0.716
1c6y MK1Protease / 0.714
1mtr PI6Gag-Pol polyprotein 3.4.23.16 0.714
1d4k PI8Gag-Pol polyprotein 3.4.23.16 0.709
3ggu 017Gag-Pol polyprotein 3.4.23.16 0.707
1izh Q50Protease / 0.706
1ec1 BEEGag-Pol polyprotein 3.4.23.16 0.705
1ffi 2NCGag-Pol polyprotein 3.4.23.16 0.705
1fg6 2NCGag-Pol polyprotein 3.4.23.16 0.703
3ok9 G52Gag-Pol polyprotein 3.4.23.16 0.702
2i0d MUTProtease / 0.700
2a1e IPFGag-Pol polyprotein 3.4.23.16 0.698
2hs1 017Protease / 0.698
2q5k AB1Protease / 0.697
3gi5 K62Gag-Pol polyprotein / 0.697
3nuo 478Gag-Pol polyprotein 3.4.23.16 0.695
3bvb 017Gag-Pol polyprotein 3.4.23.16 0.694
1hvj A78Gag-Pol polyprotein / 0.693
2hb3 GRLProtease / 0.693
3jvy 017Gag-Pol polyprotein 3.4.23.16 0.692
3d1z 017Gag-Pol polyprotein 3.4.23.16 0.690
1ec3 MS3Gag-Pol polyprotein 3.4.23.16 0.689
2qi3 MZ5Gag-Pol polyprotein / 0.689
1a9m U0EGag-Pol polyprotein / 0.688
1ebw BEIGag-Pol polyprotein 3.4.23.16 0.688
2qi5 MZ7Gag-Pol polyprotein / 0.688
2cen 4AHProtease / 0.687
2wl0 5AHGag-Pol polyprotein / 0.687
1k2b 0Q4Gag-Pol polyprotein 3.4.23.16 0.686
3o9g F53Gag-Pol polyprotein / 0.686
3sab F78Protease / 0.686
1rl8 RITGag-Pol polyprotein 3.4.23.16 0.685
2cem 2AHPol protein / 0.685
1b6k PI5Gag-Pol polyprotein 3.4.23.16 0.684
1ec2 BEJGag-Pol polyprotein 3.4.23.16 0.684
1hpv 478Gag-Pol polyprotein / 0.684
1iiq 0ZRGag-Pol polyprotein 3.4.23.16 0.683
1tcx IM1Gag-Pol polyprotein 3.4.23.16 0.683
1fgc 2NCGag-Pol polyprotein 3.4.23.16 0.682
4q1y 017Gag-Pol polyprotein 3.4.23.16 0.682
4djr 0KJPol polyprotein / 0.680
4njt 017Protease / 0.680
2fdd 385Pol protein / 0.679
2fxe DR7Gag-Pol polyprotein 3.4.23.16 0.679
2aqu DR7Gag-Pol polyprotein 3.4.23.16 0.677
3o9a K14Pol polyprotein / 0.677
3o9f K2DGag-Pol polyprotein / 0.677
3ucb 017Gag-Pol polyprotein / 0.677
1ff0 2NCGag-Pol polyprotein 3.4.23.16 0.676
2q54 MU1Protease / 0.676
3bgb LJGGag-Pol polyprotein 3.4.23.16 0.676
3i2l 2NCProtease / 0.675
2qi7 MZ9Gag-Pol polyprotein / 0.674
3kf0 3TLGag-Pol polyprotein / 0.674
2cej 1AHPol protein / 0.673
3lit E15Protease / 0.673
3lzv 017Gag-Pol polyprotein 3.4.23.16 0.672
4hdp G52Gag-Pol polyprotein 3.4.23.16 0.672
3bxr DRRGag-Pol polyprotein 3.4.23.16 0.671
3djk G55Gag-Pol polyprotein 3.4.23.16 0.671
3o9b K2APol polyprotein / 0.671
3kfr 3TLGag-Pol polyprotein / 0.670
4heg G52Gag-Pol polyprotein 3.4.23.16 0.669
3el0 1UNGag-Pol polyprotein 3.4.23.16 0.668
3liv E16Protease / 0.668
1w5y BE6Gag-Pol polyprotein 3.4.23.16 0.667
3liq E14Protease / 0.666
3ndw RITGag-Pol polyprotein 3.4.23.16 0.666
1fej 2NCGag-Pol polyprotein 3.4.23.16 0.665
3nwx KVSGag-Pol polyprotein 3.4.23.16 0.665
3vfb 031Gag-Pol polyprotein 3.4.23.16 0.665
2qd8 065Gag-Pol polyprotein 3.4.23.16 0.664
3ndx RITGag-Pol polyprotein 3.4.23.16 0.664
3nu3 478Gag-Pol polyprotein 3.4.23.16 0.663
1c70 L75Protease / 0.662
1d4j MSCGag-Pol polyprotein 3.4.23.16 0.662
1fg8 0Q4Gag-Pol polyprotein 3.4.23.16 0.662
1ody LP1Gag-Pol polyprotein 3.4.23.16 0.662
2i4u DJRProtease / 0.662
1k2c 0Q4Gag-Pol polyprotein 3.4.23.16 0.660
3nuj 478Gag-Pol polyprotein 3.4.23.16 0.660
3sa8 K83Protease / 0.660
4ye3 G04Gag-Pol polyprotein 3.4.23.16 0.660
2aoe 0Q4Gag-Pol polyprotein 3.4.23.16 0.657
3em4 DR7Gag-Pol polyprotein 3.4.23.16 0.657
1wbk 568Pol protein / 0.656
2bb9 AKCGag-Pol polyprotein 3.4.23.16 0.656
3i7e DJRGag-Pol polyprotein / 0.656
3nwq 2NCGag-Pol polyprotein 3.4.23.16 0.656
3oxx DR7Gag-Pol polyprotein 3.4.23.16 0.656
1eby BEBGag-Pol polyprotein 3.4.23.16 0.655
3o99 K13Pol polyprotein / 0.655
4hdb G52Gag-Pol polyprotein 3.4.23.16 0.655
4djq M86Pol polyprotein / 0.654
4rvj 478Protease / 0.654
1hxw RITGag-Pol polyprotein / 0.653
2bbb HH1Gag-Pol polyprotein 3.4.23.16 0.653
3lix E17Protease / 0.653
3nu4 478Gag-Pol polyprotein 3.4.23.16 0.653
1hsg MK1Gag-Pol polyprotein / 0.652