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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
1a9m U0E Gag-Pol polyprotein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1a9m U0EGag-Pol polyprotein / 1.184
1iiq 0ZRGag-Pol polyprotein 3.4.23.16 0.794
2q5k AB1Protease / 0.746
1ec1 BEEGag-Pol polyprotein 3.4.23.16 0.745
1tcx IM1Gag-Pol polyprotein 3.4.23.16 0.739
2rkf AB1Pol protein / 0.734
4dfg 0JVGag-Pol polyprotein 3.4.23.16 0.727
3i2l 2NCProtease / 0.723
2a4f AAUV-1 protease / 0.719
3kfs 3TLGag-Pol polyprotein / 0.718
1a94 0Q4Gag-Pol polyprotein 3.4.23.16 0.717
2qhc AB1Protease / 0.712
2qi7 MZ9Gag-Pol polyprotein / 0.711
2i4w KGQProtease / 0.710
1izh Q50Protease / 0.709
4djr 0KJPol polyprotein / 0.707
2wkz 5AHGag-Pol polyprotein / 0.705
1ebw BEIGag-Pol polyprotein 3.4.23.16 0.704
2avm 2NCGag-Pol polyprotein 3.4.23.16 0.704
3mxd K53Gag-Pol polyprotein 3.4.23.16 0.703
2qi5 MZ7Gag-Pol polyprotein / 0.701
3tog 079Gag-Pol polyprotein 2.7.7.49 0.701
1pro A88Gag-Pol polyprotein / 0.700
3ndt ROCGag-Pol polyprotein 3.4.23.16 0.700
3kdc JZPGag-Pol polyprotein 3.4.23.16 0.699
3kfr 3TLGag-Pol polyprotein / 0.698
2bqv A1AProtease / 0.696
3o9i A61Gag-Pol polyprotein / 0.696
1k2c 0Q4Gag-Pol polyprotein 3.4.23.16 0.695
1sbg IM1Gag-Pol polyprotein / 0.690
1xl5 190Gag-Pol polyprotein 3.4.23.16 0.690
3nls 016Gag-Pol polyprotein 3.4.23.16 0.688
3nyg 2NCGag-Pol polyprotein 3.4.23.16 0.686
4heg G52Gag-Pol polyprotein 3.4.23.16 0.685
3sa5 A69Protease / 0.683
1t7i 017Gag-Pol polyprotein 3.4.23.16 0.682
2i0a MUIProtease / 0.682
3hzc 2NCProtease / 0.681
3nwx KVSGag-Pol polyprotein 3.4.23.16 0.681
1a8g 2Z4Gag-Pol polyprotein 3.4.23.16 0.680
2nmy ROCProtease / 0.680
2qi3 MZ5Gag-Pol polyprotein / 0.680
2cem 2AHPol protein / 0.678
1ebk 0Q4Gag-Pol polyprotein 3.4.23.16 0.677
1hpv 478Gag-Pol polyprotein / 0.677
3o9d K19Pol polyprotein / 0.677
4dqe 017Gag-Pol polyprotein / 0.676
4hdf G52Gag-Pol polyprotein 3.4.23.16 0.676
4dqh 017Gag-Pol polyprotein / 0.675
1daz 0Q4Gag-Pol polyprotein 3.4.23.16 0.674
1zsf 0ZSGag-Pol polyprotein 3.4.23.16 0.674
3ndw RITGag-Pol polyprotein 3.4.23.16 0.673
1fff 0Q4Gag-Pol polyprotein 3.4.23.16 0.672
3kfn 3TLGag-Pol polyprotein / 0.672
3ndx RITGag-Pol polyprotein 3.4.23.16 0.672
4q1x 017Gag-Pol polyprotein 3.4.23.16 0.672
1fgc 2NCGag-Pol polyprotein 3.4.23.16 0.671
1k6v XN2Gag-Pol polyprotein 3.4.23.16 0.671
2aoe 0Q4Gag-Pol polyprotein 3.4.23.16 0.671
3kdb 006Gag-Pol polyprotein 3.4.23.16 0.671
1ody LP1Gag-Pol polyprotein 3.4.23.16 0.670
2qi6 MZ8Gag-Pol polyprotein / 0.670
3dck KVIProtease / 0.670
2psv MUVProtease / 0.669
1ida 0POGag-Pol polyprotein 3.4.23.47 0.668
3d1y ROCGag-Pol polyprotein 3.4.23.16 0.668
3ttp 017Gag-Pol polyprotein 3.4.23.16 0.668
1bai 0Q4Gag-Pro polyprotein / 0.667
1hiv 1ZKGag-Pol polyprotein / 0.667
1z1h HBBGag-Pol polyprotein 3.4.23.16 0.667
3mws 017Pol protein / 0.667
4i8z G08Gag-Pol polyprotein 3.4.23.16 0.667
4q1y 017Gag-Pol polyprotein 3.4.23.16 0.667
2qi4 MZ6Gag-Pol polyprotein / 0.666
3k4v ROCGag-Pol polyprotein 3.4.23.16 0.666
3gi4 K60Gag-Pol polyprotein / 0.665
3oy4 017Gag-Pol polyprotein 3.4.23.16 0.665
3sab F78Protease / 0.665
3gi6 D78Gag-Pol polyprotein / 0.664
1ffi 2NCGag-Pol polyprotein 3.4.23.16 0.663
1fg6 2NCGag-Pol polyprotein 3.4.23.16 0.662
3gi5 K62Gag-Pol polyprotein / 0.662
3sa3 23XProtease / 0.662
3tl9 ROCGag-Pol polyprotein 3.4.23.16 0.662
1hvk A79Gag-Pol polyprotein / 0.661
2p3b 3TLV-1 PROTEASE protein / 0.661
2p3b 3TLV-1 protease / 0.661
3mxe K54Gag-Pol polyprotein 3.4.23.16 0.661
1zj7 0ZTGag-Pol polyprotein 3.4.23.16 0.660
2pk6 O33V-1 protease / 0.660
1ec3 MS3Gag-Pol polyprotein 3.4.23.16 0.659
3oxx DR7Gag-Pol polyprotein 3.4.23.16 0.659
2psu MUUProtease / 0.658
3d1x ROCGag-Pol polyprotein 3.4.23.16 0.658
3oxw 017Gag-Pol polyprotein 3.4.23.16 0.658
1ebz BECGag-Pol polyprotein 3.4.23.16 0.657
1yti PHE_LEU_GLU_LYSGag-Pol polyprotein / 0.657
2fde 385Gag-Pol polyprotein 3.4.23.16 0.657
2i4x KGQProtease / 0.657
2pk5 075Protease / 0.657
3ndu ROCGag-Pol polyprotein 3.4.23.16 0.657
1k6c MK1Gag-Pol polyprotein 3.4.23.16 0.656
4k4p 3TLGag-Pol polyprotein / 0.656
2fxe DR7Gag-Pol polyprotein 3.4.23.16 0.655
3s56 ROCProtease / 0.655
1d4i BEGGag-Pol polyprotein 3.4.23.16 0.654
1dw6 0Q4Gag-Pol polyprotein 3.4.23.16 0.654
1hsh MK1Gag-Pol polyprotein / 0.654
2nnp ROCProtease / 0.654
1zsr 0ZTGag-Pol polyprotein 3.4.23.16 0.653
1bv9 XV6Gag-Pol polyprotein 3.4.23.16 0.650
1hxb ROCGag-Pol polyprotein 3.4.23.16 0.650
1ivq 0PXGag-Pol polyprotein / 0.650
2hb3 GRLProtease / 0.650
2i4d QFIProtease / 0.650
3bva 2NCGag-Pol polyprotein 3.4.23.16 0.650
3ekx 1UNGag-Pol polyprotein 3.4.23.16 0.650