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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
1cbf SAH Cobalt-precorrin-4 C(11)-methyltransferase 2.1.1.271

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1cbf SAHCobalt-precorrin-4 C(11)-methyltransferase 2.1.1.271 1.055
1v9a SAHUncharacterized protein / 0.868
3ndc SAHPrecorrin-4 C(11)-methyltransferase 2.1.1.133 0.815
2ybo SAHMethyltransferase / 0.812
1s4d SAHUroporphyrinogen-III C-methyltransferase 2.1.1.107 0.804
3nd1 SAHPrecorrin-6A synthase (Deacetylating) / 0.761
2e0n SAHPrecorrin-2 C20-methyltransferase / 0.752
2npn SAMPutative cobalamin synthesis related protein / 0.741
2qbu SAHPrecorrin-2 methyltransferase / 0.736
2zvc SAHPrecorrin-3 C17-methyltransferase / 0.722
2bb3 SAHCobalamin biosynthesis precorrin-6Y methylase (CbiE) / 0.720
2zvb SAHPrecorrin-3 C17-methyltransferase / 0.717
3nut SAHPrecorrin-3 methylase / 0.707
2owu SAHDiphthine synthase / 0.706
2p6k SAHDiphthine synthase / 0.698
2ek7 SAHDiphthine synthase / 0.695
2owv SAHDiphthine synthase / 0.695
2egs SAHDiphthine synthase / 0.694
2emr SAHDiphthine synthase / 0.694
2eni SAHDiphthine synthase / 0.694
2pcm SAHDiphthine synthase / 0.693
2e7r SAHDiphthine synthase / 0.691
2egb SAHDiphthine synthase / 0.691
2eka SAHDiphthine synthase / 0.691
2eld SAHDiphthine synthase / 0.691
2dxw SAHDiphthine synthase / 0.690
2e15 SAHDiphthine synthase / 0.690
2eh2 SAHDiphthine synthase / 0.690
2en5 SAHDiphthine synthase / 0.690
2p9d SAHDiphthine synthase / 0.690
2z6r SAHDiphthine synthase / 0.690
2e17 SAHDiphthine synthase / 0.689
2p6i SAHDiphthine synthase / 0.689
2e08 SAHDiphthine synthase / 0.688
2e4n SAHDiphthine synthase / 0.685
2pca SAHDiphthine synthase / 0.685
2dxv SAHDiphthine synthase / 0.684
2dxx SAHDiphthine synthase / 0.684
2dsg SAHDiphthine synthase / 0.683
2e16 SAHDiphthine synthase / 0.683
2ejj SAHDiphthine synthase / 0.683
2el3 SAHDiphthine synthase / 0.683
2owg SAHDiphthine synthase / 0.683
1kor ANPArgininosuccinate synthase / 0.682
2dsi SAHDiphthine synthase / 0.681
2e07 SAHDiphthine synthase / 0.681
2hut SAHDiphthine synthase / 0.681
2egl SAHDiphthine synthase / 0.680
2pb5 SAHDiphthine synthase / 0.679
2dek SAHDiphthine synthase / 0.677
2owk SAHDiphthine synthase / 0.677
2dsh SAHDiphthine synthase / 0.673
2el0 SAHDiphthine synthase / 0.673
2pck SAHDiphthine synthase / 0.673
2huq SAHDiphthine synthase / 0.671
2p5f SAHDiphthine synthase / 0.671
2ele SAHDiphthine synthase / 0.670
2ehl SAHDiphthine synthase / 0.669
2dv3 SAHDiphthine synthase / 0.668
2dv7 SAHDiphthine synthase / 0.668
2eh4 SAHDiphthine synthase / 0.667
2p6l SAHDiphthine synthase / 0.666
2hr8 SAHDiphthine synthase / 0.664
2z08 ATPUniversal stress protein family / 0.664
4cnf MTASpoU rRNA methylase / 0.664
2dv4 SAHDiphthine synthase / 0.663
1kh2 ATPArgininosuccinate synthase / 0.662
1j21 ATPArgininosuccinate synthase / 0.661
1mjh ATPUniversal stress protein MJ0577 / 0.660
2e8h SAHDiphthine synthase / 0.660
2ek3 SAHDiphthine synthase / 0.659
2eh5 SAHDiphthine synthase / 0.658
2dv5 SAHDiphthine synthase / 0.656
2egv SAMRibosomal RNA small subunit methyltransferase E 2.1.1.193 0.656
2ek4 SAHDiphthine synthase / 0.655
2yy8 SAMtRNA (cytidine(56)-2'-O)-methyltransferase / 0.655
1kh3 ANPArgininosuccinate synthase / 0.652
3ab8 ATPUncharacterized protein / 0.652
4xfj ANPArgininosuccinate synthase / 0.652
1jgt APCCarboxyethyl-arginine beta-lactam-synthase 6.3.3.4 0.651
2hma SAMtRNA-specific 2-thiouridylase MnmA / 0.650