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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
4x3q SAH SibL

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4x3q SAHSibL / 1.086
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.779
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.776
3fri SAH16S rRNA methylase / 0.767
3e8s SAHUncharacterized protein / 0.765
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.754
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.753
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.752
3ou2 SAHSAM-dependent methyltransferase / 0.750
3e23 SAMUncharacterized protein / 0.749
4a6d SAMAcetylserotonin O-methyltransferase 2.1.1.4 0.749
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.749
3p9k SAHCaffeic acid O-methyltransferase / 0.745
4nec SAHPutative SAM-dependent methyltransferase / 0.744
3kkz SAMUncharacterized protein / 0.742
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.738
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.735
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.734
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.731
2qe6 SAMUncharacterized protein / 0.725
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.721
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.719
2zfu SAHRibosomal RNA-processing protein 8 / 0.719
3t7s SAMUncharacterized protein / 0.714
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.711
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.710
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.710
5bp9 SAHPutative methyltransferase protein / 0.706
3vc1 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.705
5je2 SAHMethyl transferase / 0.702
2gs9 SAHUncharacterized protein / 0.701
2xvm SAHTellurite methyltransferase 2.1.1.265 0.701
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.701
1f3l SAHProtein arginine N-methyltransferase 3 / 0.699
5je3 SAHMethyl transferase / 0.699
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.698
3lst SAHCalO1 / 0.696
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.696
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.694
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.692
3vc2 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.692
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.692
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.691
4ckb SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.689
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.687
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.687
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.686
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.682
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.682
5epe SAHUncharacterized protein / 0.682
4c03 SFGProtein arginine N-methyltransferase 6 / 0.681
4e2x SAHMethyltransferase / 0.681
5jdz SAHMethyl transferase / 0.680
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.679
2zw9 SAMtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.679
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.679
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.679
1yf3 SAHDNA adenine methylase / 0.677
4hh4 SAHCcbJ / 0.677
3go4 SAHUncharacterized protein / 0.675
1r37 NADNAD-dependent alcohol dehydrogenase 1.1.1.1 0.674
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.674
3t0i SAHPutative methyltransferase / 0.673
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.672
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.671
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.670
4rvd SAMD-mycarose 3-C-methyltransferase / 0.670
2ji6 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.669
5bxy SAHPutative RNA methylase family UPF0020 / 0.669
2jib ADPOxalyl-CoA decarboxylase 4.1.1.8 0.667
2c31 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.665
3ldf SAHUncharacterized protein / 0.664
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.663
3t7t SAHUncharacterized protein / 0.663
1wy7 SAHUncharacterized protein / 0.662
1xdu SFGAclacinomycin 10-hydroxylase RdmB 4.1.1 0.662
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.659
1y9d FADPyruvate oxidase 1.2.3.3 0.657
4fr0 SAMArsenic methyltransferase / 0.657
4dmg SAMUncharacterized protein / 0.654
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.652
1npd NADQuinate/shikimate dehydrogenase / 0.651
1x1b SAHC-20 methyltransferase / 0.651
2q28 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.651
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.651
3i53 SAH2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase / 0.651
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.650
3nn6 FB06-hydroxy-L-nicotine oxidase / 0.650
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.650