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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
4ce0 SAH Probable O-methyltransferase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4ce0 SAHProbable O-methyltransferase / 1.087
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.804
4gf5 SAHCalS11 / 0.745
3tos SAHCalS11 / 0.742
1nbh SAMGlycine N-methyltransferase 2.1.1.20 0.735
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.716
3c3y SAHO-methyltransferase / 0.707
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.706
3ssm SAHMycinamicin VI 2''-O-methyltransferase / 0.706
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.704
1nbi SAMGlycine N-methyltransferase 2.1.1.20 0.693
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.692
2v7g NADUrocanate hydratase 4.2.1.49 0.691
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.690
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.689
4fr0 SAMArsenic methyltransferase / 0.683
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.677
2plw SAMRibosomal RNA methyltransferase, putative / 0.676
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.675
3gwz SAHMitomycin biosynthesis 6-O-methyltransferase / 0.672
2br5 SAHCephalosporin hydroxylase CmcI / 0.671
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.671
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.670
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.669
1p1b SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.667
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.665
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.665
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.664
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.664
5fa8 SAMRibosomal protein L11 methyltransferase, putative / 0.664
3lcc SAHThiocyanate methyltransferase 1 / 0.662
1l3i SAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) / 0.661
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.660
4e2x SAHMethyltransferase / 0.660
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.658
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.657
2hnk SAHSAM-dependent O-methyltransferase / 0.656
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.655
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.654
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.654
5bxy SAHPutative RNA methylase family UPF0020 / 0.654
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.653
2ji7 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.652
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.652
2cdu ADPNADH oxidase / 0.651
2ji6 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.651
3ict FADCoenzyme A disulfide reductase / 0.651
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.650
3atr FDAConserved Archaeal protein / 0.650
4hh4 SAHCcbJ / 0.650