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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
3ssm SAH Mycinamicin VI 2''-O-methyltransferase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3ssm SAHMycinamicin VI 2''-O-methyltransferase / 1.121
3sso SAHMycinamicin VI 2''-O-methyltransferase / 1.023
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.790
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.779
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.778
3cbg SAHO-methyltransferase / 0.773
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.773
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.770
4oa5 SAHO-methyltransferase family protein / 0.764
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.756
3duw SAHO-methyltransferase, putative / 0.749
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.747
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.744
1yf3 SAHDNA adenine methylase / 0.741
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.740
2o07 MTASpermidine synthase 2.5.1.16 0.739
3gry SAMProbable ribosomal RNA small subunit methyltransferase A / 0.739
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.736
3c3y SAHO-methyltransferase / 0.736
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.731
3iv6 SAMUncharacterized protein / 0.730
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.729
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.726
3grv ADNProbable ribosomal RNA small subunit methyltransferase A / 0.724
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.723
4kvz SAHPtnL protein / 0.723
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.719
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.718
3tos SAHCalS11 / 0.717
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.717
4gf5 SAHCalS11 / 0.717
2hnk SAHSAM-dependent O-methyltransferase / 0.712
2zzn SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.712
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.711
1af7 SAHChemotaxis protein methyltransferase 2.1.1.80 0.709
2g1p SAHDNA adenine methylase 2.1.1.72 0.708
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.708
2cww SAHUncharacterized protein / 0.707
4ce0 SAHProbable O-methyltransferase / 0.706
3tr6 SAHO-methyltransferase / 0.703
4ctk SAMGenome polyprotein / 0.702
3ou6 SAMSAM-dependent methyltransferase / 0.701
4uy6 SAHHistidine N-alpha-methyltransferase / 0.701
3gwz SAHMitomycin biosynthesis 6-O-methyltransferase / 0.700
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.700
2gs9 SAHUncharacterized protein / 0.698
2c31 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.697
1khh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.695
1p1b SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.695
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.695
2ji6 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.695
2jib ADPOxalyl-CoA decarboxylase 4.1.1.8 0.694
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.693
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.693
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.693
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.692
4ctj SAMGenome polyprotein / 0.691
3p9c SAHCaffeic acid O-methyltransferase / 0.690
5d4u SAMUncharacterized protein MJ0489 / 0.690
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.690
2fkn NADUrocanate hydratase 4.2.1.49 0.688
2ji7 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.688
4kwc SAHMethyltransferase domain family / 0.687
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.686
3lcc SAHThiocyanate methyltransferase 1 / 0.686
4blw SAHRibosomal RNA large subunit methyltransferase J / 0.686
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.685
1nai NADUDP-glucose 4-epimerase 5.1.3.2 0.684
2bm9 SAMCephalosporin hydroxylase CmcI / 0.684
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.684
4nbu NAI3-oxoacyl-(Acyl-carrier-protein) reductase / 0.684
1nbi SAMGlycine N-methyltransferase 2.1.1.20 0.683
2br5 SAHCephalosporin hydroxylase CmcI / 0.683
4dmg SAMUncharacterized protein / 0.682
1g60 SAMModification methylase MboII 2.1.1.72 0.681
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.680
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.679
4fr0 SAMArsenic methyltransferase / 0.679
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.678
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.677
2q28 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.676
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.674
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.673
3vyw SAMUncharacterized protein / 0.673
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.672
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.672
1ori SAHProtein arginine N-methyltransferase 1 / 0.671
4pyo SAHCatechol O-methyltransferase 2.1.1.6 0.671
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.671
2plw SAMRibosomal RNA methyltransferase, putative / 0.669
3i53 SAH2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase / 0.668
4gh5 NADShort-chain dehydrogenase/reductase SDR / 0.668
3m6v SAMRibosomal RNA small subunit methyltransferase F / 0.667
4blv SAMRibosomal RNA large subunit methyltransferase J / 0.665
4yag NAIC alpha-dehydrogenase / 0.665
5d4v SAHUncharacterized protein MJ0489 / 0.665
3lby SAHUncharacterized protein / 0.664
3nug NADPyridoxal 4-dehydrogenase 1.1.1.107 0.664
3bwc SAMSpermidine synthase, putative / 0.662
3ka7 FADPutative oxidoreductase / 0.662
4eqs FADCoenzyme A disulfide reductase / 0.661
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.660
2x2r X2OKinesin-like protein KIF11 / 0.660
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.660
5bxy SAHPutative RNA methylase family UPF0020 / 0.660
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.658
1l3i SAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) / 0.656
3eey SAMrRNA methylase / 0.656
4g56 SAHProtein arginine N-methyltransferase 5 / 0.656
4j2w FADKynurenine 3-monooxygenase / 0.656
5eku SAHArginine N-methyltransferase, putative / 0.656
3sgl SAMtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.655
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.654
1wy7 SAHUncharacterized protein / 0.654
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.654
5jdz SAHMethyl transferase / 0.654
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.652
4g67 SAHUncharacterized ACR, COG1565 superfamily / 0.651