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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
2zcj SAH Modification methylase HhaI 2.1.1.37

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2zcj SAHModification methylase HhaI 2.1.1.37 0.959
2z6u SAHModification methylase HhaI 2.1.1.37 0.928
2i9k SAHModification methylase HhaI 2.1.1.37 0.912
2c7q SAHModification methylase HhaI 2.1.1.37 0.903
1skm SAHModification methylase HhaI 2.1.1.37 0.871
4mht SAHModification methylase HhaI 2.1.1.37 0.863
3mht SAHModification methylase HhaI 2.1.1.37 0.852
2uyh SAHModification methylase HhaI 2.1.1.37 0.831
7mht SAHModification methylase HhaI 2.1.1.37 0.830
1fjx SAHModification methylase HhaI 2.1.1.37 0.820
1mht SAHModification methylase HhaI 2.1.1.37 0.815
10mh SAHModification methylase HhaI 2.1.1.37 0.810
5mht SAHModification methylase HhaI 2.1.1.37 0.791
9mht SAHModification methylase HhaI 2.1.1.37 0.788
4dkj SAHCytosine-specific methyltransferase / 0.780
3ldg SAHUncharacterized protein / 0.767
8mht SAHModification methylase HhaI 2.1.1.37 0.757
1boo SAHModification methylase PvuII 2.1.1.113 0.754
2f8l SAMLmo1582 protein / 0.754
2hmy SAMModification methylase HhaI 2.1.1.37 0.748
3swr SFGDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.742
2g1p SAHDNA adenine methylase 2.1.1.72 0.739
2zif SAMMethyltransferase / 0.736
1g60 SAMModification methylase MboII 2.1.1.72 0.735
1nw5 SAMModification methylase RsrI 2.1.1.72 0.732
1yf3 SAHDNA adenine methylase / 0.729
3qv2 SAH5-cytosine DNA methyltransferase / 0.729
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.719
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.719
4poo SAMPutative RNA methylase / 0.718
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.714
1eg2 MTAModification methylase RsrI 2.1.1.72 0.713
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.713
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.710
2ore SAHDNA adenine methylase 2.1.1.72 0.705
4c03 SFGProtein arginine N-methyltransferase 6 / 0.704
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.702
4rtm SAMDNA adenine methylase 2.1.1.72 0.701
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.698
2yxl SFG450aa long hypothetical fmu protein / 0.698
4rtk SAHDNA adenine methylase 2.1.1.72 0.698
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.696
3c3y SAHO-methyltransferase / 0.696
1kr5 SAHProtein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77 0.695
5bxy SAHPutative RNA methylase family UPF0020 / 0.693
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.692
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.690
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.688
3ldf SAHUncharacterized protein / 0.687
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.685
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.684
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.683
3pt6 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.683
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.682
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.682
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.681
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.681
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.679
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.678
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.678
4c05 SAHProtein arginine N-methyltransferase 6 / 0.678
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.678
2px2 SAHGenome polyprotein 2.7.7.48 0.677
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.676
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.675
4gbe SAHDNA adenine methylase 2.1.1.72 0.675
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.675
5k7w SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.675
3cjt SAHRibosomal protein L11 methyltransferase 2.1.1 0.674
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.674
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.673
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.672
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.672
4rtj SFGDNA adenine methylase 2.1.1.72 0.672
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.671
4oa5 SAHO-methyltransferase family protein / 0.670
4rts SAMDNA adenine methylase 2.1.1.72 0.670
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.669
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.669
4kvz SAHPtnL protein / 0.669
4rto SFGDNA adenine methylase 2.1.1.72 0.669
2xyr SFGReplicase polyprotein 1ab 2.1.1 0.668
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.668
3cbg SAHO-methyltransferase / 0.668
4rtq SAHDNA adenine methylase 2.1.1.72 0.668
2cww SAHUncharacterized protein / 0.667
2vou FAD2,6-dihydroxypyridine 3-monooxygenase 1.14.13.10 0.667
3eey SAMrRNA methylase / 0.667
1nw6 SFGModification methylase RsrI 2.1.1.72 0.666
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.666
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.666
2o07 MTASpermidine synthase 2.5.1.16 0.665
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.665
2bm9 SAMCephalosporin hydroxylase CmcI / 0.664
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.663
4rtp SAMDNA adenine methylase 2.1.1.72 0.663
2gsd NADFormate dehydrogenase / 0.662
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.661
4xcx SAHSmall RNA 2'-O-methyltransferase / 0.661
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.660
3tm4 SAMUncharacterized protein / 0.660
1f3l SAHProtein arginine N-methyltransferase 3 / 0.659
1g1a NADdTDP-glucose 4,6-dehydratase / 0.659
3e8s SAHUncharacterized protein / 0.659
3tm5 SFGUncharacterized protein / 0.659
4yuz S4MSpermidine synthase, putative / 0.659
3tlj SAHUncharacterized protein / 0.658
4nec SAHPutative SAM-dependent methyltransferase / 0.658
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.658
2o06 MTASpermidine synthase 2.5.1.16 0.657
4h0n SAHDnmt2 / 0.656
3icp NADNAD-dependent epimerase/dehydratase / 0.655
4uck SAMLarge structural protein / 0.655
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.654
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.654
5je4 SAHMethyl transferase / 0.654
2plw SAMRibosomal RNA methyltransferase, putative / 0.653
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.653
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.653
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.652
4c04 SFGProtein arginine N-methyltransferase 6 / 0.652
3ruf NADUDP-N-acetylglucosamine 4-epimerase / 0.651
4tm3 FADKtzI / 0.651
4qpp SAHProtein arginine N-methyltransferase 6 / 0.650