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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
3pt9 SAH DNA (cytosine-5)-methyltransferase 1 2.1.1.37

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.953
3swr SFGDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.801
2yxl SFG450aa long hypothetical fmu protein / 0.795
3pt6 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.790
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.781
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.778
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.763
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.760
1boo SAHModification methylase PvuII 2.1.1.113 0.754
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.738
4da4 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.730
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.729
4rtk SAHDNA adenine methylase 2.1.1.72 0.726
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.720
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.714
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.714
2g1p SAHDNA adenine methylase 2.1.1.72 0.712
3tm4 SAMUncharacterized protein / 0.711
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.711
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.710
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.709
10mh SAHModification methylase HhaI 2.1.1.37 0.708
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.706
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.706
4rtj SFGDNA adenine methylase 2.1.1.72 0.706
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.706
2hnk SAHSAM-dependent O-methyltransferase / 0.703
7mht SAHModification methylase HhaI 2.1.1.37 0.703
4gbe SAHDNA adenine methylase 2.1.1.72 0.702
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.699
3sgl SAMtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.699
1skm SAHModification methylase HhaI 2.1.1.37 0.698
2px2 SAHGenome polyprotein 2.7.7.48 0.698
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.698
2i9k SAHModification methylase HhaI 2.1.1.37 0.696
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.696
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.695
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.694
1yf3 SAHDNA adenine methylase / 0.694
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.694
3ldg SAHUncharacterized protein / 0.691
5jdz SAHMethyl transferase / 0.691
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.689
5je3 SAHMethyl transferase / 0.688
3ou2 SAHSAM-dependent methyltransferase / 0.687
1fjx SAHModification methylase HhaI 2.1.1.37 0.686
2c7q SAHModification methylase HhaI 2.1.1.37 0.686
5je2 SAHMethyl transferase / 0.685
4k6m SAHGenome polyprotein / 0.684
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.683
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.682
3mht SAHModification methylase HhaI 2.1.1.37 0.682
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.682
9mht SAHModification methylase HhaI 2.1.1.37 0.681
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.679
1eg2 MTAModification methylase RsrI 2.1.1.72 0.678
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.678
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.678
1kr5 SAHProtein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77 0.677
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.677
4rtq SAHDNA adenine methylase 2.1.1.72 0.677
5je4 SAHMethyl transferase / 0.677
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.675
3lkz SFGGenome polyprotein / 0.675
3ely SAHMethyltransferase / 0.674
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.671
2uyh SAHModification methylase HhaI 2.1.1.37 0.671
2z6u SAHModification methylase HhaI 2.1.1.37 0.670
4blw SAHRibosomal RNA large subunit methyltransferase J / 0.670
3go4 SAHUncharacterized protein / 0.669
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.668
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.668
3tos SAHCalS11 / 0.667
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.667
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.665
3qv2 SAH5-cytosine DNA methyltransferase / 0.664
4mht SAHModification methylase HhaI 2.1.1.37 0.664
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.662
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.662
3tlj SAHUncharacterized protein / 0.662
4rtm SAMDNA adenine methylase 2.1.1.72 0.662
2zif SAMMethyltransferase / 0.661
3p97 SAMGenome polyprotein 2.1.1.56 0.661
2wa2 SAMGenome polyprotein / 0.660
1mht SAHModification methylase HhaI 2.1.1.37 0.659
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.659
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.658
4dkj SAHCytosine-specific methyltransferase / 0.658
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.658
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.657
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.655
2p3q SAHGenome polyprotein / 0.655
3eva SAHGenome polyprotein 2.1.1.56 0.655
3evc SAHGenome polyprotein 2.1.1.56 0.654
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.654
4c03 SFGProtein arginine N-methyltransferase 6 / 0.654
2zcj SAHModification methylase HhaI 2.1.1.37 0.653
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.653
4pyo SAHCatechol O-methyltransferase 2.1.1.6 0.653
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.653
2np6 NEAModification methylase TaqI 2.1.1.72 0.652
5bp9 SAHPutative methyltransferase protein / 0.652
2cww SAHUncharacterized protein / 0.651
2f8l SAMLmo1582 protein / 0.651
4kvz SAHPtnL protein / 0.651
1aqi SAHModification methylase TaqI 2.1.1.72 0.650
2eg5 SAH7-methylxanthosine synthase 1 / 0.650
2ytz SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.650
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.650