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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
4rtm SAM DNA adenine methylase 2.1.1.72

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4rtm SAMDNA adenine methylase 2.1.1.72 0.943
4rtk SAHDNA adenine methylase 2.1.1.72 0.885
4rtp SAMDNA adenine methylase 2.1.1.72 0.841
4rtj SFGDNA adenine methylase 2.1.1.72 0.837
4gbe SAHDNA adenine methylase 2.1.1.72 0.809
4rto SFGDNA adenine methylase 2.1.1.72 0.803
2g1p SAHDNA adenine methylase 2.1.1.72 0.778
1yf3 SAHDNA adenine methylase / 0.776
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.765
4rts SAMDNA adenine methylase 2.1.1.72 0.756
2ore SAHDNA adenine methylase 2.1.1.72 0.754
4rtn SAHDNA adenine methylase 2.1.1.72 0.752
4gol SA8DNA adenine methylase 2.1.1.72 0.738
4rtq SAHDNA adenine methylase 2.1.1.72 0.730
4rtr SAMDNA adenine methylase 2.1.1.72 0.726
1nw5 SAMModification methylase RsrI 2.1.1.72 0.721
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.719
1eg2 MTAModification methylase RsrI 2.1.1.72 0.717
3qv2 SAH5-cytosine DNA methyltransferase / 0.709
3tm5 SFGUncharacterized protein / 0.708
4rtl SFGDNA adenine methylase 2.1.1.72 0.704
2zcj SAHModification methylase HhaI 2.1.1.37 0.701
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.700
4dmg SAMUncharacterized protein / 0.700
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.700
3eey SAMrRNA methylase / 0.698
1g60 SAMModification methylase MboII 2.1.1.72 0.696
3tm4 SAMUncharacterized protein / 0.696
1boo SAHModification methylase PvuII 2.1.1.113 0.695
3ldg SAHUncharacterized protein / 0.693
4blv SAMRibosomal RNA large subunit methyltransferase J / 0.690
1nw6 SFGModification methylase RsrI 2.1.1.72 0.689
2yxl SFG450aa long hypothetical fmu protein / 0.689
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.688
2uyh SAHModification methylase HhaI 2.1.1.37 0.687
2c7q SAHModification methylase HhaI 2.1.1.37 0.686
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.686
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.684
1skm SAHModification methylase HhaI 2.1.1.37 0.681
9mht SAHModification methylase HhaI 2.1.1.37 0.681
10mh SAHModification methylase HhaI 2.1.1.37 0.679
2i9k SAHModification methylase HhaI 2.1.1.37 0.678
3mht SAHModification methylase HhaI 2.1.1.37 0.678
3tlj SAHUncharacterized protein / 0.676
4poo SAMPutative RNA methylase / 0.676
1uay ADNOxidoreductase / 0.675
2f8l SAMLmo1582 protein / 0.673
4ft4 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.673
4mht SAHModification methylase HhaI 2.1.1.37 0.673
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.671
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.668
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.667
5mht SAHModification methylase HhaI 2.1.1.37 0.663
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.662
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.661
3s1s SAHRestriction endonuclease BpuSI / 0.660
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.660
3m6v SAMRibosomal RNA small subunit methyltransferase F / 0.659
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.659
7mht SAHModification methylase HhaI 2.1.1.37 0.659
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.657
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.657
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.657
1qlh NADAlcohol dehydrogenase E chain 1.1.1.1 0.655
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.655
1mht SAHModification methylase HhaI 2.1.1.37 0.654
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.654
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.652
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.652
3m6w SAMRibosomal RNA small subunit methyltransferase F / 0.651
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.651
4dkj SAHCytosine-specific methyltransferase / 0.651
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.650