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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
2eg5 SAH 7-methylxanthosine synthase 1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2eg5 SAH7-methylxanthosine synthase 1 / 0.940
1g7u PEP2-dehydro-3-deoxyphosphooctonate aldolase 2.5.1.55 0.744
4e5i 0N9Polymerase acidic protein / 0.744
5f2k SAHUncharacterized protein / 0.738
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.737
4poo SAMPutative RNA methylase / 0.723
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.721
1ve3 SAMUncharacterized protein / 0.719
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.718
3go4 SAHUncharacterized protein / 0.714
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.710
3e23 SAMUncharacterized protein / 0.709
3fri SAH16S rRNA methylase / 0.698
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.695
5je4 SAHMethyl transferase / 0.694
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.692
3b5i SAHIndole-3-acetate O-methyltransferase 1 / 0.690
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.689
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.684
5jdz SAHMethyl transferase / 0.684
4dmg SAMUncharacterized protein / 0.683
4pne SAHMethyltransferase-like protein / 0.682
3lst SAHCalO1 / 0.680
4dkj SAHCytosine-specific methyltransferase / 0.680
4ek9 EP4Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.679
3c3y SAHO-methyltransferase / 0.678
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.678
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.676
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.676
5k7w SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.675
1eg2 MTAModification methylase RsrI 2.1.1.72 0.674
4e2x SAHMethyltransferase / 0.672
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.672
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.671
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.669
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.667
4lwp SAHArginine N-methyltransferase, putative / 0.667
1skm SAHModification methylase HhaI 2.1.1.37 0.666
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.665
10mh SAHModification methylase HhaI 2.1.1.37 0.664
3qv2 SAH5-cytosine DNA methyltransferase / 0.664
4hh4 SAHCcbJ / 0.663
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.662
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.662
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.662
4rvd SAMD-mycarose 3-C-methyltransferase / 0.661
5je3 SAHMethyl transferase / 0.661
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.660
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.659
4blv SAMRibosomal RNA large subunit methyltransferase J / 0.658
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.658
1kr5 SAHProtein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77 0.657
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.656
1boo SAHModification methylase PvuII 2.1.1.113 0.655
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.655
2uyh SAHModification methylase HhaI 2.1.1.37 0.654
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.654
4ckb SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.654
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.654
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.654
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.653
4uy6 SAHHistidine N-alpha-methyltransferase / 0.652
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.650
3ha3 SAHHydroxymycolate synthase MmaA4 2.1.1 0.650
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.650