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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
4mb2 ATP Uncharacterized protein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4mb2 ATPUncharacterized protein / 0.947
2yxl SFG450aa long hypothetical fmu protein / 0.722
1boo SAHModification methylase PvuII 2.1.1.113 0.718
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.711
3ldf SAHUncharacterized protein / 0.698
4rtk SAHDNA adenine methylase 2.1.1.72 0.697
9mht SAHModification methylase HhaI 2.1.1.37 0.697
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.695
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.691
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.690
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.690
5je4 SAHMethyl transferase / 0.688
2g1p SAHDNA adenine methylase 2.1.1.72 0.687
5jdz SAHMethyl transferase / 0.686
5je3 SAHMethyl transferase / 0.686
1f8w FADNADH peroxidase 1.11.1.1 0.685
2ore SAHDNA adenine methylase 2.1.1.72 0.683
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.682
2qe6 SAMUncharacterized protein / 0.681
3ko8 NADNAD-dependent epimerase/dehydratase / 0.681
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.681
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.678
4icy FADPgaE / 0.678
2np6 NEAModification methylase TaqI 2.1.1.72 0.677
2z6u SAHModification methylase HhaI 2.1.1.37 0.677
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.677
1eg2 MTAModification methylase RsrI 2.1.1.72 0.676
4twr NADNAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase / 0.676
2i9k SAHModification methylase HhaI 2.1.1.37 0.673
3mht SAHModification methylase HhaI 2.1.1.37 0.673
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.672
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.672
4rts SAMDNA adenine methylase 2.1.1.72 0.671
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.671
1skm SAHModification methylase HhaI 2.1.1.37 0.670
3tm4 SAMUncharacterized protein / 0.670
1fjx SAHModification methylase HhaI 2.1.1.37 0.669
2uyh SAHModification methylase HhaI 2.1.1.37 0.669
3go4 SAHUncharacterized protein / 0.666
2zif SAMMethyltransferase / 0.665
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.663
4blw SAHRibosomal RNA large subunit methyltransferase J / 0.662
2rgh FADAlpha-Glycerophosphate Oxidase / 0.661
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.660
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.660
4eqg A5AHistidine triad nucleotide-binding protein 1 3 0.660
3lcc SAHThiocyanate methyltransferase 1 / 0.659
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.659
4eqe KAAHistidine triad nucleotide-binding protein 1 3 0.659
1uay ADNOxidoreductase / 0.658
2ih2 NEAModification methylase TaqI 2.1.1.72 0.658
3tos SAHCalS11 / 0.658
3wdm ADN4-phosphopantoate--beta-alanine ligase 6.3.2.36 0.658
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.658
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.657
2p5y NADUDP-glucose 4-epimerase / 0.657
4lv5 ADPRhoptry protein 5B / 0.657
4yai NAIC alpha-dehydrogenase / 0.657
1i8t FADUDP-galactopyranose mutase 5.4.99.9 0.656
3aw9 NADNAD-dependent epimerase/dehydratase / 0.656
4yag NAIC alpha-dehydrogenase / 0.656
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.655
3oe4 610Catechol O-methyltransferase 2.1.1.6 0.655
2c7q SAHModification methylase HhaI 2.1.1.37 0.654
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.654
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.654
5je2 SAHMethyl transferase / 0.654
1cbo FADCholesterol oxidase 1.1.3.6 0.653
1nah NADUDP-glucose 4-epimerase 5.1.3.2 0.653
4rtj SFGDNA adenine methylase 2.1.1.72 0.653
5f8f SFGPossible transcriptional regulatory protein / 0.653
3swr SFGDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.652
4nec SAHPutative SAM-dependent methyltransferase / 0.652
1g60 SAMModification methylase MboII 2.1.1.72 0.651
2f8l SAMLmo1582 protein / 0.651
2hms NAIKtr system potassium uptake protein A / 0.651
2c31 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.650
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.650
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.650