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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
2plw SAM Ribosomal RNA methyltransferase, putative

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2plw SAMRibosomal RNA methyltransferase, putative / 0.974
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.815
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.791
2px2 SAHGenome polyprotein 2.7.7.48 0.777
3lga SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.771
3c3y SAHO-methyltransferase / 0.765
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.761
3emd SFGMethyltransferase / 0.747
2hnk SAHSAM-dependent O-methyltransferase / 0.732
4gf5 SAHCalS11 / 0.729
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.723
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.723
4k6m SAHGenome polyprotein / 0.717
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.716
2g1p SAHDNA adenine methylase 2.1.1.72 0.715
3cbg SAHO-methyltransferase / 0.714
4ctj SAMGenome polyprotein / 0.713
3vyw SAMUncharacterized protein / 0.708
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.705
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.705
3evb SAHGenome polyprotein 2.1.1.56 0.700
4ctk SAMGenome polyprotein / 0.699
3tr6 SAHO-methyltransferase / 0.697
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.696
4uck SAMLarge structural protein / 0.696
2yxl SFG450aa long hypothetical fmu protein / 0.695
4rtj SFGDNA adenine methylase 2.1.1.72 0.694
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.692
4n48 SAMCap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1 2.1.1.57 0.691
2px5 SAHGenome polyprotein 2.7.7.48 0.689
2xyr SFGReplicase polyprotein 1ab 2.1.1 0.689
3eld SFGMethyltransferase / 0.688
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.687
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.687
2bm9 SAMCephalosporin hydroxylase CmcI / 0.683
3p8z 36AGenome polyprotein 2.1.1.56 0.681
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.681
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.681
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.680
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.678
5g3s FDAFlavin-dependent L-tryptophan oxidase VioA / 0.678
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.677
3wv8 ATPHmd co-occurring protein HcgE / 0.676
4ce0 SAHProbable O-methyltransferase / 0.676
4pyo SAHCatechol O-methyltransferase 2.1.1.6 0.676
5jdz SAHMethyl transferase / 0.676
3evc SAHGenome polyprotein 2.1.1.56 0.673
3lcc SAHThiocyanate methyltransferase 1 / 0.673
3lkz SFGGenome polyprotein / 0.673
3tos SAHCalS11 / 0.672
3m6w SAMRibosomal RNA small subunit methyltransferase F / 0.671
2oy0 SAHGenome polyprotein / 0.669
3ssm SAHMycinamicin VI 2''-O-methyltransferase / 0.669
4d79 ATPtRNA threonylcarbamoyladenosine dehydratase 6.1 0.669
2cww SAHUncharacterized protein / 0.668
2pxa SAHGenome polyprotein 2.7.7.48 0.668
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.668
3ldf SAHUncharacterized protein / 0.667
3ely SAHMethyltransferase / 0.666
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.666
1rp0 AHZThiamine thiazole synthase, chloroplastic / 0.665
3eva SAHGenome polyprotein 2.1.1.56 0.665
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.663
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.662
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.662
1yf3 SAHDNA adenine methylase / 0.661
2xbm SAHGenome polyprotein / 0.661
3fri SAH16S rRNA methylase / 0.661
3p8z SAHGenome polyprotein 2.1.1.56 0.661
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.660
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.660
5je2 SAHMethyl transferase / 0.660
5je4 SAHMethyl transferase / 0.659
1la2 NADInositol-3-phosphate synthase 5.5.1.4 0.658
5je3 SAHMethyl transferase / 0.657
1r6a SAHGenome polyprotein 2.7.7.48 0.656
2e1m FADL-glutamate oxidase / 0.656
2i9k SAHModification methylase HhaI 2.1.1.37 0.656
4tlx FDAKtzI / 0.656
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.656
5dto SAHGenome polyprotein / 0.656
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.655
3h5n ATPMccB protein / 0.655
3p97 SAMGenome polyprotein 2.1.1.56 0.654
4tm4 FDAKtzI / 0.654
2zcj SAHModification methylase HhaI 2.1.1.37 0.653
4a99 FADTetX family tetracycline inactivation enzyme / 0.653
4j36 FADKynurenine 3-monooxygenase / 0.653
2np6 NEAModification methylase TaqI 2.1.1.72 0.652
2yr4 FADPhenylalanine 2-monooxygenase precursor 1.13.12.9 0.651
10mh SAHModification methylase HhaI 2.1.1.37 0.650
1boo SAHModification methylase PvuII 2.1.1.113 0.650
2q0l FADThioredoxin reductase 1.8.1.9 0.650
2q28 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.650
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.650
3cjt SAHRibosomal protein L11 methyltransferase 2.1.1 0.650
3g5q FADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO / 0.650
4dkj SAHCytosine-specific methyltransferase / 0.650
5eow FAD6-hydroxynicotinate 3-monooxygenase 1.14.13.114 0.650
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.650
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.650