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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
1d2h SAH Glycine N-methyltransferase 2.1.1.20

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1d2h SAHGlycine N-methyltransferase 2.1.1.20 0.883
1nbh SAMGlycine N-methyltransferase 2.1.1.20 0.734
4yac NAIC alpha-dehydrogenase / 0.716
4hh4 SAHCcbJ / 0.708
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.707
1nbi SAMGlycine N-methyltransferase 2.1.1.20 0.706
2o07 MTASpermidine synthase 2.5.1.16 0.706
3nug NADPyridoxal 4-dehydrogenase 1.1.1.107 0.702
3go4 SAHUncharacterized protein / 0.701
5je2 SAHMethyl transferase / 0.699
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.696
4nbu NAI3-oxoacyl-(Acyl-carrier-protein) reductase / 0.695
3ou6 SAMSAM-dependent methyltransferase / 0.694
1orr NADCDP-paratose 2-epimerase / 0.693
4kvz SAHPtnL protein / 0.693
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.693
2b69 NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.692
2pan FADGlyoxylate carboligase 4.1.1.47 0.690
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.690
4wec NADShort chain dehydrogenase / 0.690
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.689
2i9k SAHModification methylase HhaI 2.1.1.37 0.688
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.687
3lhd SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.687
3e23 SAMUncharacterized protein / 0.686
4nec SAHPutative SAM-dependent methyltransferase / 0.685
1khh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.684
3hvi 619Catechol O-methyltransferase 2.1.1.6 0.684
3c3y SAHO-methyltransferase / 0.683
4fn4 NADShort chain dehydrogenase / 0.683
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.683
1boo SAHModification methylase PvuII 2.1.1.113 0.682
2c31 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.681
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.681
7mht SAHModification methylase HhaI 2.1.1.37 0.681
1i3l NADUDP-glucose 4-epimerase / 0.680
2ji6 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.680
2qe6 SAMUncharacterized protein / 0.680
4gh5 NADShort-chain dehydrogenase/reductase SDR / 0.680
2np6 NEAModification methylase TaqI 2.1.1.72 0.679
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.679
1y9d FADPyruvate oxidase 1.2.3.3 0.678
2ji7 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.678
2o06 MTASpermidine synthase 2.5.1.16 0.678
2q28 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.678
3geg NADShort-chain dehydrogenase/reductase SDR / 0.678
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.677
3ou7 SAMSAM-dependent methyltransferase / 0.677
2c20 NADUDP-glucose 4-epimerase / 0.675
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.675
1kvr NADUDP-glucose 4-epimerase 5.1.3.2 0.674
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.674
1zmc NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.674
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.674
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.674
3bwc SAMSpermidine synthase, putative / 0.673
1kia SAMGlycine N-methyltransferase 2.1.1.20 0.672
1nai NADUDP-glucose 4-epimerase 5.1.3.2 0.672
2yqz SAMUncharacterized protein / 0.672
3wds NADNADH-dependent quinuclidinone reductase / 0.672
3iv6 SAMUncharacterized protein / 0.670
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.670
1l3i SAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) / 0.668
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.668
5je3 SAHMethyl transferase / 0.668
5jsf NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.668
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.667
3i53 SAH2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase / 0.667
3kkz SAMUncharacterized protein / 0.667
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.666
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.665
3eey SAMrRNA methylase / 0.665
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.665
5a3b APRSIR2 family protein / 0.665
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.665
1n4w FADCholesterol oxidase 1.1.3.6 0.664
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.664
4ekg 0QJHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.664
1v59 NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.663
3ict FADCoenzyme A disulfide reductase / 0.663
3sxp NADADP-L-glycero-D-mannoheptose-6-epimerase / 0.663
1wy7 SAHUncharacterized protein / 0.662
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.662
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.662
4ek9 EP4Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.662
4kwc SAHMethyltransferase domain family / 0.662
4rpg FADUDP-galactopyranose mutase 5.4.99.9 0.662
4yv2 S4MSpermidine synthase, putative / 0.662
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.662
2hms NAIKtr system potassium uptake protein A / 0.661
2jib ADPOxalyl-CoA decarboxylase 4.1.1.8 0.661
3ics ADPCoenzyme A disulfide reductase / 0.661
3rfx NADUronate dehydrogenase / 0.661
5f8f SFGPossible transcriptional regulatory protein / 0.661
1mxt FAECholesterol oxidase 1.1.3.6 0.660
1n1p FADCholesterol oxidase 1.1.3.6 0.660
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.660
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.659
5js6 NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.659
4u2s FDACholesterol oxidase 1.1.3.6 0.658
1b8s FADCholesterol oxidase 1.1.3.6 0.657
1ek5 NADUDP-glucose 4-epimerase / 0.657
1g1a NADdTDP-glucose 4,6-dehydratase / 0.657
1txz APRProbable ADP-ribose 1''-phosphate phosphatase YML087W 3.1.3.84 0.657
3tos SAHCalS11 / 0.657
4yv1 S4MSpermidine synthase, putative / 0.656
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.656
1bxk NADdTDP-glucose 4,6-dehydratase 2 / 0.655
1g60 SAMModification methylase MboII 2.1.1.72 0.655
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.655
5je4 SAHMethyl transferase / 0.655
1n4u FAECholesterol oxidase 1.1.3.6 0.654
1yqz FADCoenzyme A disulfide reductase / 0.654
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.654
5jla NADPutative short-chain dehydrogenase/reductase / 0.654
5l3d FADLysine-specific histone demethylase 1A 1 0.654
3cnj FADCholesterol oxidase 1.1.3.6 0.653
3gyi FADCholesterol oxidase 1.1.3.6 0.653
3lzw FADFerredoxin--NADP reductase 2 1.18.1.2 0.653
3sm8 FNKFAD-dependent catabolic D-arginine dehydrogenase DauA / 0.653
3mht SAHModification methylase HhaI 2.1.1.37 0.652
3t7s SAMUncharacterized protein / 0.651
4gf5 SAHCalS11 / 0.651
4x9n FADUncharacterized protein MG039 homolog / 0.651
4yuz S4MSpermidine synthase, putative / 0.651
3ndr NADPyridoxal 4-dehydrogenase 1.1.1.107 0.650
3sgl SAMtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.650