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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
3gry SAM Probable ribosomal RNA small subunit methyltransferase A

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3gry SAMProbable ribosomal RNA small subunit methyltransferase A / 1.109
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.895
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.794
4c03 SFGProtein arginine N-methyltransferase 6 / 0.773
3grv ADNProbable ribosomal RNA small subunit methyltransferase A / 0.772
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.768
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.756
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.754
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.743
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.743
3lcc SAHThiocyanate methyltransferase 1 / 0.743
3sgl SAMtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.741
3ssm SAHMycinamicin VI 2''-O-methyltransferase / 0.739
2hnk SAHSAM-dependent O-methyltransferase / 0.735
4uy6 SAHHistidine N-alpha-methyltransferase / 0.733
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.733
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.731
3ou2 SAHSAM-dependent methyltransferase / 0.728
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.726
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.722
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.715
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.714
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.713
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.713
5je3 SAHMethyl transferase / 0.710
1skm SAHModification methylase HhaI 2.1.1.37 0.709
3vyw SAMUncharacterized protein / 0.709
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.709
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.708
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.708
3cbg SAHO-methyltransferase / 0.707
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.704
4rvd SAMD-mycarose 3-C-methyltransferase / 0.703
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.702
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.701
4c04 SFGProtein arginine N-methyltransferase 6 / 0.701
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.699
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.698
3cjt SAHRibosomal protein L11 methyltransferase 2.1.1 0.697
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.695
1f3l SAHProtein arginine N-methyltransferase 3 / 0.694
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.693
3duw SAHO-methyltransferase, putative / 0.692
1wy7 SAHUncharacterized protein / 0.691
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.691
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.690
4nec SAHPutative SAM-dependent methyltransferase / 0.690
4hh4 SAHCcbJ / 0.688
5jdz SAHMethyl transferase / 0.688
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.686
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.686
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.685
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.685
4blw SAHRibosomal RNA large subunit methyltransferase J / 0.683
2p35 SAHTrans-aconitate 2-methyltransferase / 0.682
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.682
2yxl SFG450aa long hypothetical fmu protein / 0.681
5d4v SAHUncharacterized protein MJ0489 / 0.681
1ori SAHProtein arginine N-methyltransferase 1 / 0.680
2o07 MTASpermidine synthase 2.5.1.16 0.679
4lwp SAHArginine N-methyltransferase, putative / 0.677
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.675
7mht SAHModification methylase HhaI 2.1.1.37 0.674
2gs9 SAHUncharacterized protein / 0.673
1rp0 AHZThiamine thiazole synthase, chloroplastic / 0.672
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.672
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.669
1g1a NADdTDP-glucose 4,6-dehydratase / 0.668
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.666
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.666
2ji7 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.665
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.665
3tos SAHCalS11 / 0.664
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.663
2np6 NEAModification methylase TaqI 2.1.1.72 0.662
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.661
1boo SAHModification methylase PvuII 2.1.1.113 0.660
2y8q ADP5'-AMP-activated protein kinase subunit gamma-1 / 0.660
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.660
4xcx SAHSmall RNA 2'-O-methyltransferase / 0.660
5bp9 SAHPutative methyltransferase protein / 0.660
3lby SAHUncharacterized protein / 0.659
4qnu GEKtRNA U34 carboxymethyltransferase / 0.659
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.659
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.657
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.657
2br5 SAHCephalosporin hydroxylase CmcI / 0.656
4c3y FAD3-ketosteroid dehydrogenase / 0.656
2zw9 SAMtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.655
4oa5 SAHO-methyltransferase family protein / 0.655
3fpf MTAUncharacterized protein / 0.654
3evb SAHGenome polyprotein 2.1.1.56 0.652
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.652
1nbh SAMGlycine N-methyltransferase 2.1.1.20 0.651
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.651
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.651
2jib ADPOxalyl-CoA decarboxylase 4.1.1.8 0.651
5epe SAHUncharacterized protein / 0.651
1orh SAHProtein arginine N-methyltransferase 1 / 0.650
2zfu SAHRibosomal RNA-processing protein 8 / 0.650
4qpp SAHProtein arginine N-methyltransferase 6 / 0.650