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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
2zzm SAM tRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 1.034
3ldf SAHUncharacterized protein / 0.755
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.734
3ou2 SAHSAM-dependent methyltransferase / 0.733
3ou6 SAMSAM-dependent methyltransferase / 0.733
2qe6 SAMUncharacterized protein / 0.732
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.731
3lcc SAHThiocyanate methyltransferase 1 / 0.728
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.727
4yuz S4MSpermidine synthase, putative / 0.724
4nec SAHPutative SAM-dependent methyltransferase / 0.723
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.722
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.722
3go4 SAHUncharacterized protein / 0.720
1boo SAHModification methylase PvuII 2.1.1.113 0.719
1yf3 SAHDNA adenine methylase / 0.719
3ssm SAHMycinamicin VI 2''-O-methyltransferase / 0.718
1fjx SAHModification methylase HhaI 2.1.1.37 0.717
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.714
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.714
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.712
4yv2 S4MSpermidine synthase, putative / 0.712
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.711
1y9d FADPyruvate oxidase 1.2.3.3 0.710
2ibt NEAModification methylase TaqI 2.1.1.72 0.709
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.708
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.708
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.707
5jdz SAHMethyl transferase / 0.706
5je4 SAHMethyl transferase / 0.706
1skm SAHModification methylase HhaI 2.1.1.37 0.705
2z6u SAHModification methylase HhaI 2.1.1.37 0.703
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.703
2ih5 NEAModification methylase TaqI 2.1.1.72 0.702
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.700
5je2 SAHMethyl transferase / 0.700
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.698
2zif SAMMethyltransferase / 0.697
3c3y SAHO-methyltransferase / 0.696
3wv8 ATPHmd co-occurring protein HcgE / 0.696
2yxl SFG450aa long hypothetical fmu protein / 0.695
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.695
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.695
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.695
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.692
2plw SAMRibosomal RNA methyltransferase, putative / 0.692
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.691
4lwp SAHArginine N-methyltransferase, putative / 0.691
5je3 SAHMethyl transferase / 0.691
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.690
4kvz SAHPtnL protein / 0.689
2o06 MTASpermidine synthase 2.5.1.16 0.688
2zzn SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.688
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.688
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.687
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.686
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.685
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.685
1g60 SAMModification methylase MboII 2.1.1.72 0.684
1kr5 SAHProtein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77 0.683
2i9k SAHModification methylase HhaI 2.1.1.37 0.683
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.682
2ytz SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.681
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.680
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.680
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.679
2q28 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.678
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.678
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.678
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.676
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.674
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.674
2p35 SAHTrans-aconitate 2-methyltransferase / 0.674
3ldg SAHUncharacterized protein / 0.674
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.673
4g56 SAHProtein arginine N-methyltransferase 5 / 0.673
4qpp SAHProtein arginine N-methyltransferase 6 / 0.673
2zfu SAHRibosomal RNA-processing protein 8 / 0.672
2gs9 SAHUncharacterized protein / 0.671
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.671
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.669
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.669
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.668
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.668
3i53 SAH2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase / 0.668
4gc9 SAMDimethyladenosine transferase 1, mitochondrial 2.1.1 0.668
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.666
3tm4 SAMUncharacterized protein / 0.666
3tos SAHCalS11 / 0.666
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.666
3e23 SAMUncharacterized protein / 0.665
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.665
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.665
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.665
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.664
4yv1 S4MSpermidine synthase, putative / 0.663
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.663
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.661
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.659
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.658
2ag5 NAD3-hydroxybutyrate dehydrogenase type 2 / 0.658
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.656
4fr0 SAMArsenic methyltransferase / 0.656
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.656
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.655
4rtk SAHDNA adenine methylase 2.1.1.72 0.655
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.653
2ih2 NEAModification methylase TaqI 2.1.1.72 0.652
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.652
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.651
3e8s SAHUncharacterized protein / 0.651
2g1p SAHDNA adenine methylase 2.1.1.72 0.650
2px2 SAHGenome polyprotein 2.7.7.48 0.650
3fri SAH16S rRNA methylase / 0.650
4ek9 EP4Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.650