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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
1nw3 SAM Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 1.050
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.974
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.956
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.753
5bxy SAHPutative RNA methylase family UPF0020 / 0.750
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.741
4er6 AW2Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.740
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.740
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.737
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.733
3lcc SAHThiocyanate methyltransferase 1 / 0.731
5je2 SAHMethyl transferase / 0.731
3lst SAHCalO1 / 0.715
2zif SAMMethyltransferase / 0.713
4hh4 SAHCcbJ / 0.713
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.711
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.710
5je4 SAHMethyl transferase / 0.709
5je3 SAHMethyl transferase / 0.708
4c03 SFGProtein arginine N-methyltransferase 6 / 0.707
2zbp SAMRibosomal protein L11 methyltransferase 2.1.1 0.706
3go4 SAHUncharacterized protein / 0.706
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.706
3tm4 SAMUncharacterized protein / 0.706
5jdz SAHMethyl transferase / 0.706
1xdu SFGAclacinomycin 10-hydroxylase RdmB 4.1.1 0.703
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.703
4qpp SAHProtein arginine N-methyltransferase 6 / 0.703
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.703
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.702
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.701
4lwp SAHArginine N-methyltransferase, putative / 0.700
4c04 SFGProtein arginine N-methyltransferase 6 / 0.699
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.696
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.696
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.693
2eg5 SAH7-methylxanthosine synthase 1 / 0.692
3e23 SAMUncharacterized protein / 0.692
3p9k SAHCaffeic acid O-methyltransferase / 0.691
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.690
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.689
4uy6 SAHHistidine N-alpha-methyltransferase / 0.688
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.687
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.687
3fri SAH16S rRNA methylase / 0.687
2i9k SAHModification methylase HhaI 2.1.1.37 0.686
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.686
5bp9 SAHPutative methyltransferase protein / 0.685
5f8f SFGPossible transcriptional regulatory protein / 0.685
2zwa SAHtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.684
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.683
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.683
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.680
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.679
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.679
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.679
4ek9 EP4Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.679
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.678
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.677
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.677
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.675
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.675
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.675
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.675
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.674
3kkz SAMUncharacterized protein / 0.673
3ldg SAHUncharacterized protein / 0.672
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.672
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.672
1g38 NEAModification methylase TaqI 2.1.1.72 0.671
2np6 NEAModification methylase TaqI 2.1.1.72 0.671
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.670
2z6u SAHModification methylase HhaI 2.1.1.37 0.670
2ih5 NEAModification methylase TaqI 2.1.1.72 0.669
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.669
4kvz SAHPtnL protein / 0.668
1f3l SAHProtein arginine N-methyltransferase 3 / 0.667
1nbi SAMGlycine N-methyltransferase 2.1.1.20 0.667
2ih2 NEAModification methylase TaqI 2.1.1.72 0.667
2yxl SFG450aa long hypothetical fmu protein / 0.666
1ve3 SAMUncharacterized protein / 0.665
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.665
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.665
3cjt SAHRibosomal protein L11 methyltransferase 2.1.1 0.664
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.663
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.663
1ori SAHProtein arginine N-methyltransferase 1 / 0.662
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.662
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.662
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.661
4er7 AW3Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.661
5bp7 SAHSAM-dependent methyltransferase / 0.661
1kia SAMGlycine N-methyltransferase 2.1.1.20 0.660
2ore SAHDNA adenine methylase 2.1.1.72 0.659
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.659
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.658
1ri4 SAMmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.657
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.656
4g56 SAHProtein arginine N-methyltransferase 5 / 0.656
4rtk SAHDNA adenine methylase 2.1.1.72 0.656
4qnv GEKtRNA U34 carboxymethyltransferase / 0.655
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.655
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.654
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.654
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.653
4dc3 2FAPutative adenosine kinase / 0.653
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.652
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.652
4yac NAIC alpha-dehydrogenase / 0.652
2p35 SAHTrans-aconitate 2-methyltransferase / 0.651
3t0i SAHPutative methyltransferase / 0.651
5epe SAHUncharacterized protein / 0.651
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.650
3ely SAHMethyltransferase / 0.650
4ctk SAMGenome polyprotein / 0.650
7mht SAHModification methylase HhaI 2.1.1.37 0.650