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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
2yx1 SFG 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
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 1.069
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.830
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.797
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.791
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.790
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.782
4rtk SAHDNA adenine methylase 2.1.1.72 0.780
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.768
2yxl SFG450aa long hypothetical fmu protein / 0.766
4rtj SFGDNA adenine methylase 2.1.1.72 0.764
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.762
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.760
4dmg SAMUncharacterized protein / 0.757
1boo SAHModification methylase PvuII 2.1.1.113 0.756
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.749
4gbe SAHDNA adenine methylase 2.1.1.72 0.747
2g1p SAHDNA adenine methylase 2.1.1.72 0.744
4nec SAHPutative SAM-dependent methyltransferase / 0.744
3ldg SAHUncharacterized protein / 0.743
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.742
3ldf SAHUncharacterized protein / 0.733
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.730
4lwp SAHArginine N-methyltransferase, putative / 0.730
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.728
2z6u SAHModification methylase HhaI 2.1.1.37 0.725
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.725
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.724
3pt6 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.723
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.722
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.722
1g60 SAMModification methylase MboII 2.1.1.72 0.721
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.721
2i9k SAHModification methylase HhaI 2.1.1.37 0.721
3m6w SAMRibosomal RNA small subunit methyltransferase F / 0.721
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.721
1yf3 SAHDNA adenine methylase / 0.719
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.718
2c7q SAHModification methylase HhaI 2.1.1.37 0.717
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.717
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.716
1nw5 SAMModification methylase RsrI 2.1.1.72 0.714
4poo SAMPutative RNA methylase / 0.714
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.713
3mht SAHModification methylase HhaI 2.1.1.37 0.712
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.711
1eg2 MTAModification methylase RsrI 2.1.1.72 0.710
2zcj SAHModification methylase HhaI 2.1.1.37 0.710
3m6v SAMRibosomal RNA small subunit methyltransferase F / 0.710
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.710
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.708
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.707
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.707
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.706
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.705
1nw6 SFGModification methylase RsrI 2.1.1.72 0.703
3tm4 SAMUncharacterized protein / 0.703
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.702
3tm5 SFGUncharacterized protein / 0.702
3swr SFGDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.699
4blv SAMRibosomal RNA large subunit methyltransferase J / 0.699
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.698
1f3l SAHProtein arginine N-methyltransferase 3 / 0.697
7mht SAHModification methylase HhaI 2.1.1.37 0.697
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.696
4blw SAHRibosomal RNA large subunit methyltransferase J / 0.696
4yv2 S4MSpermidine synthase, putative / 0.696
4rtl SFGDNA adenine methylase 2.1.1.72 0.695
2hnk SAHSAM-dependent O-methyltransferase / 0.693
4rto SFGDNA adenine methylase 2.1.1.72 0.693
1ve3 SAMUncharacterized protein / 0.692
1skm SAHModification methylase HhaI 2.1.1.37 0.691
2xyr SFGReplicase polyprotein 1ab 2.1.1 0.689
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.688
4c04 SFGProtein arginine N-methyltransferase 6 / 0.688
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.688
3sgl SAMtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.687
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.687
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.687
2zif SAMMethyltransferase / 0.686
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.686
4rtq SAHDNA adenine methylase 2.1.1.72 0.686
3fri SAH16S rRNA methylase / 0.685
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.684
3p9c SAHCaffeic acid O-methyltransferase / 0.684
4rtr SAMDNA adenine methylase 2.1.1.72 0.684
1kr5 SAHProtein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77 0.683
4rts SAMDNA adenine methylase 2.1.1.72 0.683
10mh SAHModification methylase HhaI 2.1.1.37 0.682
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.682
2uyh SAHModification methylase HhaI 2.1.1.37 0.682
4mb2 ATPUncharacterized protein / 0.682
5je3 SAHMethyl transferase / 0.682
2f8l SAMLmo1582 protein / 0.680
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.679
5jdz SAHMethyl transferase / 0.679
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.678
4pyo SAHCatechol O-methyltransferase 2.1.1.6 0.678
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.675
3go4 SAHUncharacterized protein / 0.675
3tlj SAHUncharacterized protein / 0.675
4c03 SFGProtein arginine N-methyltransferase 6 / 0.675
9mht SAHModification methylase HhaI 2.1.1.37 0.675
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.674
4m37 SAHProtein arginine N-methyltransferase 7 2.1.1 0.674
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.673
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.673
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.673
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.673
2o06 MTASpermidine synthase 2.5.1.16 0.672
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.672
5eku SAHArginine N-methyltransferase, putative / 0.672
2np7 NEAModification methylase TaqI 2.1.1.72 0.671
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.671
4rtm SAMDNA adenine methylase 2.1.1.72 0.671
4xba 5GPAprataxin-like protein 3 0.671
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.670
2np6 NEAModification methylase TaqI 2.1.1.72 0.670
2yqz SAMUncharacterized protein / 0.670
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.670
8mht SAHModification methylase HhaI 2.1.1.37 0.670
2p35 SAHTrans-aconitate 2-methyltransferase / 0.669
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.669
4c05 SAHProtein arginine N-methyltransferase 6 / 0.669
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.668
1mht SAHModification methylase HhaI 2.1.1.37 0.667
4ft4 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.667
1y9d FADPyruvate oxidase 1.2.3.3 0.666
4onj SFGDNA methyltransferase / 0.666
5je4 SAHMethyl transferase / 0.666
1ori SAHProtein arginine N-methyltransferase 1 / 0.665
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.665
2zfu SAHRibosomal RNA-processing protein 8 / 0.665
4mht SAHModification methylase HhaI 2.1.1.37 0.664
3tos SAHCalS11 / 0.663
4b69 FADL-ornithine N(5)-monooxygenase / 0.663
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.663
1fjx SAHModification methylase HhaI 2.1.1.37 0.662
3eld SFGMethyltransferase / 0.662
3grv ADNProbable ribosomal RNA small subunit methyltransferase A / 0.662
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.662
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.662
1orh SAHProtein arginine N-methyltransferase 1 / 0.661
4b63 FADL-ornithine N(5)-monooxygenase / 0.661
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.661
2px2 SAHGenome polyprotein 2.7.7.48 0.660
3dh0 SAMUncharacterized protein / 0.660
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.660
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.660
3uka FADUDP-galactopyranose mutase / 0.660
4obw SAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial / 0.660
5cku FADL-ornithine N(5)-monooxygenase / 0.659
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.659
3duw SAHO-methyltransferase, putative / 0.658
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.658
2ibt NEAModification methylase TaqI 2.1.1.72 0.657
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.657
1rp0 AHZThiamine thiazole synthase, chloroplastic / 0.656
2px5 SAHGenome polyprotein 2.7.7.48 0.656
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.656
4kwc SAHMethyltransferase domain family / 0.655
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.653
1yc2 APRNAD-dependent protein deacylase 2 / 0.653
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.653
4h0n SAHDnmt2 / 0.653
4rtn SAHDNA adenine methylase 2.1.1.72 0.653
5epe SAHUncharacterized protein / 0.653
2ih2 NEAModification methylase TaqI 2.1.1.72 0.652
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.652
5f8f SFGPossible transcriptional regulatory protein / 0.652
1x1c SAHC-20 methyltransferase / 0.651
2cww SAHUncharacterized protein / 0.651
3fpf MTAUncharacterized protein / 0.651
3pl8 FADPyranose 2-oxidase / 0.651
4hh4 SAHCcbJ / 0.651
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.650
3vc1 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.650