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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
4wxx SAH DNA (cytosine-5)-methyltransferase 1 2.1.1.37

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.880
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.781
3pt6 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.761
1boo SAHModification methylase PvuII 2.1.1.113 0.736
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.731
2yxl SFG450aa long hypothetical fmu protein / 0.729
2c7q SAHModification methylase HhaI 2.1.1.37 0.723
2uyh SAHModification methylase HhaI 2.1.1.37 0.720
3swr SFGDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.719
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.710
1skm SAHModification methylase HhaI 2.1.1.37 0.709
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.707
10mh SAHModification methylase HhaI 2.1.1.37 0.704
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.700
1aqi SAHModification methylase TaqI 2.1.1.72 0.698
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.698
4nec SAHPutative SAM-dependent methyltransferase / 0.698
2hnk SAHSAM-dependent O-methyltransferase / 0.695
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.694
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.693
5jdz SAHMethyl transferase / 0.693
3mht SAHModification methylase HhaI 2.1.1.37 0.692
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.691
2ibt NEAModification methylase TaqI 2.1.1.72 0.691
4da4 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.691
5je3 SAHMethyl transferase / 0.691
1fjx SAHModification methylase HhaI 2.1.1.37 0.690
4blw SAHRibosomal RNA large subunit methyltransferase J / 0.690
2z6u SAHModification methylase HhaI 2.1.1.37 0.689
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.689
1eg2 MTAModification methylase RsrI 2.1.1.72 0.687
5je4 SAHMethyl transferase / 0.687
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.686
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.685
3go4 SAHUncharacterized protein / 0.684
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.684
2g1p SAHDNA adenine methylase 2.1.1.72 0.682
4lwp SAHArginine N-methyltransferase, putative / 0.682
4rtk SAHDNA adenine methylase 2.1.1.72 0.682
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.681
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.679
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.678
2ih2 NEAModification methylase TaqI 2.1.1.72 0.677
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.677
3ldg SAHUncharacterized protein / 0.677
4obw SAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial / 0.676
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.674
3rw9 DSHSpermidine synthase 2.5.1.16 0.674
9mht SAHModification methylase HhaI 2.1.1.37 0.674
2i9k SAHModification methylase HhaI 2.1.1.37 0.673
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.673
1mht SAHModification methylase HhaI 2.1.1.37 0.672
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.672
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.672
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.672
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.672
1nw5 SAMModification methylase RsrI 2.1.1.72 0.671
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.671
4mb2 ATPUncharacterized protein / 0.671
5mht SAHModification methylase HhaI 2.1.1.37 0.671
7mht SAHModification methylase HhaI 2.1.1.37 0.671
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.670
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.670
4gbe SAHDNA adenine methylase 2.1.1.72 0.670
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.669
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.668
2o06 MTASpermidine synthase 2.5.1.16 0.668
3iv6 SAMUncharacterized protein / 0.667
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.667
4oa5 SAHO-methyltransferase family protein / 0.667
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.666
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.666
1ve3 SAMUncharacterized protein / 0.664
2ore SAHDNA adenine methylase 2.1.1.72 0.664
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.664
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.664
2ih5 NEAModification methylase TaqI 2.1.1.72 0.662
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.662
3c3y SAHO-methyltransferase / 0.661
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.661
3nmu SAMFibrillarin-like rRNA/tRNA 2'-O-methyltransferase / 0.660
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.658
2zcj SAHModification methylase HhaI 2.1.1.37 0.658
3qv2 SAH5-cytosine DNA methyltransferase / 0.658
4rtj SFGDNA adenine methylase 2.1.1.72 0.656
4rtr SAMDNA adenine methylase 2.1.1.72 0.656
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.656
1g1a NADdTDP-glucose 4,6-dehydratase / 0.655
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.655
3cbg SAHO-methyltransferase / 0.655
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.654
3ldf SAHUncharacterized protein / 0.654
3oe4 610Catechol O-methyltransferase 2.1.1.6 0.654
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.654
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.653
2vou FAD2,6-dihydroxypyridine 3-monooxygenase 1.14.13.10 0.652
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.652
3sgl SAMtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.652
2oy0 SAHGenome polyprotein / 0.651
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.650
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.650