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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
1wg8 SAM Ribosomal RNA small subunit methyltransferase H

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 1.065
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.797
2px2 SAHGenome polyprotein 2.7.7.48 0.786
2g1p SAHDNA adenine methylase 2.1.1.72 0.785
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.779
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.774
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.766
2c7q SAHModification methylase HhaI 2.1.1.37 0.761
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.761
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.758
5k7w SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.747
4k6m SAHGenome polyprotein / 0.746
2z6u SAHModification methylase HhaI 2.1.1.37 0.744
2i9k SAHModification methylase HhaI 2.1.1.37 0.737
3mht SAHModification methylase HhaI 2.1.1.37 0.737
3ely SAHMethyltransferase / 0.735
1g60 SAMModification methylase MboII 2.1.1.72 0.734
3tos SAHCalS11 / 0.731
1l3i SAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) / 0.729
2uyh SAHModification methylase HhaI 2.1.1.37 0.729
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.729
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.727
1boo SAHModification methylase PvuII 2.1.1.113 0.726
3c3y SAHO-methyltransferase / 0.724
3eva SAHGenome polyprotein 2.1.1.56 0.723
3evc SAHGenome polyprotein 2.1.1.56 0.723
2wa2 SAMGenome polyprotein / 0.721
1skm SAHModification methylase HhaI 2.1.1.37 0.720
3evb SAHGenome polyprotein 2.1.1.56 0.719
1yf3 SAHDNA adenine methylase / 0.717
3eey SAMrRNA methylase / 0.717
3oe4 610Catechol O-methyltransferase 2.1.1.6 0.717
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.715
2zcj SAHModification methylase HhaI 2.1.1.37 0.714
4gbe SAHDNA adenine methylase 2.1.1.72 0.714
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.712
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.711
2yxl SFG450aa long hypothetical fmu protein / 0.710
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.710
4poo SAMPutative RNA methylase / 0.708
2pxa SAHGenome polyprotein 2.7.7.48 0.707
3p97 SAMGenome polyprotein 2.1.1.56 0.707
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.707
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.707
3lby SAHUncharacterized protein / 0.705
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.705
4hh4 SAHCcbJ / 0.704
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.703
4ctk SAMGenome polyprotein / 0.703
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.701
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.699
3duw SAHO-methyltransferase, putative / 0.699
3ou6 SAMSAM-dependent methyltransferase / 0.698
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.697
1d2h SAHGlycine N-methyltransferase 2.1.1.20 0.696
7mht SAHModification methylase HhaI 2.1.1.37 0.696
2hnk SAHSAM-dependent O-methyltransferase / 0.695
2px5 SAHGenome polyprotein 2.7.7.48 0.695
9mht SAHModification methylase HhaI 2.1.1.37 0.695
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.694
3swr SFGDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.694
3p8z SAHGenome polyprotein 2.1.1.56 0.693
2qe6 SAMUncharacterized protein / 0.691
4dkj SAHCytosine-specific methyltransferase / 0.691
4n48 SAMCap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1 2.1.1.57 0.691
3grv ADNProbable ribosomal RNA small subunit methyltransferase A / 0.690
1r6a SAHGenome polyprotein 2.7.7.48 0.689
2p3q SAHGenome polyprotein / 0.689
3eld SFGMethyltransferase / 0.689
5jjr SAHGenome polyprotein / 0.689
3cbg SAHO-methyltransferase / 0.688
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.687
2plw SAMRibosomal RNA methyltransferase, putative / 0.687
4ctj SAMGenome polyprotein / 0.687
1kr5 SAHProtein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77 0.686
3lkz SFGGenome polyprotein / 0.686
3tr6 SAHO-methyltransferase / 0.686
5f8f SFGPossible transcriptional regulatory protein / 0.686
1fjx SAHModification methylase HhaI 2.1.1.37 0.685
2c31 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.685
2ji6 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.684
2p41 SAHGenome polyprotein / 0.683
4eqs FADCoenzyme A disulfide reductase / 0.683
4rtk SAHDNA adenine methylase 2.1.1.72 0.683
4yac NAIC alpha-dehydrogenase / 0.683
1mht SAHModification methylase HhaI 2.1.1.37 0.682
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.682
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.682
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.682
4yuz S4MSpermidine synthase, putative / 0.682
3sgl SAMtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.681
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.681
4rtl SFGDNA adenine methylase 2.1.1.72 0.681
3elu SAMMethyltransferase / 0.680
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.680
1eg2 MTAModification methylase RsrI 2.1.1.72 0.679
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.679
4rtj SFGDNA adenine methylase 2.1.1.72 0.679
10mh SAHModification methylase HhaI 2.1.1.37 0.678
2hmy SAMModification methylase HhaI 2.1.1.37 0.677
4blv SAMRibosomal RNA large subunit methyltransferase J / 0.677
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.676
3sx2 NADUncharacterized protein / 0.676
2o06 MTASpermidine synthase 2.5.1.16 0.675
2q28 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.675
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.675
3ldg SAHUncharacterized protein / 0.675
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.675
2yqz SAMUncharacterized protein / 0.674
4mht SAHModification methylase HhaI 2.1.1.37 0.674
4tm3 FADKtzI / 0.674
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.674
5jjs SAHGenome polyprotein / 0.673
5mht SAHModification methylase HhaI 2.1.1.37 0.673
3ssm SAHMycinamicin VI 2''-O-methyltransferase / 0.672
2cww SAHUncharacterized protein / 0.671
2ji7 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.671
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.670
2yg6 FADPutrescine oxidase / 0.669
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.669
4tlx FDAKtzI / 0.669
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.668
3ou7 SAMSAM-dependent methyltransferase / 0.667
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.667
1nw5 SAMModification methylase RsrI 2.1.1.72 0.666
4em4 FADCoenzyme A disulfide reductase / 0.666
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.666
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.666
5dto SAHGenome polyprotein / 0.666
2y99 NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase 1.3.1.56 0.665
2b69 NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.664
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.664
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.663
1kf6 FADFumarate reductase flavoprotein subunit 1.3.5.4 0.662
1zq9 SAMProbable dimethyladenosine transferase / 0.662
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.662
3e23 SAMUncharacterized protein / 0.662
3nug NADPyridoxal 4-dehydrogenase 1.1.1.107 0.662
4fx9 FADCoenzyme A disulfide reductase 1.8.1.14 0.662
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.662
2gs9 SAHUncharacterized protein / 0.661
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.661
3geg NADShort-chain dehydrogenase/reductase SDR / 0.661
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.661
5je2 SAHMethyl transferase / 0.661
1h83 FADPolyamine oxidase 1.5.3.14 0.660
3ict FADCoenzyme A disulfide reductase / 0.660
4id9 NADPutative UDP-glucose 4-epimerase / 0.660
4tm4 FDAKtzI / 0.660
2np7 NEAModification methylase TaqI 2.1.1.72 0.659
3p8z 36AGenome polyprotein 2.1.1.56 0.659
4rto SFGDNA adenine methylase 2.1.1.72 0.659
8mht SAHModification methylase HhaI 2.1.1.37 0.659
5js6 NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.658
5jsf NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.658
1aqi SAHModification methylase TaqI 2.1.1.72 0.657
2jib ADPOxalyl-CoA decarboxylase 4.1.1.8 0.657
3nmu SAMFibrillarin-like rRNA/tRNA 2'-O-methyltransferase / 0.656
4b63 FADL-ornithine N(5)-monooxygenase / 0.656
2zfu SAHRibosomal RNA-processing protein 8 / 0.655
3nta FADFAD-dependent pyridine nucleotide-disulphide oxidoreductase / 0.655
4pyo SAHCatechol O-methyltransferase 2.1.1.6 0.655
4tm1 FDAKtzI / 0.655
5dbj FADFADH2-dependent halogenase PltA / 0.655
1af7 SAHChemotaxis protein methyltransferase 2.1.1.80 0.654
1khh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.654
1rp0 AHZThiamine thiazole synthase, chloroplastic / 0.654
2hms NAIKtr system potassium uptake protein A / 0.654
3tm4 SAMUncharacterized protein / 0.654
4b69 FADL-ornithine N(5)-monooxygenase / 0.654
4tlz FADKtzI / 0.654
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.654
2p1d SAHGenome polyprotein 2.7.7.48 0.653
4c04 SFGProtein arginine N-methyltransferase 6 / 0.653
4gf5 SAHCalS11 / 0.653
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.653
4nzh FADL-ornithine N(5)-monooxygenase / 0.652
4oa5 SAHO-methyltransferase family protein / 0.652
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.651
3gry SAMProbable ribosomal RNA small subunit methyltransferase A / 0.651
3ou2 SAHSAM-dependent methyltransferase / 0.651
3rha FDAPutrescine oxidase / 0.651
4ek9 EP4Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.651
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.651
3rfx NADUronate dehydrogenase / 0.650
4l7v SAHProtein-L-isoaspartate O-methyltransferase / 0.650
4yv2 S4MSpermidine synthase, putative / 0.650