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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
2bh2 SAH 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 1.017
4dkj SAHCytosine-specific methyltransferase / 0.758
2i9k SAHModification methylase HhaI 2.1.1.37 0.755
1skm SAHModification methylase HhaI 2.1.1.37 0.753
2c7q SAHModification methylase HhaI 2.1.1.37 0.749
3e8s SAHUncharacterized protein / 0.749
4c03 SFGProtein arginine N-methyltransferase 6 / 0.737
1nw5 SAMModification methylase RsrI 2.1.1.72 0.732
2uyh SAHModification methylase HhaI 2.1.1.37 0.730
3ou2 SAHSAM-dependent methyltransferase / 0.727
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.727
1fjx SAHModification methylase HhaI 2.1.1.37 0.724
3mht SAHModification methylase HhaI 2.1.1.37 0.724
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.722
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.721
1nw6 SFGModification methylase RsrI 2.1.1.72 0.718
7mht SAHModification methylase HhaI 2.1.1.37 0.718
4gbe SAHDNA adenine methylase 2.1.1.72 0.717
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.717
1eg2 MTAModification methylase RsrI 2.1.1.72 0.716
2z6u SAHModification methylase HhaI 2.1.1.37 0.716
5je2 SAHMethyl transferase / 0.716
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.715
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.714
1nbh SAMGlycine N-methyltransferase 2.1.1.20 0.710
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.710
4lwp SAHArginine N-methyltransferase, putative / 0.709
3tos SAHCalS11 / 0.707
4rtk SAHDNA adenine methylase 2.1.1.72 0.707
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.707
5je3 SAHMethyl transferase / 0.706
5bp7 SAHSAM-dependent methyltransferase / 0.705
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.703
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.703
2qe6 SAMUncharacterized protein / 0.703
3ldf SAHUncharacterized protein / 0.702
3qv2 SAH5-cytosine DNA methyltransferase / 0.701
1mht SAHModification methylase HhaI 2.1.1.37 0.699
2zcj SAHModification methylase HhaI 2.1.1.37 0.698
5jdz SAHMethyl transferase / 0.697
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.695
1yf3 SAHDNA adenine methylase / 0.694
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.694
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.694
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.694
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.691
3lcc SAHThiocyanate methyltransferase 1 / 0.691
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.691
3ou6 SAMSAM-dependent methyltransferase / 0.690
1bdb NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase / 0.689
5k7w SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.689
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.688
3e23 SAMUncharacterized protein / 0.687
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.686
2q1w NADPutative nucleotide sugar epimerase/ dehydratase / 0.686
3m6w SAMRibosomal RNA small subunit methyltransferase F / 0.685
1kvr NADUDP-glucose 4-epimerase 5.1.3.2 0.684
2cww SAHUncharacterized protein / 0.684
1g60 SAMModification methylase MboII 2.1.1.72 0.683
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.683
5mht SAHModification methylase HhaI 2.1.1.37 0.683
1boo SAHModification methylase PvuII 2.1.1.113 0.682
1f3l SAHProtein arginine N-methyltransferase 3 / 0.682
1ori SAHProtein arginine N-methyltransferase 1 / 0.682
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.682
3gry SAMProbable ribosomal RNA small subunit methyltransferase A / 0.682
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.682
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.682
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.682
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.682
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.682
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.681
2ore SAHDNA adenine methylase 2.1.1.72 0.680
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.680
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.679
10mh SAHModification methylase HhaI 2.1.1.37 0.677
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.677
9mht SAHModification methylase HhaI 2.1.1.37 0.677
1uay ADNOxidoreductase / 0.675
2o06 MTASpermidine synthase 2.5.1.16 0.675
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.675
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.673
3lst SAHCalO1 / 0.673
3p9k SAHCaffeic acid O-methyltransferase / 0.672
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.672
1x1a SAMC-20 methyltransferase / 0.671
2eg5 SAH7-methylxanthosine synthase 1 / 0.671
2hmv ADPKtr system potassium uptake protein A / 0.671
3cbg SAHO-methyltransferase / 0.671
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.671
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.670
4nec SAHPutative SAM-dependent methyltransferase / 0.670
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.669
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.669
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.669
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.668
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.668
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.668
1l3i SAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) / 0.667
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.667
4kwc SAHMethyltransferase domain family / 0.667
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.667
5bxy SAHPutative RNA methylase family UPF0020 / 0.664
1p1h NADInositol-3-phosphate synthase 5.5.1.4 0.663
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.663
3go4 SAHUncharacterized protein / 0.663
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.663
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.662
2p35 SAHTrans-aconitate 2-methyltransferase / 0.661
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.661
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.661
4xcx SAHSmall RNA 2'-O-methyltransferase / 0.661
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.661
5eow FAD6-hydroxynicotinate 3-monooxygenase 1.14.13.114 0.661
4gc9 SAMDimethyladenosine transferase 1, mitochondrial 2.1.1 0.660
4rtj SFGDNA adenine methylase 2.1.1.72 0.660
4rto SFGDNA adenine methylase 2.1.1.72 0.660
2zif SAMMethyltransferase / 0.659
4nzh FADL-ornithine N(5)-monooxygenase / 0.659
2xyr SFGReplicase polyprotein 1ab 2.1.1 0.658
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.658
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.658
1nv9 SAHRelease factor glutamine methyltransferase 2.1.1.297 0.657
1orh SAHProtein arginine N-methyltransferase 1 / 0.657
2o07 MTASpermidine synthase 2.5.1.16 0.657
2ytz SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.657
3ou7 SAMSAM-dependent methyltransferase / 0.657
4ek9 EP4Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.657
4eqs FADCoenzyme A disulfide reductase / 0.657
4rtm SAMDNA adenine methylase 2.1.1.72 0.657
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.656
3c3y SAHO-methyltransferase / 0.656
4wec NADShort chain dehydrogenase / 0.656
3pt6 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.655
3rw9 DSHSpermidine synthase 2.5.1.16 0.655
4mht SAHModification methylase HhaI 2.1.1.37 0.655
4rtq SAHDNA adenine methylase 2.1.1.72 0.655
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.654
4nbu NAI3-oxoacyl-(Acyl-carrier-protein) reductase / 0.654
4rtl SFGDNA adenine methylase 2.1.1.72 0.654
1kr5 SAHProtein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77 0.653
3cjt SAHRibosomal protein L11 methyltransferase 2.1.1 0.653
4gh5 NADShort-chain dehydrogenase/reductase SDR / 0.653
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.653
2zbp SAMRibosomal protein L11 methyltransferase 2.1.1 0.652
3fpf MTAUncharacterized protein / 0.652
3ldg SAHUncharacterized protein / 0.652
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.652
3nmu SAMFibrillarin-like rRNA/tRNA 2'-O-methyltransferase / 0.652
3sgl SAMtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.652
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.652
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.652
5je4 SAHMethyl transferase / 0.652
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.651
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.651
4gf5 SAHCalS11 / 0.651
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.650
2ih2 NEAModification methylase TaqI 2.1.1.72 0.650