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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
3lcc SAH Thiocyanate methyltransferase 1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3lcc SAHThiocyanate methyltransferase 1 / 1.066
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.835
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.834
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.821
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.814
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.806
2yqz SAMUncharacterized protein / 0.804
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.803
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.798
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.798
3go4 SAHUncharacterized protein / 0.797
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.796
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.796
4c03 SFGProtein arginine N-methyltransferase 6 / 0.795
5je3 SAHMethyl transferase / 0.795
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.792
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.791
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.790
5bp9 SAHPutative methyltransferase protein / 0.789
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.788
4hh4 SAHCcbJ / 0.787
2qe6 SAMUncharacterized protein / 0.786
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.785
5je4 SAHMethyl transferase / 0.783
4nec SAHPutative SAM-dependent methyltransferase / 0.779
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.778
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.775
3fri SAH16S rRNA methylase / 0.772
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.770
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.770
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.768
1ve3 SAMUncharacterized protein / 0.767
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.767
5jdz SAHMethyl transferase / 0.763
4qpp SAHProtein arginine N-methyltransferase 6 / 0.759
5je2 SAHMethyl transferase / 0.759
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.758
2gs9 SAHUncharacterized protein / 0.757
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.756
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.756
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.756
2p35 SAHTrans-aconitate 2-methyltransferase / 0.755
3ou6 SAMSAM-dependent methyltransferase / 0.755
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.752
4lwp SAHArginine N-methyltransferase, putative / 0.752
5epe SAHUncharacterized protein / 0.750
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.749
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.747
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.745
3gry SAMProbable ribosomal RNA small subunit methyltransferase A / 0.743
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.742
4c04 SFGProtein arginine N-methyltransferase 6 / 0.740
5bxy SAHPutative RNA methylase family UPF0020 / 0.740
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.738
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.738
1f3l SAHProtein arginine N-methyltransferase 3 / 0.735
3t7s SAMUncharacterized protein / 0.734
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.733
1y9d FADPyruvate oxidase 1.2.3.3 0.732
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.732
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.731
2zfu SAHRibosomal RNA-processing protein 8 / 0.731
3ldf SAHUncharacterized protein / 0.731
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.730
4gbe SAHDNA adenine methylase 2.1.1.72 0.730
4m37 SAHProtein arginine N-methyltransferase 7 2.1.1 0.730
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.728
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.728
1kph SAHCyclopropane mycolic acid synthase 1 2.1.1.79 0.727
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.727
3ou2 SAHSAM-dependent methyltransferase / 0.726
5bp7 SAHSAM-dependent methyltransferase / 0.726
3t7t SAHUncharacterized protein / 0.725
4rtk SAHDNA adenine methylase 2.1.1.72 0.725
2jib ADPOxalyl-CoA decarboxylase 4.1.1.8 0.724
3cjt SAHRibosomal protein L11 methyltransferase 2.1.1 0.724
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.723
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.722
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.721
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.721
4fr0 SAMArsenic methyltransferase / 0.720
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.719
3cjq SAHRibosomal protein L11 methyltransferase 2.1.1 0.719
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.719
2c7q SAHModification methylase HhaI 2.1.1.37 0.718
3tos SAHCalS11 / 0.718
4xcx SAHSmall RNA 2'-O-methyltransferase / 0.718
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.718
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.717
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.717
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.712
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.711
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.710
2ji7 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.710
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.710
4rvd SAMD-mycarose 3-C-methyltransferase / 0.710
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.709
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.709
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.709
2c31 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.707
3grv ADNProbable ribosomal RNA small subunit methyltransferase A / 0.707
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.705
2xvm SAHTellurite methyltransferase 2.1.1.265 0.705
4yac NAIC alpha-dehydrogenase / 0.705
4e2x SAHMethyltransferase / 0.703
4htf SAMtRNA 5-carboxymethoxyuridine methyltransferase / 0.703
1g60 SAMModification methylase MboII 2.1.1.72 0.702
3kkz SAMUncharacterized protein / 0.702
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.702
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.701
1ori SAHProtein arginine N-methyltransferase 1 / 0.701
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.701
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.701
3iv6 SAMUncharacterized protein / 0.701
5f2k SAHUncharacterized protein / 0.701
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.700
3fpf MTAUncharacterized protein / 0.700
2g1p SAHDNA adenine methylase 2.1.1.72 0.699
3lga SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.699
3wv8 ATPHmd co-occurring protein HcgE / 0.699
4qnu GEKtRNA U34 carboxymethyltransferase / 0.699
1skm SAHModification methylase HhaI 2.1.1.37 0.698
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.698
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.697
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.697
4qnv GEKtRNA U34 carboxymethyltransferase / 0.697
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.696
2aot SAHHistamine N-methyltransferase 2.1.1.8 0.696
4pyo SAHCatechol O-methyltransferase 2.1.1.6 0.695
1g1a NADdTDP-glucose 4,6-dehydratase / 0.694
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.694
2o06 MTASpermidine synthase 2.5.1.16 0.694
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.692
4g56 SAHProtein arginine N-methyltransferase 5 / 0.692
4oa5 SAHO-methyltransferase family protein / 0.692
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.691
2pzj NADPutative nucleotide sugar epimerase/ dehydratase / 0.691
3i53 SAH2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase / 0.690
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.688
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.688
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.687
1orh SAHProtein arginine N-methyltransferase 1 / 0.686
3ssm SAHMycinamicin VI 2''-O-methyltransferase / 0.686
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.685
2zbp SAMRibosomal protein L11 methyltransferase 2.1.1 0.685
1khh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.684
2o07 MTASpermidine synthase 2.5.1.16 0.683
4pne SAHMethyltransferase-like protein / 0.683
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.682
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.682
2i9k SAHModification methylase HhaI 2.1.1.37 0.682
4gf5 SAHCalS11 / 0.682
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.682
3cbg SAHO-methyltransferase / 0.681
3qgz ADNHistidine triad nucleotide-binding protein 1 3 0.681
4yv0 S4MSpermidine synthase, putative / 0.681
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.680
1yf3 SAHDNA adenine methylase / 0.680
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.679
2q1u NADPutative nucleotide sugar epimerase/ dehydratase / 0.678
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.678
3sxj SAMPutative methyltransferase / 0.678
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.678
1jkf NADInositol-3-phosphate synthase 5.5.1.4 0.677
3hvk 719Catechol O-methyltransferase 2.1.1.6 0.677
3p9k SAHCaffeic acid O-methyltransferase / 0.677
3tr6 SAHO-methyltransferase / 0.677
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.676
2zw9 SAMtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.676
4dmg SAMUncharacterized protein / 0.676
1jr4 CL4Catechol O-methyltransferase 2.1.1.6 0.675
3e8s SAHUncharacterized protein / 0.675
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.675
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.675
2plw SAMRibosomal RNA methyltransferase, putative / 0.673
3jyq NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.673
1nv9 SAHRelease factor glutamine methyltransferase 2.1.1.297 0.672
1ri4 SAMmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.672
3vc2 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.672
1zmc NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.671
3c3y SAHO-methyltransferase / 0.671
5f8f SFGPossible transcriptional regulatory protein / 0.671
7mht SAHModification methylase HhaI 2.1.1.37 0.671
4c3x FAD3-ketosteroid dehydrogenase / 0.669
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.669
1l7e NAINAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.668
2q1t NADPutative nucleotide sugar epimerase/ dehydratase / 0.667
3ru9 NADUDP-N-acetylglucosamine 4-epimerase / 0.667
4ek9 EP4Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.667
1l3i SAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) / 0.666
3ruh NADUDP-N-acetylglucosamine 4-epimerase / 0.666
3wv7 ADPHmd co-occurring protein HcgE / 0.666
4c05 SAHProtein arginine N-methyltransferase 6 / 0.665
4g67 SAHUncharacterized ACR, COG1565 superfamily / 0.665
2uyh SAHModification methylase HhaI 2.1.1.37 0.664
3h5n ATPMccB protein / 0.664
3ruf NADUDP-N-acetylglucosamine 4-epimerase / 0.664
1nv8 SAMRelease factor glutamine methyltransferase 2.1.1.297 0.663
2hms NAIKtr system potassium uptake protein A / 0.663
3mht SAHModification methylase HhaI 2.1.1.37 0.663
1nw5 SAMModification methylase RsrI 2.1.1.72 0.662
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.662
4ce0 SAHProbable O-methyltransferase / 0.662
5k7w SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.662
2ji6 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.661
2ytz SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.661
4yuz S4MSpermidine synthase, putative / 0.661
1b4v FADCholesterol oxidase 1.1.3.6 0.660
2fkn NADUrocanate hydratase 4.2.1.49 0.660
4ckb SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.660
3t0i SAHPutative methyltransferase / 0.659
4mb2 ATPUncharacterized protein / 0.659
1la2 NADInositol-3-phosphate synthase 5.5.1.4 0.658
1rp0 AHZThiamine thiazole synthase, chloroplastic / 0.658
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.658
2cdu ADPNADH oxidase / 0.658
4yv2 S4MSpermidine synthase, putative / 0.658
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.658
3bwc SAMSpermidine synthase, putative / 0.657
3s1s SAHRestriction endonuclease BpuSI / 0.657
4f86 SFGGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.657
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.657
2z6u SAHModification methylase HhaI 2.1.1.37 0.656
5eku SAHArginine N-methyltransferase, putative / 0.656
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.655
1wy7 SAHUncharacterized protein / 0.655
2oor NADNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.654
2v7g NADUrocanate hydratase 4.2.1.49 0.654
3cnj FADCholesterol oxidase 1.1.3.6 0.654
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.653
1xdu SFGAclacinomycin 10-hydroxylase RdmB 4.1.1 0.653
2bm9 SAMCephalosporin hydroxylase CmcI / 0.653
2q1s NAIPutative nucleotide sugar epimerase/ dehydratase / 0.653
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.653
3e23 SAMUncharacterized protein / 0.653
3k7m FAD6-hydroxy-L-nicotine oxidase / 0.653
3sgl SAMtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.653
4rdi ATPtRNA threonylcarbamoyladenosine dehydratase 6.1 0.653
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.653
1jqd SAHHistamine N-methyltransferase 2.1.1.8 0.652
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.652
2zif SAMMethyltransferase / 0.652
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.652
3gxo SAHMitomycin biosynthesis 6-O-methyltransferase / 0.652
3vyw SAMUncharacterized protein / 0.652
5d4u SAMUncharacterized protein MJ0489 / 0.652
1bxk NADdTDP-glucose 4,6-dehydratase 2 / 0.651
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.651