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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
1yf3 SAH DNA adenine methylase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1yf3 SAHDNA adenine methylase / 1.231
2g1p SAHDNA adenine methylase 2.1.1.72 0.917
4rtk SAHDNA adenine methylase 2.1.1.72 0.842
4rtj SFGDNA adenine methylase 2.1.1.72 0.820
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.815
4gbe SAHDNA adenine methylase 2.1.1.72 0.811
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.802
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.800
3duw SAHO-methyltransferase, putative / 0.791
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.778
4rtm SAMDNA adenine methylase 2.1.1.72 0.776
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.775
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.774
5je2 SAHMethyl transferase / 0.774
3swr SFGDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.771
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.769
4dmg SAMUncharacterized protein / 0.766
4rtl SFGDNA adenine methylase 2.1.1.72 0.763
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.762
2ore SAHDNA adenine methylase 2.1.1.72 0.756
4rtr SAMDNA adenine methylase 2.1.1.72 0.754
4poo SAMPutative RNA methylase / 0.753
2hnk SAHSAM-dependent O-methyltransferase / 0.747
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.747
1g60 SAMModification methylase MboII 2.1.1.72 0.746
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.744
3vyw SAMUncharacterized protein / 0.744
4rto SFGDNA adenine methylase 2.1.1.72 0.744
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.741
3ssm SAHMycinamicin VI 2''-O-methyltransferase / 0.741
4yuz S4MSpermidine synthase, putative / 0.741
5k7w SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.741
3qv2 SAH5-cytosine DNA methyltransferase / 0.739
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.738
1nw5 SAMModification methylase RsrI 2.1.1.72 0.738
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.738
2px2 SAHGenome polyprotein 2.7.7.48 0.737
2px5 SAHGenome polyprotein 2.7.7.48 0.732
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.732
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.732
2hmv ADPKtr system potassium uptake protein A / 0.731
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.730
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.730
2zcj SAHModification methylase HhaI 2.1.1.37 0.729
4nec SAHPutative SAM-dependent methyltransferase / 0.729
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.727
2ji6 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.723
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.722
3ldf SAHUncharacterized protein / 0.720
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.720
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.719
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.719
4dkj SAHCytosine-specific methyltransferase / 0.719
4kvz SAHPtnL protein / 0.719
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.717
3c3y SAHO-methyltransferase / 0.717
3eey SAMrRNA methylase / 0.717
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.716
2i9k SAHModification methylase HhaI 2.1.1.37 0.716
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.716
1boo SAHModification methylase PvuII 2.1.1.113 0.715
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.715
3tr6 SAHO-methyltransferase / 0.715
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.714
1nbi SAMGlycine N-methyltransferase 2.1.1.20 0.713
2z6u SAHModification methylase HhaI 2.1.1.37 0.712
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.712
4ctk SAMGenome polyprotein / 0.712
4pyo SAHCatechol O-methyltransferase 2.1.1.6 0.712
1r6a SAHGenome polyprotein 2.7.7.48 0.710
1ve3 SAMUncharacterized protein / 0.710
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.710
3lkz SFGGenome polyprotein / 0.708
4rtp SAMDNA adenine methylase 2.1.1.72 0.708
5jjr SAHGenome polyprotein / 0.708
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.707
1kr5 SAHProtein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77 0.707
1nw6 SFGModification methylase RsrI 2.1.1.72 0.707
3p97 SAMGenome polyprotein 2.1.1.56 0.707
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.705
4kwc SAHMethyltransferase domain family / 0.705
10mh SAHModification methylase HhaI 2.1.1.37 0.704
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.703
1eg2 MTAModification methylase RsrI 2.1.1.72 0.702
4xcx SAHSmall RNA 2'-O-methyltransferase / 0.702
3gxo SAHMitomycin biosynthesis 6-O-methyltransferase / 0.700
3rw9 DSHSpermidine synthase 2.5.1.16 0.700
3tm4 SAMUncharacterized protein / 0.700
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.700
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.700
3dh0 SAMUncharacterized protein / 0.699
4obw SAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial / 0.699
1kia SAMGlycine N-methyltransferase 2.1.1.20 0.698
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.697
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.697
3dzi RGTADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 3.2.2.6 0.697
4ctj SAMGenome polyprotein / 0.697
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.696
3ou2 SAHSAM-dependent methyltransferase / 0.696
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.696
3ldg SAHUncharacterized protein / 0.695
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.694
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.694
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.694
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.694
4rts SAMDNA adenine methylase 2.1.1.72 0.694
5dto SAHGenome polyprotein / 0.694
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.693
3eld SFGMethyltransferase / 0.693
1nbh SAMGlycine N-methyltransferase 2.1.1.20 0.692
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.692
2f8l SAMLmo1582 protein / 0.692
3eva SAHGenome polyprotein 2.1.1.56 0.692
4rtn SAHDNA adenine methylase 2.1.1.72 0.691
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.690
2pkm ADNAdenosine kinase 2.7.1.20 0.689
3lby SAHUncharacterized protein / 0.689
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.689
2np6 NEAModification methylase TaqI 2.1.1.72 0.688
3lga SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.688
3m6v SAMRibosomal RNA small subunit methyltransferase F / 0.688
4hh4 SAHCcbJ / 0.688
3mht SAHModification methylase HhaI 2.1.1.37 0.687
3qgz ADNHistidine triad nucleotide-binding protein 1 3 0.687
4n48 SAMCap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1 2.1.1.57 0.687
4rvd SAMD-mycarose 3-C-methyltransferase / 0.687
2c7q SAHModification methylase HhaI 2.1.1.37 0.686
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.686
3dzk NMNADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 3.2.2.6 0.686
3evc SAHGenome polyprotein 2.1.1.56 0.686
4gf5 SAHCalS11 / 0.686
4yac NAIC alpha-dehydrogenase / 0.686
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.685
1skm SAHModification methylase HhaI 2.1.1.37 0.684
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.684
4mht SAHModification methylase HhaI 2.1.1.37 0.684
2uyh SAHModification methylase HhaI 2.1.1.37 0.683
3tlj SAHUncharacterized protein / 0.682
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.682
3m6w SAMRibosomal RNA small subunit methyltransferase F / 0.681
3p8z SAHGenome polyprotein 2.1.1.56 0.681
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.681
3lcc SAHThiocyanate methyltransferase 1 / 0.680
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.679
2np7 NEAModification methylase TaqI 2.1.1.72 0.679
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.679
4blw SAHRibosomal RNA large subunit methyltransferase J / 0.678
4yv2 S4MSpermidine synthase, putative / 0.678
4x3q SAHSibL / 0.677
2gs9 SAHUncharacterized protein / 0.676
3tos SAHCalS11 / 0.676
4y9d NAIC alpha-dehydrogenase / 0.676
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.675
3ou6 SAMSAM-dependent methyltransferase / 0.674
3pt6 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.674
4eak ATP5'-AMP-activated protein kinase subunit gamma-1 / 0.674
1fjx SAHModification methylase HhaI 2.1.1.37 0.673
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.673
3e8s SAHUncharacterized protein / 0.673
2yxl SFG450aa long hypothetical fmu protein / 0.672
1isj NMNADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 2 3.2.2.6 0.671
1uay ADNOxidoreductase / 0.671
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.671
2ih2 NEAModification methylase TaqI 2.1.1.72 0.670
5d4v SAHUncharacterized protein MJ0489 / 0.670
1kph SAHCyclopropane mycolic acid synthase 1 2.1.1.79 0.669
1mht SAHModification methylase HhaI 2.1.1.37 0.669
2pkk 2FAAdenosine kinase 2.7.1.20 0.669
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.669
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.668
4c04 SFGProtein arginine N-methyltransferase 6 / 0.668
2oyl IDCEndoglycoceramidase II / 0.666
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.666
5jjs SAHGenome polyprotein / 0.666
2p41 SAHGenome polyprotein / 0.665
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.665
5mht SAHModification methylase HhaI 2.1.1.37 0.664
2oy0 SAHGenome polyprotein / 0.663
5f8f SFGPossible transcriptional regulatory protein / 0.663
2ji7 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.662
2c4c FAD[F-actin]-methionine sulfoxide oxidase MICAL1 1.14.13 0.661
2plw SAMRibosomal RNA methyltransferase, putative / 0.661
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.661
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.661
5jsf NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.661
1u28 NADNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.660
1p1b SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.659
3elu SAMMethyltransferase / 0.658
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.658
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.657
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.657
2zzn SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.657
4a6d SAMAcetylserotonin O-methyltransferase 2.1.1.4 0.657
2ign FADPyranose 2-oxidase / 0.656
2qe6 SAMUncharacterized protein / 0.656
2vhv NAIAlanine dehydrogenase 1.4.1.1 0.656
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.656
3cbg SAHO-methyltransferase / 0.656
3k4c FADPyranose 2-oxidase / 0.656
3lsh FADPyranose 2-oxidase / 0.656
4gol SA8DNA adenine methylase 2.1.1.72 0.656
3evg SAHGenome polyprotein 2.1.1.56 0.655
7mht SAHModification methylase HhaI 2.1.1.37 0.655
2p3q SAHGenome polyprotein / 0.654
5d4u SAMUncharacterized protein MJ0489 / 0.654
1ori SAHProtein arginine N-methyltransferase 1 / 0.653
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.653
2cww SAHUncharacterized protein / 0.653
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.652
2zif SAMMethyltransferase / 0.651
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.651