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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
2g1p SAH DNA adenine methylase 2.1.1.72

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2g1p SAHDNA adenine methylase 2.1.1.72 1.081
1yf3 SAHDNA adenine methylase / 0.917
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.911
4rtk SAHDNA adenine methylase 2.1.1.72 0.890
4gbe SAHDNA adenine methylase 2.1.1.72 0.862
4rtj SFGDNA adenine methylase 2.1.1.72 0.828
4rtq SAHDNA adenine methylase 2.1.1.72 0.804
1nw5 SAMModification methylase RsrI 2.1.1.72 0.803
2ore SAHDNA adenine methylase 2.1.1.72 0.802
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.798
2px2 SAHGenome polyprotein 2.7.7.48 0.794
1eg2 MTAModification methylase RsrI 2.1.1.72 0.787
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.787
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.785
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.784
4rtm SAMDNA adenine methylase 2.1.1.72 0.778
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.775
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.771
4rtr SAMDNA adenine methylase 2.1.1.72 0.769
1boo SAHModification methylase PvuII 2.1.1.113 0.766
4rtl SFGDNA adenine methylase 2.1.1.72 0.764
2yxl SFG450aa long hypothetical fmu protein / 0.761
1g60 SAMModification methylase MboII 2.1.1.72 0.758
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.757
4rto SFGDNA adenine methylase 2.1.1.72 0.755
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.751
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.751
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.751
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.744
3emd SFGMethyltransferase / 0.742
4ctk SAMGenome polyprotein / 0.742
4rts SAMDNA adenine methylase 2.1.1.72 0.742
2zcj SAHModification methylase HhaI 2.1.1.37 0.739
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.739
2z6u SAHModification methylase HhaI 2.1.1.37 0.738
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.736
5jdz SAHMethyl transferase / 0.736
5jjr SAHGenome polyprotein / 0.736
2i9k SAHModification methylase HhaI 2.1.1.37 0.735
4uck SAMLarge structural protein / 0.734
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.732
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.732
3ldg SAHUncharacterized protein / 0.730
4k6m SAHGenome polyprotein / 0.729
1uay ADNOxidoreductase / 0.726
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.726
4gol SA8DNA adenine methylase 2.1.1.72 0.726
2cww SAHUncharacterized protein / 0.725
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.725
4rtp SAMDNA adenine methylase 2.1.1.72 0.724
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.724
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.723
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.723
4dmg SAMUncharacterized protein / 0.722
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.721
4rtn SAHDNA adenine methylase 2.1.1.72 0.721
5je4 SAHMethyl transferase / 0.721
3ou2 SAHSAM-dependent methyltransferase / 0.720
3p8z SAHGenome polyprotein 2.1.1.56 0.720
2zif SAMMethyltransferase / 0.717
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.717
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.716
2plw SAMRibosomal RNA methyltransferase, putative / 0.715
3lkz SFGGenome polyprotein / 0.715
4ctj SAMGenome polyprotein / 0.715
5k7w SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.715
5je3 SAHMethyl transferase / 0.714
10mh SAHModification methylase HhaI 2.1.1.37 0.713
2hnk SAHSAM-dependent O-methyltransferase / 0.712
2uyh SAHModification methylase HhaI 2.1.1.37 0.712
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.712
3tm4 SAMUncharacterized protein / 0.711
3p97 SAMGenome polyprotein 2.1.1.56 0.710
1y9d FADPyruvate oxidase 1.2.3.3 0.709
3eey SAMrRNA methylase / 0.709
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.709
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.709
4yuz S4MSpermidine synthase, putative / 0.709
3ssm SAHMycinamicin VI 2''-O-methyltransferase / 0.708
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.708
1skm SAHModification methylase HhaI 2.1.1.37 0.707
2o06 MTASpermidine synthase 2.5.1.16 0.707
2f8l SAMLmo1582 protein / 0.706
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.706
3swr SFGDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.705
3tlj SAHUncharacterized protein / 0.704
2px5 SAHGenome polyprotein 2.7.7.48 0.703
3rw9 DSHSpermidine synthase 2.5.1.16 0.703
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.703
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.702
3ely SAHMethyltransferase / 0.702
2ibt NEAModification methylase TaqI 2.1.1.72 0.701
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.701
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.701
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.701
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.700
3mht SAHModification methylase HhaI 2.1.1.37 0.700
3lcc SAHThiocyanate methyltransferase 1 / 0.699
3lga SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.698
4mht SAHModification methylase HhaI 2.1.1.37 0.698
4yac NAIC alpha-dehydrogenase / 0.698
1nw6 SFGModification methylase RsrI 2.1.1.72 0.697
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.697
1kvr NADUDP-glucose 4-epimerase 5.1.3.2 0.695
2hmv ADPKtr system potassium uptake protein A / 0.695
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.695
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.694
5jjs SAHGenome polyprotein / 0.694
3eva SAHGenome polyprotein 2.1.1.56 0.693
3evc SAHGenome polyprotein 2.1.1.56 0.693
4nbu NAI3-oxoacyl-(Acyl-carrier-protein) reductase / 0.692
4nec SAHPutative SAM-dependent methyltransferase / 0.692
4yv2 S4MSpermidine synthase, putative / 0.692
7mht SAHModification methylase HhaI 2.1.1.37 0.692
9mht SAHModification methylase HhaI 2.1.1.37 0.692
1fjx SAHModification methylase HhaI 2.1.1.37 0.691
3go4 SAHUncharacterized protein / 0.691
3duw SAHO-methyltransferase, putative / 0.690
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.690
8mht SAHModification methylase HhaI 2.1.1.37 0.690
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.689
3eld SFGMethyltransferase / 0.689
3ou6 SAMSAM-dependent methyltransferase / 0.689
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.688
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.688
2ytz SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.687
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.687
4kvz SAHPtnL protein / 0.687
4mb2 ATPUncharacterized protein / 0.687
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.687
1mht SAHModification methylase HhaI 2.1.1.37 0.686
2h39 ADQADP-glucose phosphorylase / 0.686
3pt6 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.686
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.686
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.686
2c7q SAHModification methylase HhaI 2.1.1.37 0.685
2pzj NADPutative nucleotide sugar epimerase/ dehydratase / 0.684
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.684
5d4v SAHUncharacterized protein MJ0489 / 0.684
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.683
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.683
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.683
4poo SAMPutative RNA methylase / 0.683
2np6 NEAModification methylase TaqI 2.1.1.72 0.682
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.682
1r6a SAHGenome polyprotein 2.7.7.48 0.680
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.680
4dkj SAHCytosine-specific methyltransferase / 0.679
4obw SAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial / 0.679
4yuv S4MSpermidine synthase, putative / 0.679
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.678
1f3l SAHProtein arginine N-methyltransferase 3 / 0.676
3m6v SAMRibosomal RNA small subunit methyltransferase F / 0.676
4hh4 SAHCcbJ / 0.676
3tos SAHCalS11 / 0.675
2q1u NADPutative nucleotide sugar epimerase/ dehydratase / 0.673
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.672
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.672
2p41 SAHGenome polyprotein / 0.671
2zzn SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.671
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.671
1txz APRProbable ADP-ribose 1''-phosphate phosphatase YML087W 3.1.3.84 0.670
2ih2 NEAModification methylase TaqI 2.1.1.72 0.670
2pxa SAHGenome polyprotein 2.7.7.48 0.670
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.669
4h0n SAHDnmt2 / 0.669
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.668
4blv SAMRibosomal RNA large subunit methyltransferase J / 0.668
1g1a NADdTDP-glucose 4,6-dehydratase / 0.666
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.666
1p1i NADInositol-3-phosphate synthase 5.5.1.4 0.665
2ih5 NEAModification methylase TaqI 2.1.1.72 0.665
2np7 NEAModification methylase TaqI 2.1.1.72 0.665
4blw SAHRibosomal RNA large subunit methyltransferase J / 0.665
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.663
3evb SAHGenome polyprotein 2.1.1.56 0.663
5d4u SAMUncharacterized protein MJ0489 / 0.663
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.662
3tm5 SFGUncharacterized protein / 0.662
5mht SAHModification methylase HhaI 2.1.1.37 0.662
1bxk NADdTDP-glucose 4,6-dehydratase 2 / 0.661
1xdu SFGAclacinomycin 10-hydroxylase RdmB 4.1.1 0.661
4xcx SAHSmall RNA 2'-O-methyltransferase / 0.661
2oy0 SAHGenome polyprotein / 0.660
3cbg SAHO-methyltransferase / 0.660
3qv2 SAH5-cytosine DNA methyltransferase / 0.660
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.660
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.659
3elu SAMMethyltransferase / 0.659
4rvd SAMD-mycarose 3-C-methyltransferase / 0.658
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.657
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.656
4y9d NAIC alpha-dehydrogenase / 0.655
5jsf NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.655
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.654
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.654
3lby SAHUncharacterized protein / 0.653
2gs9 SAHUncharacterized protein / 0.652
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.652
3wdm ADN4-phosphopantoate--beta-alanine ligase 6.3.2.36 0.652
3i53 SAH2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase / 0.651
3s1s SAHRestriction endonuclease BpuSI / 0.651
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.651
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.651
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.650