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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
3tm4 SAM Uncharacterized protein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3tm4 SAMUncharacterized protein / 1.012
3tm5 SFGUncharacterized protein / 0.909
3tlj SAHUncharacterized protein / 0.877
2f8l SAMLmo1582 protein / 0.840
1nw5 SAMModification methylase RsrI 2.1.1.72 0.810
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.791
3ldg SAHUncharacterized protein / 0.785
2uyh SAHModification methylase HhaI 2.1.1.37 0.768
1g60 SAMModification methylase MboII 2.1.1.72 0.755
1skm SAHModification methylase HhaI 2.1.1.37 0.755
10mh SAHModification methylase HhaI 2.1.1.37 0.752
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.752
7mht SAHModification methylase HhaI 2.1.1.37 0.752
9mht SAHModification methylase HhaI 2.1.1.37 0.745
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.743
3swr SFGDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.742
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.737
4gbe SAHDNA adenine methylase 2.1.1.72 0.734
1mht SAHModification methylase HhaI 2.1.1.37 0.731
2c7q SAHModification methylase HhaI 2.1.1.37 0.731
3ou6 SAMSAM-dependent methyltransferase / 0.731
4rtk SAHDNA adenine methylase 2.1.1.72 0.731
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.728
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.727
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.727
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.726
1fjx SAHModification methylase HhaI 2.1.1.37 0.725
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.723
4mht SAHModification methylase HhaI 2.1.1.37 0.722
3mht SAHModification methylase HhaI 2.1.1.37 0.719
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.718
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.717
4rto SFGDNA adenine methylase 2.1.1.72 0.717
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.715
2ore SAHDNA adenine methylase 2.1.1.72 0.713
2np7 NEAModification methylase TaqI 2.1.1.72 0.712
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.712
2g1p SAHDNA adenine methylase 2.1.1.72 0.711
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.711
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.711
2ih2 NEAModification methylase TaqI 2.1.1.72 0.709
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.707
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.706
2z6u SAHModification methylase HhaI 2.1.1.37 0.705
4obw SAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial / 0.705
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.705
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.703
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.703
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.703
1yf3 SAHDNA adenine methylase / 0.700
4rtj SFGDNA adenine methylase 2.1.1.72 0.696
4rtm SAMDNA adenine methylase 2.1.1.72 0.696
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.696
4rtr SAMDNA adenine methylase 2.1.1.72 0.695
3qv2 SAH5-cytosine DNA methyltransferase / 0.694
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.694
3abi NADUncharacterized protein / 0.693
2o06 MTASpermidine synthase 2.5.1.16 0.691
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.691
2zif SAMMethyltransferase / 0.690
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.690
5mht SAHModification methylase HhaI 2.1.1.37 0.690
2np6 NEAModification methylase TaqI 2.1.1.72 0.688
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.687
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.685
4rtq SAHDNA adenine methylase 2.1.1.72 0.685
4yac NAIC alpha-dehydrogenase / 0.685
5eku SAHArginine N-methyltransferase, putative / 0.684
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.683
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.682
3sxp NADADP-L-glycero-D-mannoheptose-6-epimerase / 0.680
2px2 SAHGenome polyprotein 2.7.7.48 0.679
4fn4 NADShort chain dehydrogenase / 0.679
4n48 SAMCap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1 2.1.1.57 0.679
4rtp SAMDNA adenine methylase 2.1.1.72 0.678
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.677
1nw6 SFGModification methylase RsrI 2.1.1.72 0.677
2yxl SFG450aa long hypothetical fmu protein / 0.677
1aqi SAHModification methylase TaqI 2.1.1.72 0.676
2i9k SAHModification methylase HhaI 2.1.1.37 0.676
2br5 SAHCephalosporin hydroxylase CmcI / 0.674
2p35 SAHTrans-aconitate 2-methyltransferase / 0.673
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.673
1g1a NADdTDP-glucose 4,6-dehydratase / 0.672
2ih5 NEAModification methylase TaqI 2.1.1.72 0.672
4d79 ATPtRNA threonylcarbamoyladenosine dehydratase 6.1 0.671
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.671
1boo SAHModification methylase PvuII 2.1.1.113 0.670
4dkj SAHCytosine-specific methyltransferase / 0.670
4mb2 ATPUncharacterized protein / 0.670
1pow FADPyruvate oxidase 1.2.3.3 0.669
1ori SAHProtein arginine N-methyltransferase 1 / 0.668
3n1s 5GPPurine nucleoside phosphoramidase / 0.668
4ctj SAMGenome polyprotein / 0.668
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.666
4yuz S4MSpermidine synthase, putative / 0.666
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.665
2gsd NADFormate dehydrogenase / 0.665
4blv SAMRibosomal RNA large subunit methyltransferase J / 0.665
4rts SAMDNA adenine methylase 2.1.1.72 0.663
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.662
1jqd SAHHistamine N-methyltransferase 2.1.1.8 0.661
2zcj SAHModification methylase HhaI 2.1.1.37 0.660
4emw FADCoenzyme A disulfide reductase / 0.660
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.659
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.659
5fa8 SAMRibosomal protein L11 methyltransferase, putative / 0.659
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.659
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.658
1g38 NEAModification methylase TaqI 2.1.1.72 0.657
1uay ADNOxidoreductase / 0.657
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.656
4kvz SAHPtnL protein / 0.656
4m37 SAHProtein arginine N-methyltransferase 7 2.1.1 0.656
4wec NADShort chain dehydrogenase / 0.656
4yv1 S4MSpermidine synthase, putative / 0.656
5cku FADL-ornithine N(5)-monooxygenase / 0.656
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.654
4uy6 SAHHistidine N-alpha-methyltransferase / 0.654
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.654
1eg2 MTAModification methylase RsrI 2.1.1.72 0.653
1ve3 SAMUncharacterized protein / 0.653
4ek9 EP4Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.653
2hmv ADPKtr system potassium uptake protein A / 0.652
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.652
4gol SA8DNA adenine methylase 2.1.1.72 0.652
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.652
3lhd SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.651
4c04 SFGProtein arginine N-methyltransferase 6 / 0.651
4em4 FADCoenzyme A disulfide reductase / 0.650