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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
3ldf SAH Uncharacterized protein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3ldf SAHUncharacterized protein / 1.076
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.824
2yxl SFG450aa long hypothetical fmu protein / 0.770
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.755
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.755
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.745
1nw5 SAMModification methylase RsrI 2.1.1.72 0.735
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.733
3lcc SAHThiocyanate methyltransferase 1 / 0.731
1y9d FADPyruvate oxidase 1.2.3.3 0.725
1eg2 MTAModification methylase RsrI 2.1.1.72 0.723
2i9k SAHModification methylase HhaI 2.1.1.37 0.723
1yf3 SAHDNA adenine methylase / 0.720
5je2 SAHMethyl transferase / 0.720
7mht SAHModification methylase HhaI 2.1.1.37 0.718
1boo SAHModification methylase PvuII 2.1.1.113 0.717
1skm SAHModification methylase HhaI 2.1.1.37 0.717
3duw SAHO-methyltransferase, putative / 0.712
5k7w SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.712
1ve3 SAMUncharacterized protein / 0.711
4nec SAHPutative SAM-dependent methyltransferase / 0.711
2c7q SAHModification methylase HhaI 2.1.1.37 0.710
2np6 NEAModification methylase TaqI 2.1.1.72 0.709
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.709
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.709
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.708
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.705
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.704
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.704
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.703
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.702
2ibt NEAModification methylase TaqI 2.1.1.72 0.702
2z6u SAHModification methylase HhaI 2.1.1.37 0.702
4oa5 SAHO-methyltransferase family protein / 0.702
5je4 SAHMethyl transferase / 0.702
3mht SAHModification methylase HhaI 2.1.1.37 0.700
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.699
4mb2 ATPUncharacterized protein / 0.698
5je3 SAHMethyl transferase / 0.698
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.696
2uyh SAHModification methylase HhaI 2.1.1.37 0.696
4pyo SAHCatechol O-methyltransferase 2.1.1.6 0.696
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.696
2f8l SAMLmo1582 protein / 0.694
3cbg SAHO-methyltransferase / 0.694
2hnk SAHSAM-dependent O-methyltransferase / 0.692
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.692
4rtq SAHDNA adenine methylase 2.1.1.72 0.691
4c05 SAHProtein arginine N-methyltransferase 6 / 0.690
4poo SAMPutative RNA methylase / 0.690
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.689
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.689
2zcj SAHModification methylase HhaI 2.1.1.37 0.687
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.687
5epe SAHUncharacterized protein / 0.687
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.685
1nbh SAMGlycine N-methyltransferase 2.1.1.20 0.684
1uay ADNOxidoreductase / 0.684
3go4 SAHUncharacterized protein / 0.683
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.683
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.683
5jdz SAHMethyl transferase / 0.683
3ou2 SAHSAM-dependent methyltransferase / 0.682
1fjx SAHModification methylase HhaI 2.1.1.37 0.681
4c04 SFGProtein arginine N-methyltransferase 6 / 0.681
4dmg SAMUncharacterized protein / 0.681
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.680
2cdu ADPNADH oxidase / 0.680
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.679
4obw SAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial / 0.679
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.679
5cku FADL-ornithine N(5)-monooxygenase / 0.677
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.676
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.676
2xyr SFGReplicase polyprotein 1ab 2.1.1 0.676
3jyq NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.676
3swr SFGDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.676
4nzh FADL-ornithine N(5)-monooxygenase / 0.676
10mh SAHModification methylase HhaI 2.1.1.37 0.675
2ytz SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.674
4b63 FADL-ornithine N(5)-monooxygenase / 0.674
4gdp FADPolyamine oxidase FMS1 / 0.674
2zif SAMMethyltransferase / 0.673
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.673
1nbi SAMGlycine N-methyltransferase 2.1.1.20 0.672
2plw SAMRibosomal RNA methyltransferase, putative / 0.667
3fri SAH16S rRNA methylase / 0.667
4kwc SAHMethyltransferase domain family / 0.667
3ou6 SAMSAM-dependent methyltransferase / 0.665
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.665
3lby SAHUncharacterized protein / 0.664
4x3q SAHSibL / 0.664
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.663
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.663
3wv7 ADPHmd co-occurring protein HcgE / 0.663
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.663
5mht SAHModification methylase HhaI 2.1.1.37 0.663
2xvm SAHTellurite methyltransferase 2.1.1.265 0.662
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.661
4dkj SAHCytosine-specific methyltransferase / 0.661
5f8f SFGPossible transcriptional regulatory protein / 0.661
2p35 SAHTrans-aconitate 2-methyltransferase / 0.660
5jjs SAHGenome polyprotein / 0.660
3c3y SAHO-methyltransferase / 0.659
3iv6 SAMUncharacterized protein / 0.659
4b69 FADL-ornithine N(5)-monooxygenase / 0.659
1nw6 SFGModification methylase RsrI 2.1.1.72 0.658
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.658
4hh4 SAHCcbJ / 0.657
3tos SAHCalS11 / 0.656
5bxy SAHPutative RNA methylase family UPF0020 / 0.656
2bm9 SAMCephalosporin hydroxylase CmcI / 0.655
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.654
3e8s SAHUncharacterized protein / 0.654
3tr6 SAHO-methyltransferase / 0.654
4d79 ATPtRNA threonylcarbamoyladenosine dehydratase 6.1 0.654
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.654
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.653
4gbe SAHDNA adenine methylase 2.1.1.72 0.653
1af7 SAHChemotaxis protein methyltransferase 2.1.1.80 0.652
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.652
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.652
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.651
4yuz S4MSpermidine synthase, putative / 0.651
8mht SAHModification methylase HhaI 2.1.1.37 0.651
1z7e ATPBifunctional polymyxin resistance protein ArnA / 0.650
4eqe KAAHistidine triad nucleotide-binding protein 1 3 0.650