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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
2okc SAM Probable type I restriction enzyme BthVORF4518P M protein 2.1.1.72

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 1.102
3tm4 SAMUncharacterized protein / 0.791
3tm5 SFGUncharacterized protein / 0.770
3ldg SAHUncharacterized protein / 0.756
1skm SAHModification methylase HhaI 2.1.1.37 0.754
2c7q SAHModification methylase HhaI 2.1.1.37 0.753
3mht SAHModification methylase HhaI 2.1.1.37 0.747
1nw5 SAMModification methylase RsrI 2.1.1.72 0.745
2zif SAMMethyltransferase / 0.735
2z6u SAHModification methylase HhaI 2.1.1.37 0.731
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.730
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.730
4dmg SAMUncharacterized protein / 0.729
2f8l SAMLmo1582 protein / 0.728
1g60 SAMModification methylase MboII 2.1.1.72 0.727
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.726
4poo SAMPutative RNA methylase / 0.726
1boo SAHModification methylase PvuII 2.1.1.113 0.721
4yuz S4MSpermidine synthase, putative / 0.716
10mh SAHModification methylase HhaI 2.1.1.37 0.712
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.705
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.704
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.703
3rw9 DSHSpermidine synthase 2.5.1.16 0.702
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.701
2ore SAHDNA adenine methylase 2.1.1.72 0.701
1kia SAMGlycine N-methyltransferase 2.1.1.20 0.700
2g1p SAHDNA adenine methylase 2.1.1.72 0.700
2i9k SAHModification methylase HhaI 2.1.1.37 0.698
3tlj SAHUncharacterized protein / 0.698
2o07 MTASpermidine synthase 2.5.1.16 0.697
1nw6 SFGModification methylase RsrI 2.1.1.72 0.696
2np6 NEAModification methylase TaqI 2.1.1.72 0.695
1wy7 SAHUncharacterized protein / 0.694
8mht SAHModification methylase HhaI 2.1.1.37 0.694
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.693
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.692
4n48 SAMCap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1 2.1.1.57 0.692
3eey SAMrRNA methylase / 0.691
2zcj SAHModification methylase HhaI 2.1.1.37 0.690
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.690
2pt6 S4MSpermidine synthase / 0.689
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.689
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.688
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.688
3iv6 SAMUncharacterized protein / 0.685
4obw SAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial / 0.685
2uyh SAHModification methylase HhaI 2.1.1.37 0.684
1eg2 MTAModification methylase RsrI 2.1.1.72 0.683
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.682
4yac NAIC alpha-dehydrogenase / 0.682
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.679
2hmv ADPKtr system potassium uptake protein A / 0.679
3emd SFGMethyltransferase / 0.679
3ldf SAHUncharacterized protein / 0.679
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.679
2o06 MTASpermidine synthase 2.5.1.16 0.678
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.678
2ibt NEAModification methylase TaqI 2.1.1.72 0.677
2ih2 NEAModification methylase TaqI 2.1.1.72 0.677
1yf3 SAHDNA adenine methylase / 0.675
2q28 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.675
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.675
4blw SAHRibosomal RNA large subunit methyltransferase J / 0.675
1g38 NEAModification methylase TaqI 2.1.1.72 0.674
2np7 NEAModification methylase TaqI 2.1.1.72 0.674
3gdp FAD(R)-mandelonitrile lyase 2 4.1.2.10 0.674
5jsf NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.674
1kr5 SAHProtein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77 0.673
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.673
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.673
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.673
5mht SAHModification methylase HhaI 2.1.1.37 0.673
7mht SAHModification methylase HhaI 2.1.1.37 0.673
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.672
5jjr SAHGenome polyprotein / 0.672
1i2b NADUDP-sulfoquinovose synthase, chloroplastic 3.13.1.1 0.671
2yqz SAMUncharacterized protein / 0.671
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.670
3swr SFGDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.670
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.670
5je3 SAHMethyl transferase / 0.670
1bdb NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase / 0.669
9mht SAHModification methylase HhaI 2.1.1.37 0.669
4yv2 S4MSpermidine synthase, putative / 0.668
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.667
4rtk SAHDNA adenine methylase 2.1.1.72 0.667
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.666
2fje FADAdenylylsulfate reductase, subunit A (AprA) / 0.666
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.666
2pxa SAHGenome polyprotein 2.7.7.48 0.665
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.665
4mht SAHModification methylase HhaI 2.1.1.37 0.665
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.665
1rp0 AHZThiamine thiazole synthase, chloroplastic / 0.664
1ve3 SAMUncharacterized protein / 0.664
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.664
5je4 SAHMethyl transferase / 0.664
2qa2 FADPolyketide oxygenase CabE / 0.663
2plw SAMRibosomal RNA methyltransferase, putative / 0.662
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.662
3lhd SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.662
4emw FADCoenzyme A disulfide reductase / 0.662
4oa5 SAHO-methyltransferase family protein / 0.662
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.661
3nug NADPyridoxal 4-dehydrogenase 1.1.1.107 0.661
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.660
3fri SAH16S rRNA methylase / 0.660
1nbi SAMGlycine N-methyltransferase 2.1.1.20 0.659
3p97 SAMGenome polyprotein 2.1.1.56 0.659
4gbe SAHDNA adenine methylase 2.1.1.72 0.659
5cku FADL-ornithine N(5)-monooxygenase / 0.659
5hxw FADL-amino acid deaminase / 0.659
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.658
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.657
4pyo SAHCatechol O-methyltransferase 2.1.1.6 0.657
4rtm SAMDNA adenine methylase 2.1.1.72 0.657
1mht SAHModification methylase HhaI 2.1.1.37 0.656
2zzn SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.656
4rto SFGDNA adenine methylase 2.1.1.72 0.656
4uck SAMLarge structural protein / 0.656
1g1a NADdTDP-glucose 4,6-dehydratase / 0.655
1jnz FADAdenylylsulfate reductase, subunit A (AprA) / 0.655
2ih5 NEAModification methylase TaqI 2.1.1.72 0.655
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.654
2xyr SFGReplicase polyprotein 1ab 2.1.1 0.654
3aw9 NADNAD-dependent epimerase/dehydratase / 0.654
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.653
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.653
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.652
2px5 SAHGenome polyprotein 2.7.7.48 0.652
3pt6 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.652
4ce0 SAHProbable O-methyltransferase / 0.652
4ek9 EP4Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.652
4c04 SFGProtein arginine N-methyltransferase 6 / 0.651
1aqi SAHModification methylase TaqI 2.1.1.72 0.650