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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
3a4t SFG tRNA (cytosine(48)-C(5))-methyltransferase 2.1.1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 1.135
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.814
3m6w SAMRibosomal RNA small subunit methyltransferase F / 0.813
5je2 SAHMethyl transferase / 0.788
2yxl SFG450aa long hypothetical fmu protein / 0.784
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.782
4blv SAMRibosomal RNA large subunit methyltransferase J / 0.765
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.758
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.756
3m6v SAMRibosomal RNA small subunit methyltransferase F / 0.749
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.734
5jdz SAHMethyl transferase / 0.734
5je3 SAHMethyl transferase / 0.732
4blw SAHRibosomal RNA large subunit methyltransferase J / 0.727
5bxy SAHPutative RNA methylase family UPF0020 / 0.724
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.720
5je4 SAHMethyl transferase / 0.716
1ve3 SAMUncharacterized protein / 0.715
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.715
2cww SAHUncharacterized protein / 0.714
2f8l SAMLmo1582 protein / 0.714
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.714
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.714
2o06 MTASpermidine synthase 2.5.1.16 0.712
3ldf SAHUncharacterized protein / 0.709
4dmg SAMUncharacterized protein / 0.707
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.706
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.704
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.702
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.700
3tsc NADUncharacterized protein / 0.698
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.696
2np6 NEAModification methylase TaqI 2.1.1.72 0.696
2ih5 NEAModification methylase TaqI 2.1.1.72 0.695
3swr SFGDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.693
3ssm SAHMycinamicin VI 2''-O-methyltransferase / 0.692
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.691
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.690
1boo SAHModification methylase PvuII 2.1.1.113 0.687
2pt6 S4MSpermidine synthase / 0.687
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.687
1ori SAHProtein arginine N-methyltransferase 1 / 0.686
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.685
3lga SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.684
1cbo FADCholesterol oxidase 1.1.3.6 0.681
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.681
1wy7 SAHUncharacterized protein / 0.679
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.678
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.678
4pyo SAHCatechol O-methyltransferase 2.1.1.6 0.677
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.676
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.676
4yv2 S4MSpermidine synthase, putative / 0.676
5cku FADL-ornithine N(5)-monooxygenase / 0.676
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.675
4n48 SAMCap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1 2.1.1.57 0.675
2pan FADGlyoxylate carboligase 4.1.1.47 0.674
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.674
2g1p SAHDNA adenine methylase 2.1.1.72 0.671
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.670
3tm5 SFGUncharacterized protein / 0.670
4c03 SFGProtein arginine N-methyltransferase 6 / 0.668
1g38 NEAModification methylase TaqI 2.1.1.72 0.667
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.667
4gbe SAHDNA adenine methylase 2.1.1.72 0.666
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.666
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.666
2o07 MTASpermidine synthase 2.5.1.16 0.665
2xvm SAHTellurite methyltransferase 2.1.1.265 0.665
3ou2 SAHSAM-dependent methyltransferase / 0.665
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.665
4tm1 FDAKtzI / 0.665
4rtj SFGDNA adenine methylase 2.1.1.72 0.664
1ri4 SAMmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.663
3c3y SAHO-methyltransferase / 0.663
4kwc SAHMethyltransferase domain family / 0.663
1f3l SAHProtein arginine N-methyltransferase 3 / 0.662
1jsc FADAcetolactate synthase catalytic subunit, mitochondrial 2.2.1.6 0.662
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.662
1yf3 SAHDNA adenine methylase / 0.661
2qe6 SAMUncharacterized protein / 0.661
4lwp SAHArginine N-methyltransferase, putative / 0.661
3ldg SAHUncharacterized protein / 0.660
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.660
4poo SAMPutative RNA methylase / 0.660
2np7 NEAModification methylase TaqI 2.1.1.72 0.659
3hvk 719Catechol O-methyltransferase 2.1.1.6 0.659
3tm4 SAMUncharacterized protein / 0.659
3vc1 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.659
4rtl SFGDNA adenine methylase 2.1.1.72 0.658
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.658
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.657
4ctk SAMGenome polyprotein / 0.657
4kvz SAHPtnL protein / 0.657
4yuz S4MSpermidine synthase, putative / 0.657
3pl8 FADPyranose 2-oxidase / 0.655
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.655
4tm4 FDAKtzI / 0.655
3cbg SAHO-methyltransferase / 0.654
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.653
3lbf SAHProtein-L-isoaspartate O-methyltransferase 2.1.1.77 0.653
3nn6 FB06-hydroxy-L-nicotine oxidase / 0.653
4obw SAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial / 0.653
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.653
4tm3 FADKtzI / 0.653
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.652
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.652
3wds NADNADH-dependent quinuclidinone reductase / 0.652
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.652
2fk8 SAMHydroxymycolate synthase MmaA4 2.1.1 0.651
2i9k SAHModification methylase HhaI 2.1.1.37 0.651
2ore SAHDNA adenine methylase 2.1.1.72 0.651
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.650
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.650
5epe SAHUncharacterized protein / 0.650