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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
4pne SAH Methyltransferase-like protein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4pne SAHMethyltransferase-like protein / 1.019
1kph SAHCyclopropane mycolic acid synthase 1 2.1.1.79 0.825
3vc1 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.772
4nec SAHPutative SAM-dependent methyltransferase / 0.766
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.758
3ou2 SAHSAM-dependent methyltransferase / 0.756
3vc2 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.752
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.748
2zfu SAHRibosomal RNA-processing protein 8 / 0.741
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.738
3e23 SAMUncharacterized protein / 0.734
4hh4 SAHCcbJ / 0.734
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.733
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.732
2yqz SAMUncharacterized protein / 0.730
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.724
2fk8 SAMHydroxymycolate synthase MmaA4 2.1.1 0.719
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.713
5f8f SFGPossible transcriptional regulatory protein / 0.713
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.712
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.710
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.708
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.705
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.705
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.704
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.702
2qe6 SAMUncharacterized protein / 0.701
5bp9 SAHPutative methyltransferase protein / 0.701
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.694
2gs9 SAHUncharacterized protein / 0.689
1ri4 SAMmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.688
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.688
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.687
3e8s SAHUncharacterized protein / 0.686
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.683
3lcc SAHThiocyanate methyltransferase 1 / 0.683
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.683
2eg5 SAH7-methylxanthosine synthase 1 / 0.682
4f86 SFGGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.682
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.680
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.679
5epe SAHUncharacterized protein / 0.679
3t0i SAHPutative methyltransferase / 0.678
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.678
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.677
3b5i SAHIndole-3-acetate O-methyltransferase 1 / 0.676
3p2e SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.674
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.674
7mht SAHModification methylase HhaI 2.1.1.37 0.674
3bus SAHDemethylrebeccamycin-D-glucose O-methyltransferase / 0.673
3ha5 SFGHydroxymycolate synthase MmaA4 2.1.1 0.673
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.673
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.673
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.672
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.671
4rvd SAMD-mycarose 3-C-methyltransferase / 0.671
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.670
3ha3 SAHHydroxymycolate synthase MmaA4 2.1.1 0.669
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.669
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.665
1f3l SAHProtein arginine N-methyltransferase 3 / 0.664
5f2k SAHUncharacterized protein / 0.664
4o8j ADNRNA 3'-terminal phosphate cyclase 6.5.1.4 0.663
2aot SAHHistamine N-methyltransferase 2.1.1.8 0.662
2c7q SAHModification methylase HhaI 2.1.1.37 0.661
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.659
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.657
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.657
3lst SAHCalO1 / 0.656
4ki8 ADP60 kDa chaperonin / 0.656
4dkj SAHCytosine-specific methyltransferase / 0.655
5eku SAHArginine N-methyltransferase, putative / 0.654
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.653
3p9k SAHCaffeic acid O-methyltransferase / 0.653
1x1c SAHC-20 methyltransferase / 0.652
3sxj SAMPutative methyltransferase / 0.652
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.652
2z6u SAHModification methylase HhaI 2.1.1.37 0.651
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.651
4xcx SAHSmall RNA 2'-O-methyltransferase / 0.651