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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
5f8f SFG Possible transcriptional regulatory protein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
5f8f SFGPossible transcriptional regulatory protein / 1.021
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.753
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.738
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.738
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.735
4c04 SFGProtein arginine N-methyltransferase 6 / 0.726
4hh4 SAHCcbJ / 0.719
4nec SAHPutative SAM-dependent methyltransferase / 0.718
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.715
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.714
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.713
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.713
4pne SAHMethyltransferase-like protein / 0.713
3ldg SAHUncharacterized protein / 0.712
3iv6 SAMUncharacterized protein / 0.711
2yqz SAMUncharacterized protein / 0.710
3ou2 SAHSAM-dependent methyltransferase / 0.710
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.708
3ou6 SAMSAM-dependent methyltransferase / 0.708
4c03 SFGProtein arginine N-methyltransferase 6 / 0.704
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.703
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.699
3e23 SAMUncharacterized protein / 0.698
4kvz SAHPtnL protein / 0.697
2qe6 SAMUncharacterized protein / 0.695
3ou7 SAMSAM-dependent methyltransferase / 0.693
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.693
3b5i SAHIndole-3-acetate O-methyltransferase 1 / 0.692
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.689
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.689
4uy6 SAHHistidine N-alpha-methyltransferase / 0.689
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.688
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.687
4ax8 SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.687
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.687
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.687
5epe SAHUncharacterized protein / 0.687
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.686
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.686
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.685
2np7 NEAModification methylase TaqI 2.1.1.72 0.684
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.684
4a6d SAMAcetylserotonin O-methyltransferase 2.1.1.4 0.684
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.683
1g60 SAMModification methylase MboII 2.1.1.72 0.682
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.682
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.682
1boo SAHModification methylase PvuII 2.1.1.113 0.681
3p2e SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.681
1kr5 SAHProtein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77 0.680
1wy7 SAHUncharacterized protein / 0.680
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.680
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.680
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.680
3kkz SAMUncharacterized protein / 0.679
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.679
2ibt NEAModification methylase TaqI 2.1.1.72 0.678
2p35 SAHTrans-aconitate 2-methyltransferase / 0.677
3p9k SAHCaffeic acid O-methyltransferase / 0.677
3e8s SAHUncharacterized protein / 0.676
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.676
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.676
2np6 NEAModification methylase TaqI 2.1.1.72 0.675
3lst SAHCalO1 / 0.675
3ksd NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.673
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.673
1nbi SAMGlycine N-methyltransferase 2.1.1.20 0.671
3lcc SAHThiocyanate methyltransferase 1 / 0.671
1zmc NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.670
2e1m FADL-glutamate oxidase / 0.669
2gs9 SAHUncharacterized protein / 0.669
2o07 MTASpermidine synthase 2.5.1.16 0.669
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.669
3fri SAH16S rRNA methylase / 0.669
3gu3 SAHMethyltransferase / 0.669
5bp7 SAHSAM-dependent methyltransferase / 0.669
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.668
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.668
5je4 SAHMethyl transferase / 0.668
2c7q SAHModification methylase HhaI 2.1.1.37 0.667
2ji7 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.667
3t7s SAMUncharacterized protein / 0.667
4dmg SAMUncharacterized protein / 0.667
5jdz SAHMethyl transferase / 0.667
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.666
1y9d FADPyruvate oxidase 1.2.3.3 0.666
3bus SAHDemethylrebeccamycin-D-glucose O-methyltransferase / 0.666
5f8e SAHPossible transcriptional regulatory protein / 0.666
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.664
1ve3 SAMUncharacterized protein / 0.664
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.664
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.664
4kwc SAHMethyltransferase domain family / 0.664
5fa8 SAMRibosomal protein L11 methyltransferase, putative / 0.664
1yf3 SAHDNA adenine methylase / 0.663
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.663
1d2h SAHGlycine N-methyltransferase 2.1.1.20 0.661
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.661
2xvm SAHTellurite methyltransferase 2.1.1.265 0.661
3hvi 619Catechol O-methyltransferase 2.1.1.6 0.661
3ldf SAHUncharacterized protein / 0.661
3t0i SAHPutative methyltransferase / 0.661
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.661
2ih2 NEAModification methylase TaqI 2.1.1.72 0.660
3t7t SAHUncharacterized protein / 0.660
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.660
2o06 MTASpermidine synthase 2.5.1.16 0.658
3i53 SAH2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase / 0.658
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.657
5je2 SAHMethyl transferase / 0.657
1f3l SAHProtein arginine N-methyltransferase 3 / 0.656
1xdu SFGAclacinomycin 10-hydroxylase RdmB 4.1.1 0.656
3gwz SAHMitomycin biosynthesis 6-O-methyltransferase / 0.656
1nbh SAMGlycine N-methyltransferase 2.1.1.20 0.655
4q7f 3D1Uncharacterized protein / 0.655
1i2b NADUDP-sulfoquinovose synthase, chloroplastic 3.13.1.1 0.654
3g8a SAHRibosomal RNA small subunit methyltransferase G / 0.654
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.654
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.653
1skm SAHModification methylase HhaI 2.1.1.37 0.653
4mb2 ATPUncharacterized protein / 0.653
4xba 5GPAprataxin-like protein 3 0.653
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.652
2zwa SAHtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.652
4tm3 FADKtzI / 0.652
7mht SAHModification methylase HhaI 2.1.1.37 0.652
1rp0 AHZThiamine thiazole synthase, chloroplastic / 0.651
3ruc NADUDP-N-acetylglucosamine 4-epimerase / 0.650
5je3 SAHMethyl transferase / 0.650