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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
5f2k SAH Uncharacterized protein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
5f2k SAHUncharacterized protein / 1.110
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.813
2zfu SAHRibosomal RNA-processing protein 8 / 0.786
2yqz SAMUncharacterized protein / 0.778
3go4 SAHUncharacterized protein / 0.755
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.748
2eg5 SAH7-methylxanthosine synthase 1 / 0.738
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.736
1af7 SAHChemotaxis protein methyltransferase 2.1.1.80 0.734
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.734
4e2x SAHMethyltransferase / 0.733
1f3l SAHProtein arginine N-methyltransferase 3 / 0.730
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.724
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.720
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.719
3vc2 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.719
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.718
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.717
3b5i SAHIndole-3-acetate O-methyltransferase 1 / 0.716
3lst SAHCalO1 / 0.715
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.715
3e23 SAMUncharacterized protein / 0.714
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.713
3c3y SAHO-methyltransferase / 0.712
2zwa SAHtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.711
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.711
4g67 SAHUncharacterized ACR, COG1565 superfamily / 0.708
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.706
3dh0 SAMUncharacterized protein / 0.702
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.702
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.699
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.698
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.697
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.695
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.694
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.693
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.693
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.692
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.690
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.683
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.683
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.683
5bp9 SAHPutative methyltransferase protein / 0.682
3i53 SAH2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase / 0.681
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.681
2zw9 SAMtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.680
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.678
1kr5 SAHProtein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77 0.677
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.677
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.677
3kkz SAMUncharacterized protein / 0.677
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.676
4gf5 SAHCalS11 / 0.673
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.673
2ji7 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.672
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.672
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.671
3tos SAHCalS11 / 0.671
1kph SAHCyclopropane mycolic acid synthase 1 2.1.1.79 0.670
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.670
4hh4 SAHCcbJ / 0.670
4oa5 SAHO-methyltransferase family protein / 0.669
5bxy SAHPutative RNA methylase family UPF0020 / 0.669
1khh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.668
2gs9 SAHUncharacterized protein / 0.668
4kvz SAHPtnL protein / 0.668
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.668
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.668
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.668
5jdz SAHMethyl transferase / 0.668
5je2 SAHMethyl transferase / 0.668
1l3i SAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) / 0.667
1wy7 SAHUncharacterized protein / 0.666
5k7w SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.666
1ori SAHProtein arginine N-methyltransferase 1 / 0.664
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.664
3duw SAHO-methyltransferase, putative / 0.664
3p9k SAHCaffeic acid O-methyltransferase / 0.664
4pne SAHMethyltransferase-like protein / 0.664
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.664
4kwc SAHMethyltransferase domain family / 0.663
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.660
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.659
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.659
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.657
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.656
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.655
4pgh SAMCaffeic acid O-methyltransferase / 0.655
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.655
3t7s SAMUncharacterized protein / 0.654
4qnv GEKtRNA U34 carboxymethyltransferase / 0.654
2fk8 SAMHydroxymycolate synthase MmaA4 2.1.1 0.653
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.653
5je3 SAHMethyl transferase / 0.653
4ckb SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.652
1sg9 SAMRelease factor glutamine methyltransferase 2.1.1.297 0.650
3bus SAHDemethylrebeccamycin-D-glucose O-methyltransferase / 0.650
3lcc SAHThiocyanate methyltransferase 1 / 0.650