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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
4qdk SAH Magnesium-protoporphyrin O-methyltransferase 2.1.1.11

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 1.136
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.811
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.802
4kvz SAHPtnL protein / 0.801
5je2 SAHMethyl transferase / 0.798
5jdz SAHMethyl transferase / 0.787
3e23 SAMUncharacterized protein / 0.783
4htf SAMtRNA 5-carboxymethoxyuridine methyltransferase / 0.778
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.776
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.774
5bxy SAHPutative RNA methylase family UPF0020 / 0.774
2zfu SAHRibosomal RNA-processing protein 8 / 0.769
3lcc SAHThiocyanate methyltransferase 1 / 0.768
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.768
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.767
3go4 SAHUncharacterized protein / 0.767
2yqz SAMUncharacterized protein / 0.765
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.764
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.763
4e2x SAHMethyltransferase / 0.762
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.758
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.758
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.758
5je3 SAHMethyl transferase / 0.756
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.755
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.755
2qe6 SAMUncharacterized protein / 0.748
5bp7 SAHSAM-dependent methyltransferase / 0.747
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.746
3t7t SAHUncharacterized protein / 0.743
2gs9 SAHUncharacterized protein / 0.742
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.741
5epe SAHUncharacterized protein / 0.740
3fri SAH16S rRNA methylase / 0.738
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.737
3p9k SAHCaffeic acid O-methyltransferase / 0.735
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.735
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.732
3rw9 DSHSpermidine synthase 2.5.1.16 0.729
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.729
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.727
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.727
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.725
3cbg SAHO-methyltransferase / 0.725
3gxo SAHMitomycin biosynthesis 6-O-methyltransferase / 0.725
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.724
4yv2 S4MSpermidine synthase, putative / 0.724
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.724
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.721
3t7s SAMUncharacterized protein / 0.721
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.721
3c3y SAHO-methyltransferase / 0.720
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.719
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.718
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.716
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.715
4c04 SFGProtein arginine N-methyltransferase 6 / 0.714
4g67 SAHUncharacterized ACR, COG1565 superfamily / 0.714
3fpf MTAUncharacterized protein / 0.713
1ve3 SAMUncharacterized protein / 0.712
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.712
3vc2 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.712
3dh0 SAMUncharacterized protein / 0.711
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.711
2o06 MTASpermidine synthase 2.5.1.16 0.709
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.709
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.708
4c05 SAHProtein arginine N-methyltransferase 6 / 0.708
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.708
5bp9 SAHPutative methyltransferase protein / 0.708
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.707
2ih2 NEAModification methylase TaqI 2.1.1.72 0.707
1g1a NADdTDP-glucose 4,6-dehydratase / 0.705
4uy6 SAHHistidine N-alpha-methyltransferase / 0.705
2o07 MTASpermidine synthase 2.5.1.16 0.704
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.704
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.703
4nec SAHPutative SAM-dependent methyltransferase / 0.703
2hnk SAHSAM-dependent O-methyltransferase / 0.702
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.702
4l7v SAHProtein-L-isoaspartate O-methyltransferase / 0.702
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.701
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.701
4qpp SAHProtein arginine N-methyltransferase 6 / 0.701
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.701
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.701
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.700
3lst SAHCalO1 / 0.700
3ou6 SAMSAM-dependent methyltransferase / 0.700
2pan FADGlyoxylate carboligase 4.1.1.47 0.699
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.699
4yv1 S4MSpermidine synthase, putative / 0.699
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.698
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.698
2p35 SAHTrans-aconitate 2-methyltransferase / 0.698
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.697
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.697
1ri4 SAMmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.696
3i53 SAH2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase / 0.696
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.696
1kph SAHCyclopropane mycolic acid synthase 1 2.1.1.79 0.695
3kkz SAMUncharacterized protein / 0.695
4c03 SFGProtein arginine N-methyltransferase 6 / 0.695
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.694
5f2k SAHUncharacterized protein / 0.694
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.693
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.693
2ytz SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.692
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.692
3gwz SAHMitomycin biosynthesis 6-O-methyltransferase / 0.691
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.691
1wy7 SAHUncharacterized protein / 0.690
4pyo SAHCatechol O-methyltransferase 2.1.1.6 0.690
1kr5 SAHProtein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77 0.688
3bus SAHDemethylrebeccamycin-D-glucose O-methyltransferase / 0.688
3ou2 SAHSAM-dependent methyltransferase / 0.688
4qnu GEKtRNA U34 carboxymethyltransferase / 0.685
3tos SAHCalS11 / 0.684
4gbe SAHDNA adenine methylase 2.1.1.72 0.684
4xcx SAHSmall RNA 2'-O-methyltransferase / 0.683
1nv8 SAMRelease factor glutamine methyltransferase 2.1.1.297 0.682
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.682
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.682
3e8s SAHUncharacterized protein / 0.682
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.680
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.680
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.680
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.679
2eg5 SAH7-methylxanthosine synthase 1 / 0.678
4lwp SAHArginine N-methyltransferase, putative / 0.678
3g8a SAHRibosomal RNA small subunit methyltransferase G / 0.677
3vc1 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.676
2hmv ADPKtr system potassium uptake protein A / 0.675
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.675
4ce0 SAHProbable O-methyltransferase / 0.675
4hh4 SAHCcbJ / 0.674
4dmg SAMUncharacterized protein / 0.672
4kwc SAHMethyltransferase domain family / 0.672
7mht SAHModification methylase HhaI 2.1.1.37 0.672
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.671
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.671
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.671
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.670
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.670
3mht SAHModification methylase HhaI 2.1.1.37 0.669
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.669
1skm SAHModification methylase HhaI 2.1.1.37 0.668
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.668
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.668
1af7 SAHChemotaxis protein methyltransferase 2.1.1.80 0.667
3p2e SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.667
3pb3 SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.667
3wv8 ATPHmd co-occurring protein HcgE / 0.667
1nv9 SAHRelease factor glutamine methyltransferase 2.1.1.297 0.666
4gf5 SAHCalS11 / 0.666
5dbj FADFADH2-dependent halogenase PltA / 0.666
1d2h SAHGlycine N-methyltransferase 2.1.1.20 0.665
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.665
4qnv GEKtRNA U34 carboxymethyltransferase / 0.665
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.665
2c7q SAHModification methylase HhaI 2.1.1.37 0.664
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.664
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.663
4rvd SAMD-mycarose 3-C-methyltransferase / 0.663
1f3l SAHProtein arginine N-methyltransferase 3 / 0.662
2uyh SAHModification methylase HhaI 2.1.1.37 0.662
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.662
5eku SAHArginine N-methyltransferase, putative / 0.662
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.661
1eg2 MTAModification methylase RsrI 2.1.1.72 0.661
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.660
2hms NAIKtr system potassium uptake protein A / 0.660
2z6u SAHModification methylase HhaI 2.1.1.37 0.660
3lby SAHUncharacterized protein / 0.660
9mht SAHModification methylase HhaI 2.1.1.37 0.660
4pne SAHMethyltransferase-like protein / 0.659
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.659
1rp0 AHZThiamine thiazole synthase, chloroplastic / 0.658
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.657
2zwa SAHtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.657
2ibt NEAModification methylase TaqI 2.1.1.72 0.656
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.655
3t0i SAHPutative methyltransferase / 0.654
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.654
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.654
1boo SAHModification methylase PvuII 2.1.1.113 0.653
4yuz S4MSpermidine synthase, putative / 0.653
4h0n SAHDnmt2 / 0.652
1fjx SAHModification methylase HhaI 2.1.1.37 0.651
1uay ADNOxidoreductase / 0.651
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.651
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.650
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.650