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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
4fgz SAH Phosphoethanolamine N-methyltransferase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4fgz SAHPhosphoethanolamine N-methyltransferase / 1.054
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 1.011
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.995
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.985
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.922
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.888
5je2 SAHMethyl transferase / 0.870
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.809
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.803
3lcc SAHThiocyanate methyltransferase 1 / 0.796
2zfu SAHRibosomal RNA-processing protein 8 / 0.781
3t7s SAMUncharacterized protein / 0.779
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.777
2gs9 SAHUncharacterized protein / 0.777
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.777
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.776
4hh4 SAHCcbJ / 0.776
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.772
5epe SAHUncharacterized protein / 0.769
3fri SAH16S rRNA methylase / 0.768
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.766
3kkz SAMUncharacterized protein / 0.765
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.765
3t7t SAHUncharacterized protein / 0.761
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.761
1ri4 SAMmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.760
2p35 SAHTrans-aconitate 2-methyltransferase / 0.760
3e23 SAMUncharacterized protein / 0.760
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.759
5je3 SAHMethyl transferase / 0.758
3go4 SAHUncharacterized protein / 0.753
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.753
4yuz S4MSpermidine synthase, putative / 0.753
2qe6 SAMUncharacterized protein / 0.752
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.752
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.752
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.750
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.750
1kph SAHCyclopropane mycolic acid synthase 1 2.1.1.79 0.749
3vc1 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.749
5bp7 SAHSAM-dependent methyltransferase / 0.746
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.743
5jdz SAHMethyl transferase / 0.743
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.742
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.741
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.741
3t0i SAHPutative methyltransferase / 0.740
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.740
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.739
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.739
3p2e SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.738
3vc2 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.738
3bwc SAMSpermidine synthase, putative / 0.736
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.733
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.733
4c03 SFGProtein arginine N-methyltransferase 6 / 0.732
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.732
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.731
4rvd SAMD-mycarose 3-C-methyltransferase / 0.731
4kvz SAHPtnL protein / 0.728
4kwc SAHMethyltransferase domain family / 0.728
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.727
4pne SAHMethyltransferase-like protein / 0.724
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.723
3ssm SAHMycinamicin VI 2''-O-methyltransferase / 0.723
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.723
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.722
3gwz SAHMitomycin biosynthesis 6-O-methyltransferase / 0.720
3e8s SAHUncharacterized protein / 0.718
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.717
3mht SAHModification methylase HhaI 2.1.1.37 0.717
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.717
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.717
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.717
1wy7 SAHUncharacterized protein / 0.715
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.715
4yv2 S4MSpermidine synthase, putative / 0.715
5f2k SAHUncharacterized protein / 0.715
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.712
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.712
4qpp SAHProtein arginine N-methyltransferase 6 / 0.709
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.706
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.706
2i9k SAHModification methylase HhaI 2.1.1.37 0.705
3cbg SAHO-methyltransferase / 0.705
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.705
3tos SAHCalS11 / 0.705
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.705
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.704
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.704
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.704
3b5i SAHIndole-3-acetate O-methyltransferase 1 / 0.701
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.700
1nai NADUDP-glucose 4-epimerase 5.1.3.2 0.698
4yv0 S4MSpermidine synthase, putative / 0.698
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.698
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.697
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.697
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.697
3sxj SAMPutative methyltransferase / 0.696
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.696
4wec NADShort chain dehydrogenase / 0.696
1f3l SAHProtein arginine N-methyltransferase 3 / 0.695
2eg5 SAH7-methylxanthosine synthase 1 / 0.695
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.695
3gxo SAHMitomycin biosynthesis 6-O-methyltransferase / 0.695
3lst SAHCalO1 / 0.695
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.695
3c3y SAHO-methyltransferase / 0.694
4nec SAHPutative SAM-dependent methyltransferase / 0.694
4yv1 S4MSpermidine synthase, putative / 0.694
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.693
3ou6 SAMSAM-dependent methyltransferase / 0.693
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.693
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.692
3rw9 DSHSpermidine synthase 2.5.1.16 0.691
1kr5 SAHProtein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77 0.690
2o07 MTASpermidine synthase 2.5.1.16 0.690
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.690
3pb3 SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.690
1y9d FADPyruvate oxidase 1.2.3.3 0.689
5bxy SAHPutative RNA methylase family UPF0020 / 0.688
5f8f SFGPossible transcriptional regulatory protein / 0.687
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.686
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.686
2g1p SAHDNA adenine methylase 2.1.1.72 0.684
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.684
4gf5 SAHCalS11 / 0.683
4pyo SAHCatechol O-methyltransferase 2.1.1.6 0.683
2ji7 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.681
3ou2 SAHSAM-dependent methyltransferase / 0.681
1bdb NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase / 0.680
2v7g NADUrocanate hydratase 4.2.1.49 0.680
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.680
3fpf MTAUncharacterized protein / 0.680
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.679
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.678
4yac NAIC alpha-dehydrogenase / 0.678
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.677
1kia SAMGlycine N-methyltransferase 2.1.1.20 0.677
2hnk SAHSAM-dependent O-methyltransferase / 0.677
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.677
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.677
4g67 SAHUncharacterized ACR, COG1565 superfamily / 0.677
4lwp SAHArginine N-methyltransferase, putative / 0.677
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.676
2ytz SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.676
2zw9 SAMtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.676
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.674
1g1a NADdTDP-glucose 4,6-dehydratase / 0.673
1l3i SAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) / 0.673
4c04 SFGProtein arginine N-methyltransferase 6 / 0.673
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.672
3g8a SAHRibosomal RNA small subunit methyltransferase G / 0.672
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.671
1zmc NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.671
1fjx SAHModification methylase HhaI 2.1.1.37 0.669
10mh SAHModification methylase HhaI 2.1.1.37 0.668
1nbh SAMGlycine N-methyltransferase 2.1.1.20 0.668
3lby SAHUncharacterized protein / 0.668
3p9k SAHCaffeic acid O-methyltransferase / 0.667
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.666
1xdu SFGAclacinomycin 10-hydroxylase RdmB 4.1.1 0.666
2np6 NEAModification methylase TaqI 2.1.1.72 0.665
1jr4 CL4Catechol O-methyltransferase 2.1.1.6 0.664
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.663
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.662
2c7q SAHModification methylase HhaI 2.1.1.37 0.662
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.662
2z6u SAHModification methylase HhaI 2.1.1.37 0.662
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.662
2pan FADGlyoxylate carboligase 4.1.1.47 0.660
4rpg FADUDP-galactopyranose mutase 5.4.99.9 0.660
4c05 SAHProtein arginine N-methyltransferase 6 / 0.659
4em3 FADCoenzyme A disulfide reductase / 0.659
4qnu GEKtRNA U34 carboxymethyltransferase / 0.659
4b63 FADL-ornithine N(5)-monooxygenase / 0.658
4eqx FADCoenzyme A disulfide reductase / 0.657
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.656
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.656
4ek9 EP4Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.656
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.655
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.654
2pt6 S4MSpermidine synthase / 0.654
3dh0 SAMUncharacterized protein / 0.654
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.653
2uyh SAHModification methylase HhaI 2.1.1.37 0.651
3bus SAHDemethylrebeccamycin-D-glucose O-methyltransferase / 0.651
3grv ADNProbable ribosomal RNA small subunit methyltransferase A / 0.650
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.650
4g56 SAHProtein arginine N-methyltransferase 5 / 0.650