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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
4kvz SAH PtnL protein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4kvz SAHPtnL protein / 0.972
4kwc SAHMethyltransferase domain family / 0.825
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.801
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.784
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.760
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.754
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.750
5je2 SAHMethyl transferase / 0.747
3go4 SAHUncharacterized protein / 0.745
3kkz SAMUncharacterized protein / 0.744
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.742
1ve3 SAMUncharacterized protein / 0.741
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.740
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.739
3p2e SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.734
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.734
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.732
3bwc SAMSpermidine synthase, putative / 0.730
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.730
2gs9 SAHUncharacterized protein / 0.729
1nbh SAMGlycine N-methyltransferase 2.1.1.20 0.728
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.728
3ou2 SAHSAM-dependent methyltransferase / 0.728
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.728
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.728
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.727
5epe SAHUncharacterized protein / 0.725
5bxy SAHPutative RNA methylase family UPF0020 / 0.724
3ssm SAHMycinamicin VI 2''-O-methyltransferase / 0.723
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.722
3pb3 SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.722
4hh4 SAHCcbJ / 0.720
1yf3 SAHDNA adenine methylase / 0.719
3t7s SAMUncharacterized protein / 0.719
3cbg SAHO-methyltransferase / 0.715
3t7t SAHUncharacterized protein / 0.714
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.713
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.711
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.711
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.711
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.708
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.705
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.704
1skm SAHModification methylase HhaI 2.1.1.37 0.704
2hnk SAHSAM-dependent O-methyltransferase / 0.702
3vc1 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.702
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.701
4uy6 SAHHistidine N-alpha-methyltransferase / 0.701
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.700
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.700
1kr5 SAHProtein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77 0.699
1y9d FADPyruvate oxidase 1.2.3.3 0.698
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.698
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.697
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.697
3ldg SAHUncharacterized protein / 0.697
5f8f SFGPossible transcriptional regulatory protein / 0.697
2pan FADGlyoxylate carboligase 4.1.1.47 0.696
2xvm SAHTellurite methyltransferase 2.1.1.265 0.695
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.695
4qnu GEKtRNA U34 carboxymethyltransferase / 0.694
1d2h SAHGlycine N-methyltransferase 2.1.1.20 0.693
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.693
3e8s SAHUncharacterized protein / 0.693
3lst SAHCalO1 / 0.693
3nn6 FB06-hydroxy-L-nicotine oxidase / 0.692
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.692
4yv2 S4MSpermidine synthase, putative / 0.692
4dmg SAMUncharacterized protein / 0.691
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.691
4rvd SAMD-mycarose 3-C-methyltransferase / 0.691
1l3i SAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) / 0.690
2z6u SAHModification methylase HhaI 2.1.1.37 0.690
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.689
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.689
5bp7 SAHSAM-dependent methyltransferase / 0.688
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.688
2g1p SAHDNA adenine methylase 2.1.1.72 0.687
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.686
2np6 NEAModification methylase TaqI 2.1.1.72 0.686
3vc2 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.686
1zmc NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.684
5bp9 SAHPutative methyltransferase protein / 0.684
3dh0 SAMUncharacterized protein / 0.683
3fri SAH16S rRNA methylase / 0.683
3i53 SAH2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase / 0.683
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.683
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.683
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.682
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.682
3c3y SAHO-methyltransferase / 0.681
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.681
3nmu SAMFibrillarin-like rRNA/tRNA 2'-O-methyltransferase / 0.680
3grv ADNProbable ribosomal RNA small subunit methyltransferase A / 0.679
3gwz SAHMitomycin biosynthesis 6-O-methyltransferase / 0.679
3gxo SAHMitomycin biosynthesis 6-O-methyltransferase / 0.679
3tos SAHCalS11 / 0.679
4gf5 SAHCalS11 / 0.679
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.679
1wy7 SAHUncharacterized protein / 0.678
4yac NAIC alpha-dehydrogenase / 0.678
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.678
1khh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.677
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.677
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.677
2q28 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.676
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.675
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.675
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.674
1f3l SAHProtein arginine N-methyltransferase 3 / 0.672
1xwf ADNAdenosylhomocysteinase 3.3.1.1 0.672
4obw SAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial / 0.672
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.672
2uyh SAHModification methylase HhaI 2.1.1.37 0.671
3tr6 SAHO-methyltransferase / 0.671
1xdu SFGAclacinomycin 10-hydroxylase RdmB 4.1.1 0.670
2c7q SAHModification methylase HhaI 2.1.1.37 0.670
4qnv GEKtRNA U34 carboxymethyltransferase / 0.670
4rtk SAHDNA adenine methylase 2.1.1.72 0.670
1nv8 SAMRelease factor glutamine methyltransferase 2.1.1.297 0.669
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.669
2zcj SAHModification methylase HhaI 2.1.1.37 0.669
3p9k SAHCaffeic acid O-methyltransferase / 0.669
4a6d SAMAcetylserotonin O-methyltransferase 2.1.1.4 0.669
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.669
1eg2 MTAModification methylase RsrI 2.1.1.72 0.668
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.668
2ji7 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.668
3t0i SAHPutative methyltransferase / 0.668
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.668
5f2k SAHUncharacterized protein / 0.668
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.667
2i9k SAHModification methylase HhaI 2.1.1.37 0.667
2ji6 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.667
2p35 SAHTrans-aconitate 2-methyltransferase / 0.667
2wsb NADGalactitol dehydrogenase / 0.667
3sxj SAMPutative methyltransferase / 0.667
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.667
3ak4 NADNADH-dependent quinuclidinone reductase / 0.666
3fpf MTAUncharacterized protein / 0.666
3mht SAHModification methylase HhaI 2.1.1.37 0.666
3nug NADPyridoxal 4-dehydrogenase 1.1.1.107 0.666
1bdb NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase / 0.665
2c31 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.665
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.665
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.664
2jib ADPOxalyl-CoA decarboxylase 4.1.1.8 0.664
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.663
4eqr FADCoenzyme A disulfide reductase / 0.662
4yuz S4MSpermidine synthase, putative / 0.662
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.662
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.661
1ri4 SAMmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.661
3pt6 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.661
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.661
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.661
1uay ADNOxidoreductase / 0.660
3kh5 ADPUncharacterized protein MJ1225 / 0.660
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.659
3cjt SAHRibosomal protein L11 methyltransferase 2.1.1 0.659
3s5w FADL-ornithine N(5)-monooxygenase / 0.659
3uth FDAUDP-galactopyranose mutase / 0.659
4nec SAHPutative SAM-dependent methyltransferase / 0.659
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.659
1nbi SAMGlycine N-methyltransferase 2.1.1.20 0.658
2zfu SAHRibosomal RNA-processing protein 8 / 0.658
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.657
4eqw FADCoenzyme A disulfide reductase / 0.657
4lis NADUDP-glucose 4-epimerase (Eurofung) / 0.657
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.656
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.656
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.656
3tm4 SAMUncharacterized protein / 0.656
4dkj SAHCytosine-specific methyltransferase / 0.656
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.654
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.653
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.653
4gh5 NADShort-chain dehydrogenase/reductase SDR / 0.653
4c04 SFGProtein arginine N-methyltransferase 6 / 0.652
5fa8 SAMRibosomal protein L11 methyltransferase, putative / 0.652
1ori SAHProtein arginine N-methyltransferase 1 / 0.651
2vvl FADMonoamine oxidase N 1.4.3.4 0.651
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.651
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.650
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.650