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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
4gqb 0XU Protein arginine N-methyltransferase 5

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4gqb 0XUProtein arginine N-methyltransferase 5 / 1.172
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.893
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.851
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.850
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.836
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.809
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.803
4c03 SFGProtein arginine N-methyltransferase 6 / 0.800
2qe6 SAMUncharacterized protein / 0.796
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.795
4hh4 SAHCcbJ / 0.788
5jdz SAHMethyl transferase / 0.786
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.783
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.779
3fri SAH16S rRNA methylase / 0.777
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.776
3t7s SAMUncharacterized protein / 0.775
2yqz SAMUncharacterized protein / 0.772
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.768
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.767
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.765
3gwz SAHMitomycin biosynthesis 6-O-methyltransferase / 0.762
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.762
5je3 SAHMethyl transferase / 0.761
4uy6 SAHHistidine N-alpha-methyltransferase / 0.759
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.756
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.755
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.754
3p9k SAHCaffeic acid O-methyltransferase / 0.751
2o06 MTASpermidine synthase 2.5.1.16 0.750
4a6d SAMAcetylserotonin O-methyltransferase 2.1.1.4 0.750
4kvz SAHPtnL protein / 0.750
1f3l SAHProtein arginine N-methyltransferase 3 / 0.745
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.745
2ji7 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.740
2ji6 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.739
5je4 SAHMethyl transferase / 0.734
2c31 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.733
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.732
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.731
2jib ADPOxalyl-CoA decarboxylase 4.1.1.8 0.729
3kkz SAMUncharacterized protein / 0.729
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.727
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.726
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.726
3ldg SAHUncharacterized protein / 0.726
4c04 SFGProtein arginine N-methyltransferase 6 / 0.726
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.726
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.725
3ou2 SAHSAM-dependent methyltransferase / 0.723
4yac NAIC alpha-dehydrogenase / 0.723
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.721
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.721
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.720
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.719
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.718
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.718
3lst SAHCalO1 / 0.718
3lcc SAHThiocyanate methyltransferase 1 / 0.717
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.717
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.715
4lwp SAHArginine N-methyltransferase, putative / 0.715
4rvd SAMD-mycarose 3-C-methyltransferase / 0.715
3t0i SAHPutative methyltransferase / 0.714
2gs9 SAHUncharacterized protein / 0.713
3bwc SAMSpermidine synthase, putative / 0.713
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.712
4pne SAHMethyltransferase-like protein / 0.712
2ih2 NEAModification methylase TaqI 2.1.1.72 0.711
3e23 SAMUncharacterized protein / 0.711
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.711
5f2k SAHUncharacterized protein / 0.711
1orh SAHProtein arginine N-methyltransferase 1 / 0.710
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.710
4e2x SAHMethyltransferase / 0.710
2rgh FADAlpha-Glycerophosphate Oxidase / 0.708
3gry SAMProbable ribosomal RNA small subunit methyltransferase A / 0.708
4qpp SAHProtein arginine N-methyltransferase 6 / 0.707
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.707
1kph SAHCyclopropane mycolic acid synthase 1 2.1.1.79 0.705
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.705
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.705
1nai NADUDP-glucose 4-epimerase 5.1.3.2 0.704
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.704
4nec SAHPutative SAM-dependent methyltransferase / 0.704
2o07 MTASpermidine synthase 2.5.1.16 0.703
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.703
5f8f SFGPossible transcriptional regulatory protein / 0.703
1wy7 SAHUncharacterized protein / 0.702
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.702
3t7t SAHUncharacterized protein / 0.702
3ua3 SAHProtein arginine N-methyltransferase 5 / 0.700
5bp9 SAHPutative methyltransferase protein / 0.700
3sxj SAMPutative methyltransferase / 0.699
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.699
1i2b NADUDP-sulfoquinovose synthase, chloroplastic 3.13.1.1 0.698
3ru9 NADUDP-N-acetylglucosamine 4-epimerase / 0.698
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.698
5bxy SAHPutative RNA methylase family UPF0020 / 0.698
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.698
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.697
3e8s SAHUncharacterized protein / 0.697
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.697
4yv2 S4MSpermidine synthase, putative / 0.697
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.696
2p35 SAHTrans-aconitate 2-methyltransferase / 0.695
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.694
4x3q SAHSibL / 0.694
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.693
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.693
3sgl SAMtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.692
1yf3 SAHDNA adenine methylase / 0.690
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.690
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.690
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.690
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.689
3hvi 619Catechol O-methyltransferase 2.1.1.6 0.688
3pb3 SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.688
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.688
3kkj FADRenalase / 0.687
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.686
3gxo SAHMitomycin biosynthesis 6-O-methyltransferase / 0.686
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.686
4wec NADShort chain dehydrogenase / 0.686
5je2 SAHMethyl transferase / 0.686
4fr0 SAMArsenic methyltransferase / 0.685
3gwf FADCyclohexanone monooxygenase / 0.684
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.684
1l3i SAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) / 0.683
3ruh NADUDP-N-acetylglucosamine 4-epimerase / 0.683
1khh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.680
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.678
2zfu SAHRibosomal RNA-processing protein 8 / 0.678
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.678
3c3y SAHO-methyltransferase / 0.678
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.677
3ruc NADUDP-N-acetylglucosamine 4-epimerase / 0.677
4yuz S4MSpermidine synthase, putative / 0.677
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.676
2fjb SFDAdenylylsulfate reductase, subunit A (AprA) / 0.676
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.676
4yuv S4MSpermidine synthase, putative / 0.676
3g8a SAHRibosomal RNA small subunit methyltransferase G / 0.675
1kr5 SAHProtein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77 0.674
1ori SAHProtein arginine N-methyltransferase 1 / 0.674
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.672
4qnv GEKtRNA U34 carboxymethyltransferase / 0.672
5bp7 SAHSAM-dependent methyltransferase / 0.672
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.671
4hb9 FADUncharacterized protein / 0.671
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.670
3ha5 SFGHydroxymycolate synthase MmaA4 2.1.1 0.670
2b69 NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.669
3nmu SAMFibrillarin-like rRNA/tRNA 2'-O-methyltransferase / 0.669
3cjt SAHRibosomal protein L11 methyltransferase 2.1.1 0.668
1x1b SAHC-20 methyltransferase / 0.667
2aot SAHHistamine N-methyltransferase 2.1.1.8 0.667
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.666
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.665
3ukf FDAUDP-galactopyranose mutase / 0.665
1g60 SAMModification methylase MboII 2.1.1.72 0.664
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.664
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.663
1aqi SAHModification methylase TaqI 2.1.1.72 0.663
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.663
4d04 FADPhenylacetone monooxygenase 1.14.13.92 0.663
5epe SAHUncharacterized protein / 0.663
3nwb 659Catechol O-methyltransferase 2.1.1.6 0.662
3ruf NADUDP-N-acetylglucosamine 4-epimerase / 0.662
1mht SAHModification methylase HhaI 2.1.1.37 0.661
1e1k FADNADPH:adrenodoxin oxidoreductase, mitochondrial 1.18.1.6 0.660
1ve3 SAMUncharacterized protein / 0.660
2plw SAMRibosomal RNA methyltransferase, putative / 0.660
5fm6 ADPRuvB-like helicase / 0.660
1v59 FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.659
1zk7 FADMercuric reductase 1.16.1.1 0.659
3vc1 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.659
1jr4 CL4Catechol O-methyltransferase 2.1.1.6 0.658
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.658
1y9d FADPyruvate oxidase 1.2.3.3 0.657
2fk8 SAMHydroxymycolate synthase MmaA4 2.1.1 0.657
3rfx NADUronate dehydrogenase / 0.657
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.656
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.656
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.656
3vyw SAMUncharacterized protein / 0.656
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.655
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.654
3vc2 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.654
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.653
2px5 SAHGenome polyprotein 2.7.7.48 0.653
3cbg SAHO-methyltransferase / 0.653
3gwd FADCyclohexanone monooxygenase / 0.653
5g3t FDAFlavin-dependent L-tryptophan oxidase VioA / 0.653
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.652
3fpf MTAUncharacterized protein / 0.652
2xvm SAHTellurite methyltransferase 2.1.1.265 0.651
4jq9 FADDihydrolipoyl dehydrogenase / 0.651
1boo SAHModification methylase PvuII 2.1.1.113 0.650
1nbh SAMGlycine N-methyltransferase 2.1.1.20 0.650
2qt0 NNRNicotinamide riboside kinase 1 / 0.650