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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
5fa5 MTA Protein arginine N-methyltransferase 5

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
5fa5 MTAProtein arginine N-methyltransferase 5 / 1.010
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.893
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.789
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.778
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.772
2qe6 SAMUncharacterized protein / 0.771
3rw9 DSHSpermidine synthase 2.5.1.16 0.771
3ou6 SAMSAM-dependent methyltransferase / 0.767
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.758
2q28 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.756
4lwp SAHArginine N-methyltransferase, putative / 0.756
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.755
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.755
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.751
4g56 SAHProtein arginine N-methyltransferase 5 / 0.751
1f3l SAHProtein arginine N-methyltransferase 3 / 0.750
3lcc SAHThiocyanate methyltransferase 1 / 0.749
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.747
2ji7 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.745
4uy6 SAHHistidine N-alpha-methyltransferase / 0.745
2c31 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.742
2ji6 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.741
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.741
2jib ADPOxalyl-CoA decarboxylase 4.1.1.8 0.740
3ou2 SAHSAM-dependent methyltransferase / 0.739
2o06 MTASpermidine synthase 2.5.1.16 0.738
3tos SAHCalS11 / 0.736
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.736
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.735
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.734
4a6d SAMAcetylserotonin O-methyltransferase 2.1.1.4 0.729
4nec SAHPutative SAM-dependent methyltransferase / 0.728
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.728
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.727
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.724
1y9d FADPyruvate oxidase 1.2.3.3 0.723
2o07 MTASpermidine synthase 2.5.1.16 0.723
3e8s SAHUncharacterized protein / 0.722
3bwc SAMSpermidine synthase, putative / 0.720
4yac NAIC alpha-dehydrogenase / 0.720
1nai NADUDP-glucose 4-epimerase 5.1.3.2 0.719
2pan FADGlyoxylate carboligase 4.1.1.47 0.719
4c03 SFGProtein arginine N-methyltransferase 6 / 0.719
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.718
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.715
1nbi SAMGlycine N-methyltransferase 2.1.1.20 0.714
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.714
1ori SAHProtein arginine N-methyltransferase 1 / 0.712
2yg4 FADPutrescine oxidase / 0.712
1wy7 SAHUncharacterized protein / 0.708
3p9k SAHCaffeic acid O-methyltransferase / 0.708
5epe SAHUncharacterized protein / 0.708
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.705
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.705
1eg2 MTAModification methylase RsrI 2.1.1.72 0.704
3grv ADNProbable ribosomal RNA small subunit methyltransferase A / 0.704
3hvi 619Catechol O-methyltransferase 2.1.1.6 0.704
4gf5 SAHCalS11 / 0.704
4yv2 S4MSpermidine synthase, putative / 0.702
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.702
3ua3 SAHProtein arginine N-methyltransferase 5 / 0.701
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.699
1khh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.698
4tm1 FDAKtzI / 0.698
2gs9 SAHUncharacterized protein / 0.697
2hnk SAHSAM-dependent O-methyltransferase / 0.697
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.697
3lby SAHUncharacterized protein / 0.697
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.697
1l3i SAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) / 0.696
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.696
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.695
1ryi FADGlycine oxidase 1.4.3.19 0.694
4ce0 SAHProbable O-methyltransferase / 0.692
4c04 SFGProtein arginine N-methyltransferase 6 / 0.691
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.691
3c3y SAHO-methyltransferase / 0.690
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.690
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.690
1orr NADCDP-paratose 2-epimerase / 0.689
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.688
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.688
2yr5 FADPhenylalanine 2-monooxygenase precursor 1.13.12.9 0.686
3ru9 NADUDP-N-acetylglucosamine 4-epimerase / 0.685
3ruh NADUDP-N-acetylglucosamine 4-epimerase / 0.685
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.685
4tlx FDAKtzI / 0.685
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.684
2yg7 FADPutrescine oxidase / 0.684
4oa5 SAHO-methyltransferase family protein / 0.684
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.683
1yqz FADCoenzyme A disulfide reductase / 0.683
3fpf MTAUncharacterized protein / 0.683
5eow FAD6-hydroxynicotinate 3-monooxygenase 1.14.13.114 0.683
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.682
4tm4 FDAKtzI / 0.682
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.681
4nzh FADL-ornithine N(5)-monooxygenase / 0.681
1y56 FAD382aa long hypothetical sarcosine oxidase / 0.679
3nn6 FB06-hydroxy-L-nicotine oxidase / 0.679
4qpp SAHProtein arginine N-methyltransferase 6 / 0.679
1skm SAHModification methylase HhaI 2.1.1.37 0.678
3nmu SAMFibrillarin-like rRNA/tRNA 2'-O-methyltransferase / 0.678
4b63 FADL-ornithine N(5)-monooxygenase / 0.678
5je2 SAHMethyl transferase / 0.678
1orh SAHProtein arginine N-methyltransferase 1 / 0.677
2i0z FADNAD(FAD)-utilizing dehydrogenases / 0.677
3iv6 SAMUncharacterized protein / 0.677
1e1m FADNADPH:adrenodoxin oxidoreductase, mitochondrial 1.18.1.6 0.676
3gry SAMProbable ribosomal RNA small subunit methyltransferase A / 0.675
4ek9 EP4Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.675
7mht SAHModification methylase HhaI 2.1.1.37 0.675
4pne SAHMethyltransferase-like protein / 0.674
3cjt SAHRibosomal protein L11 methyltransferase 2.1.1 0.673
3duw SAHO-methyltransferase, putative / 0.673
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.672
2fjb SFDAdenylylsulfate reductase, subunit A (AprA) / 0.672
2jb2 FADL-amino acid oxidase / 0.672
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.672
4eqg A5AHistidine triad nucleotide-binding protein 1 3 0.672
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.672
1ju2 FAD(R)-mandelonitrile lyase 2 4.1.2.10 0.671
2yqz SAMUncharacterized protein / 0.671
2zfu SAHRibosomal RNA-processing protein 8 / 0.671
3gdp FAD(R)-mandelonitrile lyase 2 4.1.2.10 0.671
2ih2 NEAModification methylase TaqI 2.1.1.72 0.670
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.670
4eqe KAAHistidine triad nucleotide-binding protein 1 3 0.670
4yxd FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.670
2i9k SAHModification methylase HhaI 2.1.1.37 0.669
4b69 FADL-ornithine N(5)-monooxygenase / 0.669
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.668
1kph SAHCyclopropane mycolic acid synthase 1 2.1.1.79 0.668
3qvw NADMyo-inositol-1-phosphate synthase (Ino1) / 0.668
3rfx NADUronate dehydrogenase / 0.668
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.668
3wv7 ADPHmd co-occurring protein HcgE / 0.667
4gc9 SAMDimethyladenosine transferase 1, mitochondrial 2.1.1 0.667
5fa8 SAMRibosomal protein L11 methyltransferase, putative / 0.667
3cbg SAHO-methyltransferase / 0.666
3kkz SAMUncharacterized protein / 0.666
4qnv GEKtRNA U34 carboxymethyltransferase / 0.666
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.665
1v59 NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.665
1zmc NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.664
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.664
4xxg FADCholesterol oxidase 1.1.3.6 0.664
2gew FADCholesterol oxidase 1.1.3.6 0.663
4bjz FADProbable salicylate monooxygenase / 0.663
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.663
4icy FADPgaE / 0.663
2xve FADPutative flavin-containing monooxygenase / 0.662
4kvz SAHPtnL protein / 0.662
4nbu NAI3-oxoacyl-(Acyl-carrier-protein) reductase / 0.662
1gal FADGlucose oxidase 1.1.3.4 0.661
1ptj SNDNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.661
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.661
3lhd SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.661
1jr4 CL4Catechol O-methyltransferase 2.1.1.6 0.660
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.660
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.660
4u2t FADCholesterol oxidase 1.1.3.6 0.659
2bm9 SAMCephalosporin hydroxylase CmcI / 0.658
2f5z FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.658
2jb1 FADL-amino acid oxidase / 0.658
3gwd FADCyclohexanone monooxygenase / 0.658
4u2l SFDCholesterol oxidase 1.1.3.6 0.658
1nbh SAMGlycine N-methyltransferase 2.1.1.20 0.657
4opd FDAConserved Archaeal protein / 0.657
3e23 SAMUncharacterized protein / 0.656
3p2e SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.656
3q2k NAIProbable oxidoreductase / 0.656
3q60 ATPRhoptry protein 5B / 0.656
3uov FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase 1.14.13.160 0.656
4mok FADPyranose 2-oxidase / 0.656
2c7g FADNADPH-ferredoxin reductase FprA 1.18.1.2 0.655
3b6d FAECholesterol oxidase 1.1.3.6 0.655
3ihg FADAklavinone 12-hydroxylase RdmE / 0.655
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.655
10mh SAHModification methylase HhaI 2.1.1.37 0.654
2c4c FAD[F-actin]-methionine sulfoxide oxidase MICAL1 1.14.13 0.654
3cjq SAHRibosomal protein L11 methyltransferase 2.1.1 0.654
4x9n FADUncharacterized protein MG039 homolog / 0.654
1kia SAMGlycine N-methyltransferase 2.1.1.20 0.653
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.653
4at0 FADPossible succinate dehydrogenase / 0.653
4c05 SAHProtein arginine N-methyltransferase 6 / 0.653
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.652
2eq7 NADDihydrolipoyl dehydrogenase / 0.652
3atq FDAConserved Archaeal protein / 0.652
3o9z NADLipopolysaccaride biosynthesis protein wbpB / 0.652
4fwj FADLysine-specific histone demethylase 1B 1 0.652
4m37 SAHProtein arginine N-methyltransferase 7 2.1.1 0.652
4tlz FADKtzI / 0.652
1nfr NAD3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase 1.1.1.53 0.651
1y56 ATPUncharacterized protein / 0.651
3g8a SAHRibosomal RNA small subunit methyltransferase G / 0.651
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.651
3uox FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase 1.14.13.160 0.651
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.651
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.650
2qt0 NNRNicotinamide riboside kinase 1 / 0.650
4nbw NADShort-chain dehydrogenase/reductase SDR / 0.650