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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
3a26 MTA tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.845
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.801
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.757
2yxl SFG450aa long hypothetical fmu protein / 0.739
1skm SAHModification methylase HhaI 2.1.1.37 0.733
2zif SAMMethyltransferase / 0.733
2ore SAHDNA adenine methylase 2.1.1.72 0.729
3mht SAHModification methylase HhaI 2.1.1.37 0.722
2c7q SAHModification methylase HhaI 2.1.1.37 0.721
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.721
4oa5 SAHO-methyltransferase family protein / 0.721
2i9k SAHModification methylase HhaI 2.1.1.37 0.719
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.717
3tm4 SAMUncharacterized protein / 0.717
3ldg SAHUncharacterized protein / 0.716
7mht SAHModification methylase HhaI 2.1.1.37 0.714
3ou2 SAHSAM-dependent methyltransferase / 0.712
1boo SAHModification methylase PvuII 2.1.1.113 0.711
4pyo SAHCatechol O-methyltransferase 2.1.1.6 0.709
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.708
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.707
1nw6 SFGModification methylase RsrI 2.1.1.72 0.706
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.706
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.706
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.704
4nec SAHPutative SAM-dependent methyltransferase / 0.704
2e1m FADL-glutamate oxidase / 0.703
2vou FAD2,6-dihydroxypyridine 3-monooxygenase 1.14.13.10 0.703
4c03 SFGProtein arginine N-methyltransferase 6 / 0.702
4c04 SFGProtein arginine N-methyltransferase 6 / 0.702
2uyh SAHModification methylase HhaI 2.1.1.37 0.701
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.701
2f8l SAMLmo1582 protein / 0.700
2ibt NEAModification methylase TaqI 2.1.1.72 0.699
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.699
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.699
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.698
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.698
3ou6 SAMSAM-dependent methyltransferase / 0.696
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.696
9mht SAHModification methylase HhaI 2.1.1.37 0.696
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.695
4mb2 ATPUncharacterized protein / 0.695
3grv ADNProbable ribosomal RNA small subunit methyltransferase A / 0.694
1ori SAHProtein arginine N-methyltransferase 1 / 0.693
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.692
2ih2 NEAModification methylase TaqI 2.1.1.72 0.691
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.691
3swr SFGDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.690
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.690
2g1p SAHDNA adenine methylase 2.1.1.72 0.689
2yqz SAMUncharacterized protein / 0.689
3ldf SAHUncharacterized protein / 0.689
1eg2 MTAModification methylase RsrI 2.1.1.72 0.688
3lcc SAHThiocyanate methyltransferase 1 / 0.688
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.688
5bp7 SAHSAM-dependent methyltransferase / 0.688
5epe SAHUncharacterized protein / 0.688
1tdo FADL-amino-acid oxidase 1.4.3.2 0.687
1reo FADL-amino-acid oxidase 1.4.3.2 0.686
2np6 NEAModification methylase TaqI 2.1.1.72 0.686
3duw SAHO-methyltransferase, putative / 0.686
1tdk FADL-amino-acid oxidase 1.4.3.2 0.685
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.685
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.684
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.684
1rp0 AHZThiamine thiazole synthase, chloroplastic / 0.683
2o06 MTASpermidine synthase 2.5.1.16 0.683
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.683
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.683
5je2 SAHMethyl transferase / 0.683
3cbg SAHO-methyltransferase / 0.682
4tm4 FDAKtzI / 0.682
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.681
2np7 NEAModification methylase TaqI 2.1.1.72 0.681
2rgh FADAlpha-Glycerophosphate Oxidase / 0.681
4rtk SAHDNA adenine methylase 2.1.1.72 0.681
2hms NAIKtr system potassium uptake protein A / 0.680
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.680
3iv6 SAMUncharacterized protein / 0.680
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.680
4eqx FADCoenzyme A disulfide reductase / 0.678
4kvz SAHPtnL protein / 0.677
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.677
2cdu ADPNADH oxidase / 0.676
3wdm ADN4-phosphopantoate--beta-alanine ligase 6.3.2.36 0.676
4egu 5GPPutative histidine triad (HIT) protein / 0.676
4em4 FADCoenzyme A disulfide reductase / 0.676
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.675
2oy0 SAHGenome polyprotein / 0.675
1yf3 SAHDNA adenine methylase / 0.673
2dki FAD3-hydroxybenzoate 4-monooxygenase 1.14.13.23 0.673
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.673
10mh SAHModification methylase HhaI 2.1.1.37 0.672
1g1a NADdTDP-glucose 4,6-dehydratase / 0.672
3lov FADProtoporphyrinogen oxidase / 0.672
3rw9 DSHSpermidine synthase 2.5.1.16 0.672
1e6e FADNADPH:adrenodoxin oxidoreductase, mitochondrial 1.18.1.6 0.671
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.671
1nw5 SAMModification methylase RsrI 2.1.1.72 0.671
2rgj FADFlavin-containing monooxygenase / 0.671
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.671
2hmv ADPKtr system potassium uptake protein A / 0.670
2z6u SAHModification methylase HhaI 2.1.1.37 0.670
3go4 SAHUncharacterized protein / 0.670
4g6h NAIRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial 1.6.5.9 0.670
1f8r FADL-amino-acid oxidase 1.4.3.2 0.669
1tdn FADL-amino-acid oxidase 1.4.3.2 0.669
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.669
1y56 FAD382aa long hypothetical sarcosine oxidase / 0.669
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.669
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.669
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.669
4c3y FAD3-ketosteroid dehydrogenase / 0.669
4qi4 FADCellobiose dehydrogenase / 0.669
1f8s FADL-amino-acid oxidase 1.4.3.2 0.668
1mxt FAECholesterol oxidase 1.1.3.6 0.668
1n4u FAECholesterol oxidase 1.1.3.6 0.668
3b6d FAECholesterol oxidase 1.1.3.6 0.668
3emd SFGMethyltransferase / 0.668
3kve FADL-amino-acid oxidase / 0.668
3p8z SAHGenome polyprotein 2.1.1.56 0.668
4b63 FADL-ornithine N(5)-monooxygenase / 0.668
1n1p FADCholesterol oxidase 1.1.3.6 0.667
1n4v FADCholesterol oxidase 1.1.3.6 0.667
1n4w FADCholesterol oxidase 1.1.3.6 0.667
2gew FADCholesterol oxidase 1.1.3.6 0.667
3alm FAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase / 0.667
3cnj FADCholesterol oxidase 1.1.3.6 0.667
3gyi FADCholesterol oxidase 1.1.3.6 0.667
3gyj FADCholesterol oxidase 1.1.3.6 0.667
3n1s 5GPPurine nucleoside phosphoramidase / 0.667
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.667
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.667
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.667
4hh4 SAHCcbJ / 0.667
4xwr FADCholesterol oxidase 1.1.3.6 0.667
4xxg FADCholesterol oxidase 1.1.3.6 0.667
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.667
1b8s FADCholesterol oxidase 1.1.3.6 0.666
2qe6 SAMUncharacterized protein / 0.666
3bwc SAMSpermidine synthase, putative / 0.666
4u2t FADCholesterol oxidase 1.1.3.6 0.666
4gbe SAHDNA adenine methylase 2.1.1.72 0.665
4guv FADTetX family tetracycline inactivation enzyme / 0.665
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.665
5bp9 SAHPutative methyltransferase protein / 0.665
2ih5 NEAModification methylase TaqI 2.1.1.72 0.664
2o07 MTASpermidine synthase 2.5.1.16 0.664
2pxa SAHGenome polyprotein 2.7.7.48 0.663
4tlx FDAKtzI / 0.663
1jnz FADAdenylylsulfate reductase, subunit A (AprA) / 0.662
1v59 NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.662
2g82 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.662
2gs9 SAHUncharacterized protein / 0.662
3fpz AHZThiamine thiazole synthase / 0.662
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.662
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.661
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.661
3hvk 719Catechol O-methyltransferase 2.1.1.6 0.661
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.661
4blv SAMRibosomal RNA large subunit methyltransferase J / 0.661
1fjx SAHModification methylase HhaI 2.1.1.37 0.660
1g60 SAMModification methylase MboII 2.1.1.72 0.660
1ptj SNDNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.660
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.660
2plw SAMRibosomal RNA methyltransferase, putative / 0.660
2pzj NADPutative nucleotide sugar epimerase/ dehydratase / 0.660
4yuz S4MSpermidine synthase, putative / 0.660
2bra FAD[F-actin]-methionine sulfoxide oxidase MICAL1 1.14.13 0.658
2q1t NADPutative nucleotide sugar epimerase/ dehydratase / 0.658
3lkz SFGGenome polyprotein / 0.658
4a99 FADTetX family tetracycline inactivation enzyme / 0.658
4eqg A5AHistidine triad nucleotide-binding protein 1 3 0.658
4fn4 NADShort chain dehydrogenase / 0.658
4k5r FADOxygenase / 0.658
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.657
4c05 SAHProtein arginine N-methyltransferase 6 / 0.657
4eqe KAAHistidine triad nucleotide-binding protein 1 3 0.657
4xcx SAHSmall RNA 2'-O-methyltransferase / 0.657
1zmc NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.656
5bv3 M7Gm7GpppX diphosphatase 3.6.1.59 0.656
8mht SAHModification methylase HhaI 2.1.1.37 0.656
2b9y FADPutative aminooxidase / 0.655
2bac FADPutative aminooxidase / 0.655
2p35 SAHTrans-aconitate 2-methyltransferase / 0.655
3gdp FAD(R)-mandelonitrile lyase 2 4.1.2.10 0.655
3nmu SAMFibrillarin-like rRNA/tRNA 2'-O-methyltransferase / 0.655
4ctk SAMGenome polyprotein / 0.655
4u2l SFDCholesterol oxidase 1.1.3.6 0.655
1cbo FADCholesterol oxidase 1.1.3.6 0.654
1cc2 FADCholesterol oxidase 1.1.3.6 0.654
4b66 FADL-ornithine N(5)-monooxygenase / 0.654
5eow FAD6-hydroxynicotinate 3-monooxygenase 1.14.13.114 0.653
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.652
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.652
3lga SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.652
4htf SAMtRNA 5-carboxymethoxyuridine methyltransferase / 0.652
4rtj SFGDNA adenine methylase 2.1.1.72 0.652
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.652
2ep7 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.651
3ou7 SAMSAM-dependent methyltransferase / 0.651
4rek FADCholesterol oxidase 1.1.3.6 0.651
1e1m FADNADPH:adrenodoxin oxidoreductase, mitochondrial 1.18.1.6 0.650
3qgz ADNHistidine triad nucleotide-binding protein 1 3 0.650
3tlj SAHUncharacterized protein / 0.650
4xba 5GPAprataxin-like protein 3 0.650