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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
2o06 MTA Spermidine synthase 2.5.1.16

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity
Align
2o06 MTASpermidine synthase 2.5.1.16 0.900
2o07 MTASpermidine synthase 2.5.1.16 0.847
2pt6 S4MSpermidine synthase / 0.800
4yv2 S4MSpermidine synthase, putative / 0.793
3rw9 DSHSpermidine synthase 2.5.1.16 0.789
4yv1 S4MSpermidine synthase, putative / 0.779
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.751
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.750
3go4 SAHUncharacterized protein / 0.739
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.738
5je2 SAHMethyl transferase / 0.735
2ibt NEAModification methylase TaqI 2.1.1.72 0.729
2q28 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.729
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.728
3grv ADNProbable ribosomal RNA small subunit methyltransferase A / 0.728
1nah NADUDP-glucose 4-epimerase 5.1.3.2 0.726
3bwc SAMSpermidine synthase, putative / 0.726
3tsc NADUncharacterized protein / 0.726
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.724
4yuv S4MSpermidine synthase, putative / 0.724
2np7 NEAModification methylase TaqI 2.1.1.72 0.723
5je4 SAHMethyl transferase / 0.720
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.718
5jdz SAHMethyl transferase / 0.718
5je3 SAHMethyl transferase / 0.718
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.716
3mht SAHModification methylase HhaI 2.1.1.37 0.716
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.714
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.713
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.713
3ea4 FABAcetolactate synthase, chloroplastic 2.2.1.6 0.713
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.713
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.712
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.711
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.709
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.709
2hun NAD336aa long hypothetical dTDP-glucose 4,6-dehydratase / 0.708
3fpf MTAUncharacterized protein / 0.708
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.708
3pgx NADUncharacterized NAD-dependent oxidoreductase MAP_4146 / 0.708
1bdb NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase / 0.707
2g1p SAHDNA adenine methylase 2.1.1.72 0.707
2q1u NADPutative nucleotide sugar epimerase/ dehydratase / 0.707
4c03 SFGProtein arginine N-methyltransferase 6 / 0.707
4yv0 S4MSpermidine synthase, putative / 0.706
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.705
3s55 NADPutative short-chain dehydrogenase/reductase / 0.705
2hmv ADPKtr system potassium uptake protein A / 0.704
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.704
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.703
4tm4 FDAKtzI / 0.702
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.701
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.701
5eow FAD6-hydroxynicotinate 3-monooxygenase 1.14.13.114 0.701
1y9d FADPyruvate oxidase 1.2.3.3 0.700
2pzj NADPutative nucleotide sugar epimerase/ dehydratase / 0.700
3ko8 NADNAD-dependent epimerase/dehydratase / 0.700
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.700
4tlz FADKtzI / 0.700
3icp NADNAD-dependent epimerase/dehydratase / 0.699
1rp0 AHZThiamine thiazole synthase, chloroplastic / 0.698
4gbe SAHDNA adenine methylase 2.1.1.72 0.697
1g1a NADdTDP-glucose 4,6-dehydratase / 0.696
1zq9 SAMProbable dimethyladenosine transferase / 0.696
2ih5 NEAModification methylase TaqI 2.1.1.72 0.696
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.694
2ih2 NEAModification methylase TaqI 2.1.1.72 0.694
2q1t NADPutative nucleotide sugar epimerase/ dehydratase / 0.694
2q1w NADPutative nucleotide sugar epimerase/ dehydratase / 0.694
3lcc SAHThiocyanate methyltransferase 1 / 0.694
1kr5 SAHProtein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77 0.693
5cku FADL-ornithine N(5)-monooxygenase / 0.693
2qe6 SAMUncharacterized protein / 0.692
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.692
3ru9 NADUDP-N-acetylglucosamine 4-epimerase / 0.692
3sx2 NADUncharacterized protein / 0.692
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.692
2q1s NAIPutative nucleotide sugar epimerase/ dehydratase / 0.691
3ruf NADUDP-N-acetylglucosamine 4-epimerase / 0.691
3tm4 SAMUncharacterized protein / 0.691
7mht SAHModification methylase HhaI 2.1.1.37 0.691
2fkn NADUrocanate hydratase 4.2.1.49 0.690
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.690
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.690
4twr NADNAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase / 0.690
4poo SAMPutative RNA methylase / 0.689
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.689
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.688
2z6u SAHModification methylase HhaI 2.1.1.37 0.688
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.688
2ji6 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.687
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.687
4nzh FADL-ornithine N(5)-monooxygenase / 0.687
4yuz S4MSpermidine synthase, putative / 0.687
1boo SAHModification methylase PvuII 2.1.1.113 0.686
1skm SAHModification methylase HhaI 2.1.1.37 0.686
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.686
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.686
2c7g FADNADPH-ferredoxin reductase FprA 1.18.1.2 0.685
4yac NAIC alpha-dehydrogenase / 0.685
1zx9 FADMercuric reductase 1.16.1.1 0.684
4rtk SAHDNA adenine methylase 2.1.1.72 0.684
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.684
1ryi FADGlycine oxidase 1.4.3.19 0.683
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.683
3cox FADCholesterol oxidase 1.1.3.6 0.683
4obw SAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial / 0.683
4kwc SAHMethyltransferase domain family / 0.682
1lqu FADNADPH-ferredoxin reductase FprA 1.18.1.2 0.681
3e9y FABAcetolactate synthase, chloroplastic 2.2.1.6 0.681
5g3t FDAFlavin-dependent L-tryptophan oxidase VioA / 0.681
4b65 FADL-ornithine N(5)-monooxygenase / 0.680
1p1h NADInositol-3-phosphate synthase 5.5.1.4 0.679
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.679
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.679
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.679
1d2h SAHGlycine N-methyltransferase 2.1.1.20 0.678
1nw6 SFGModification methylase RsrI 2.1.1.72 0.678
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.678
2uxx FAJLysine-specific histone demethylase 1A 1 0.678
4b69 FADL-ornithine N(5)-monooxygenase / 0.678
5hxw FADL-amino acid deaminase / 0.678
1nbi SAMGlycine N-methyltransferase 2.1.1.20 0.677
3ka7 FADPutative oxidoreductase / 0.677
3lby SAHUncharacterized protein / 0.677
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.677
2b69 NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.676
2c20 NADUDP-glucose 4-epimerase / 0.676
2i9k SAHModification methylase HhaI 2.1.1.37 0.676
3oe4 610Catechol O-methyltransferase 2.1.1.6 0.676
5g3s FDAFlavin-dependent L-tryptophan oxidase VioA / 0.676
1g60 SAMModification methylase MboII 2.1.1.72 0.675
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.675
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.675
2wsb NADGalactitol dehydrogenase / 0.675
1g38 NEAModification methylase TaqI 2.1.1.72 0.674
2jb2 FADL-amino acid oxidase / 0.674
3ruh NADUDP-N-acetylglucosamine 4-epimerase / 0.674
4tm3 FADKtzI / 0.674
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.673
3sgl SAMtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.673
1f3l SAHProtein arginine N-methyltransferase 3 / 0.672
1i2b NADUDP-sulfoquinovose synthase, chloroplastic 3.13.1.1 0.672
2bry FAD[F-actin]-methionine sulfoxide oxidase MICAL1 1.14.13 0.672
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.672
3ruc NADUDP-N-acetylglucosamine 4-epimerase / 0.672
4rtq SAHDNA adenine methylase 2.1.1.72 0.672
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.672
1p1i NADInositol-3-phosphate synthase 5.5.1.4 0.671
2c31 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.671
3gyj FADCholesterol oxidase 1.1.3.6 0.671
4uy6 SAHHistidine N-alpha-methyltransferase / 0.671
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.671
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.670
3kkj FADRenalase / 0.670
4gll NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.670
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.669
5eku SAHArginine N-methyltransferase, putative / 0.669
1uay ADNOxidoreductase / 0.668
2ji7 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.668
3ldg SAHUncharacterized protein / 0.668
3lu1 NADUDP-N-acetylglucosamine 4-epimerase / 0.668
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.668
1e6w NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.667
1n4v FADCholesterol oxidase 1.1.3.6 0.667
1n4w FADCholesterol oxidase 1.1.3.6 0.667
2vou FAD2,6-dihydroxypyridine 3-monooxygenase 1.14.13.10 0.667
4guv FADTetX family tetracycline inactivation enzyme / 0.667
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.667
4rek FADCholesterol oxidase 1.1.3.6 0.667
5bxy SAHPutative RNA methylase family UPF0020 / 0.667
1eg2 MTAModification methylase RsrI 2.1.1.72 0.666
1wy7 SAHUncharacterized protein / 0.666
2jib ADPOxalyl-CoA decarboxylase 4.1.1.8 0.666
3nn6 FB06-hydroxy-L-nicotine oxidase / 0.666
4eqs FADCoenzyme A disulfide reductase / 0.666
1yqz FADCoenzyme A disulfide reductase / 0.665
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.665
2v7g NADUrocanate hydratase 4.2.1.49 0.665
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.665
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.665
4qpp SAHProtein arginine N-methyltransferase 6 / 0.665
2yqz SAMUncharacterized protein / 0.664
2igo FADPyranose 2-oxidase / 0.663
3c3y SAHO-methyltransferase / 0.663
3lga SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.663
3tos SAHCalS11 / 0.663
2qa2 FADPolyketide oxygenase CabE / 0.662
3kkz SAMUncharacterized protein / 0.662
3lhd SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.662
3lsi FADPyranose 2-oxidase / 0.662
4u8k FDAUDP-galactopyranose mutase / 0.662
2yg3 FADPutrescine oxidase / 0.661
2yg7 FADPutrescine oxidase / 0.661
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.661
3nlc FADUncharacterized protein / 0.661
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.661
4htf SAMtRNA 5-carboxymethoxyuridine methyltransferase / 0.661
4nbu NAI3-oxoacyl-(Acyl-carrier-protein) reductase / 0.661
9mht SAHModification methylase HhaI 2.1.1.37 0.661
2f5z FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.660
2gdz NAD15-hydroxyprostaglandin dehydrogenase [NAD(+)] 1.1.1.141 0.660
3k30 ADPHistamine dehydrogenase / 0.660
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.660
1ve3 SAMUncharacterized protein / 0.659
2aot SAHHistamine N-methyltransferase 2.1.1.8 0.659
3cmc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.659
3eey SAMrRNA methylase / 0.659
3ou2 SAHSAM-dependent methyltransferase / 0.659
3ou6 SAMSAM-dependent methyltransferase / 0.659
3p9u FADTetX family tetracycline inactivation enzyme / 0.659
4dmg SAMUncharacterized protein / 0.659
1nai NADUDP-glucose 4-epimerase 5.1.3.2 0.658
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.658
4bjz FADProbable salicylate monooxygenase / 0.658
4gde FDAUDP-galactopyranose mutase / 0.658
4mok FADPyranose 2-oxidase / 0.658
5f8f SFGPossible transcriptional regulatory protein / 0.658
2oy0 SAHGenome polyprotein / 0.657
2rgj FADFlavin-containing monooxygenase / 0.657
2vyn NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.657
2zcj SAHModification methylase HhaI 2.1.1.37 0.657
3alm FAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase / 0.657
3nug NADPyridoxal 4-dehydrogenase 1.1.1.107 0.657
3uth FDAUDP-galactopyranose mutase / 0.657
3wdm ADN4-phosphopantoate--beta-alanine ligase 6.3.2.36 0.657
3we0 FADLysine 2-monooxygenase / 0.657
1aqi SAHModification methylase TaqI 2.1.1.72 0.656
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.656
2px2 SAHGenome polyprotein 2.7.7.48 0.656
2vqb FADPutative flavin-containing monooxygenase / 0.656
3lkz SFGGenome polyprotein / 0.656
3qv1 NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.656
3sxp NADADP-L-glycero-D-mannoheptose-6-epimerase / 0.656
3utf FDAUDP-galactopyranose mutase / 0.656
5jjr SAHGenome polyprotein / 0.656
10mh SAHModification methylase HhaI 2.1.1.37 0.655
1pdh FASp-hydroxybenzoate hydroxylase / 0.655
3alj FAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase / 0.655
5i39 FADL-amino acid deaminase / 0.655
1tdo FADL-amino-acid oxidase 1.4.3.2 0.654
2yg4 FADPutrescine oxidase / 0.654
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.654
3all FAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase / 0.654
4k2x FADPolyketide oxygenase/hydroxylase / 0.654
4l7v SAHProtein-L-isoaspartate O-methyltransferase / 0.654
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.654
1kvr NADUDP-glucose 4-epimerase 5.1.3.2 0.653
1mht SAHModification methylase HhaI 2.1.1.37 0.653
3pl8 FADPyranose 2-oxidase / 0.653
4bk2 FADProbable salicylate monooxygenase / 0.653
4lwp SAHArginine N-methyltransferase, putative / 0.653
5js6 NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.653
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.652
1la2 NADInositol-3-phosphate synthase 5.5.1.4 0.652
2yg5 FADPutrescine oxidase / 0.652
3lst SAHCalO1 / 0.652
3m13 FADMonomeric sarcosine oxidase 1.5.3.1 0.652
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.652
4rtj SFGDNA adenine methylase 2.1.1.72 0.652
5jsf NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.652
1rsg FADPolyamine oxidase FMS1 / 0.651
1tdn FADL-amino-acid oxidase 1.4.3.2 0.651
2c54 NADGDP-mannose 3,5-epimerase 5.1.3.18 0.651
4at0 FADPossible succinate dehydrogenase / 0.651
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.650
1reo FADL-amino-acid oxidase 1.4.3.2 0.650
2gh5 FADGlutathione reductase, mitochondrial 1.8.1.7 0.650
3lsm SFDPyranose 2-oxidase / 0.650
3nmu SAMFibrillarin-like rRNA/tRNA 2'-O-methyltransferase / 0.650
4eqr FADCoenzyme A disulfide reductase / 0.650
4hb9 FADUncharacterized protein / 0.650
4k5r FADOxygenase / 0.650
4x4j FADPutative oxygenase / 0.650