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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
3a27 SAM tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.914
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.771
1boo SAHModification methylase PvuII 2.1.1.113 0.763
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.761
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.757
3tm4 SAMUncharacterized protein / 0.752
2yxl SFG450aa long hypothetical fmu protein / 0.746
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.744
2ore SAHDNA adenine methylase 2.1.1.72 0.729
2f8l SAMLmo1582 protein / 0.723
3bwc SAMSpermidine synthase, putative / 0.720
2o07 MTASpermidine synthase 2.5.1.16 0.717
2o06 MTASpermidine synthase 2.5.1.16 0.716
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.716
2zif SAMMethyltransferase / 0.715
1nw5 SAMModification methylase RsrI 2.1.1.72 0.711
1eg2 MTAModification methylase RsrI 2.1.1.72 0.710
3swr SFGDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.710
5bxy SAHPutative RNA methylase family UPF0020 / 0.709
2np6 NEAModification methylase TaqI 2.1.1.72 0.708
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.707
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.707
4rtk SAHDNA adenine methylase 2.1.1.72 0.707
2g1p SAHDNA adenine methylase 2.1.1.72 0.706
1nw6 SFGModification methylase RsrI 2.1.1.72 0.705
3ldf SAHUncharacterized protein / 0.705
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.705
2ih2 NEAModification methylase TaqI 2.1.1.72 0.704
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.704
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.703
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.703
2ibt NEAModification methylase TaqI 2.1.1.72 0.702
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.701
7mht SAHModification methylase HhaI 2.1.1.37 0.700
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.698
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.697
2np7 NEAModification methylase TaqI 2.1.1.72 0.695
1skm SAHModification methylase HhaI 2.1.1.37 0.693
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.693
9mht SAHModification methylase HhaI 2.1.1.37 0.693
2c7q SAHModification methylase HhaI 2.1.1.37 0.692
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.691
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.690
4mb2 ATPUncharacterized protein / 0.690
2uyh SAHModification methylase HhaI 2.1.1.37 0.689
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.689
10mh SAHModification methylase HhaI 2.1.1.37 0.688
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.688
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.687
4tm3 FADKtzI / 0.687
2pan FADGlyoxylate carboligase 4.1.1.47 0.686
4tm4 FDAKtzI / 0.686
1zmc NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.685
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.685
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.684
5je2 SAHMethyl transferase / 0.684
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.682
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.682
2zcj SAHModification methylase HhaI 2.1.1.37 0.681
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.681
3mht SAHModification methylase HhaI 2.1.1.37 0.680
2q28 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.679
2i9k SAHModification methylase HhaI 2.1.1.37 0.677
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.676
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.676
2hmv ADPKtr system potassium uptake protein A / 0.675
4kvz SAHPtnL protein / 0.675
5eow FAD6-hydroxynicotinate 3-monooxygenase 1.14.13.114 0.675
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.674
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.674
2ih5 NEAModification methylase TaqI 2.1.1.72 0.674
2z6u SAHModification methylase HhaI 2.1.1.37 0.673
4egu 5GPPutative histidine triad (HIT) protein / 0.673
3ldg SAHUncharacterized protein / 0.672
3nmu SAMFibrillarin-like rRNA/tRNA 2'-O-methyltransferase / 0.672
4rek FADCholesterol oxidase 1.1.3.6 0.672
5mht SAHModification methylase HhaI 2.1.1.37 0.672
3alj FAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase / 0.671
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.671
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.669
3alm FAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase / 0.669
3rw9 DSHSpermidine synthase 2.5.1.16 0.669
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.669
4rts SAMDNA adenine methylase 2.1.1.72 0.669
3all FAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase / 0.668
3cbg SAHO-methyltransferase / 0.668
3grv ADNProbable ribosomal RNA small subunit methyltransferase A / 0.668
1v59 NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.666
2px2 SAHGenome polyprotein 2.7.7.48 0.666
3ad9 FADSubunit beta of sarcosine oxidase / 0.666
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.666
3tm5 SFGUncharacterized protein / 0.665
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.665
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.664
2zzn SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.663
2hmy SAMModification methylase HhaI 2.1.1.37 0.662
3pt6 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.662
4blv SAMRibosomal RNA large subunit methyltransferase J / 0.662
8mht SAHModification methylase HhaI 2.1.1.37 0.662
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.661
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.661
4wec NADShort chain dehydrogenase / 0.661
4yac NAIC alpha-dehydrogenase / 0.661
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.660
3tlj SAHUncharacterized protein / 0.660
3fpz AHZThiamine thiazole synthase / 0.659
3k30 ADPHistamine dehydrogenase / 0.659
4ek9 EP4Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.659
4gbe SAHDNA adenine methylase 2.1.1.72 0.659
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.659
5bw4 SAMUncharacterized protein / 0.659
1jqd SAHHistamine N-methyltransferase 2.1.1.8 0.658
1ori SAHProtein arginine N-methyltransferase 1 / 0.657
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.657
4eki 0QKHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.656
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.655
3nix FADFlavoprotein/dehydrogenase / 0.655
4b66 FADL-ornithine N(5)-monooxygenase / 0.655
4kwc SAHMethyltransferase domain family / 0.655
4xba 5GPAprataxin-like protein 3 0.655
5fa8 SAMRibosomal protein L11 methyltransferase, putative / 0.655
1g38 NEAModification methylase TaqI 2.1.1.72 0.654
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.654
2p35 SAHTrans-aconitate 2-methyltransferase / 0.654
4rtm SAMDNA adenine methylase 2.1.1.72 0.654
1wy7 SAHUncharacterized protein / 0.653
4x4j FADPutative oxygenase / 0.653
4ykl GMPAprataxin-like protein 3 0.653
1g60 SAMModification methylase MboII 2.1.1.72 0.652
2fk8 SAMHydroxymycolate synthase MmaA4 2.1.1 0.652
3lcc SAHThiocyanate methyltransferase 1 / 0.652
1grg FADGlutathione reductase, mitochondrial 1.8.1.7 0.651
1yf3 SAHDNA adenine methylase / 0.651
3cge FADCoenzyme A disulfide reductase / 0.651
4dmg SAMUncharacterized protein / 0.651
4fn4 NADShort chain dehydrogenase / 0.651
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.651
1dnc FADGlutathione reductase, mitochondrial 1.8.1.7 0.650
1grh FADGlutathione reductase, mitochondrial 1.8.1.7 0.650
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.650
3lby SAHUncharacterized protein / 0.650
4ctk SAMGenome polyprotein / 0.650
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.650