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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
2np7 NEA Modification methylase TaqI 2.1.1.72

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2np7 NEAModification methylase TaqI 2.1.1.72 0.941
2ibt NEAModification methylase TaqI 2.1.1.72 0.894
2ih2 NEAModification methylase TaqI 2.1.1.72 0.880
2ih5 NEAModification methylase TaqI 2.1.1.72 0.861
1g38 NEAModification methylase TaqI 2.1.1.72 0.846
2np6 NEAModification methylase TaqI 2.1.1.72 0.825
5je4 SAHMethyl transferase / 0.753
5jdz SAHMethyl transferase / 0.751
5je3 SAHMethyl transferase / 0.751
1boo SAHModification methylase PvuII 2.1.1.113 0.730
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.730
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.726
2o06 MTASpermidine synthase 2.5.1.16 0.723
2uyh SAHModification methylase HhaI 2.1.1.37 0.720
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.720
2o07 MTASpermidine synthase 2.5.1.16 0.719
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.719
5je2 SAHMethyl transferase / 0.719
3tm4 SAMUncharacterized protein / 0.712
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.707
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.706
3mht SAHModification methylase HhaI 2.1.1.37 0.706
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.706
4c03 SFGProtein arginine N-methyltransferase 6 / 0.705
2f8l SAMLmo1582 protein / 0.702
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.702
4nec SAHPutative SAM-dependent methyltransferase / 0.701
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.697
2yqz SAMUncharacterized protein / 0.697
1y9d FADPyruvate oxidase 1.2.3.3 0.696
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.695
7mht SAHModification methylase HhaI 2.1.1.37 0.695
2ore SAHDNA adenine methylase 2.1.1.72 0.693
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.692
1aqi SAHModification methylase TaqI 2.1.1.72 0.688
1mht SAHModification methylase HhaI 2.1.1.37 0.685
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.685
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.684
5f8f SFGPossible transcriptional regulatory protein / 0.684
4rtk SAHDNA adenine methylase 2.1.1.72 0.682
2gs9 SAHUncharacterized protein / 0.681
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.681
3kkz SAMUncharacterized protein / 0.681
1yf3 SAHDNA adenine methylase / 0.679
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.678
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.678
9mht SAHModification methylase HhaI 2.1.1.37 0.677
3ldg SAHUncharacterized protein / 0.676
2px2 SAHGenome polyprotein 2.7.7.48 0.675
4yv0 S4MSpermidine synthase, putative / 0.675
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.674
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.674
3rw9 DSHSpermidine synthase 2.5.1.16 0.674
4rtj SFGDNA adenine methylase 2.1.1.72 0.674
4rtq SAHDNA adenine methylase 2.1.1.72 0.674
3fri SAH16S rRNA methylase / 0.672
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.671
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.671
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.670
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.670
3grv ADNProbable ribosomal RNA small subunit methyltransferase A / 0.669
1skm SAHModification methylase HhaI 2.1.1.37 0.667
4fr0 SAMArsenic methyltransferase / 0.667
1p1h NADInositol-3-phosphate synthase 5.5.1.4 0.666
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.666
2g1p SAHDNA adenine methylase 2.1.1.72 0.665
3tm5 SFGUncharacterized protein / 0.665
4rts SAMDNA adenine methylase 2.1.1.72 0.665
2pkm ADNAdenosine kinase 2.7.1.20 0.664
4kwc SAHMethyltransferase domain family / 0.664
4mo2 FDAUDP-galactopyranose mutase / 0.664
2p35 SAHTrans-aconitate 2-methyltransferase / 0.663
3n1s 5GPPurine nucleoside phosphoramidase / 0.663
5ig2 NADShort-chain dehydrogenase/reductase SDR / 0.663
4wec NADShort chain dehydrogenase / 0.662
2gdz NAD15-hydroxyprostaglandin dehydrogenase [NAD(+)] 1.1.1.141 0.660
4qnv GEKtRNA U34 carboxymethyltransferase / 0.660
1jr4 CL4Catechol O-methyltransferase 2.1.1.6 0.659
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.659
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.659
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.659
1nw6 SFGModification methylase RsrI 2.1.1.72 0.658
4eqg A5AHistidine triad nucleotide-binding protein 1 3 0.658
4qpp SAHProtein arginine N-methyltransferase 6 / 0.658
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.657
2yxl SFG450aa long hypothetical fmu protein / 0.657
4er6 AW2Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.656
2gmh FADElectron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial 1.5.5.1 0.655
4gh5 NADShort-chain dehydrogenase/reductase SDR / 0.655
2fkn NADUrocanate hydratase 4.2.1.49 0.654
3e9y FABAcetolactate synthase, chloroplastic 2.2.1.6 0.654
2igo FADPyranose 2-oxidase / 0.652
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.652
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.651
5ahk FADAcetolactate synthase II, large subunit / 0.651
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.651
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.651
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.650