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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
3qgz ADN Histidine triad nucleotide-binding protein 1 3

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3qgz ADNHistidine triad nucleotide-binding protein 1 3 0.841
1rzy 5ASHistidine triad nucleotide-binding protein 1 3 0.769
4e5i 0N9Polymerase acidic protein / 0.744
3n1s 5GPPurine nucleoside phosphoramidase / 0.733
5i2f BS5Histidine triad nucleotide-binding protein 1 3 0.717
4egu 5GPPutative histidine triad (HIT) protein / 0.700
3ou2 SAHSAM-dependent methyltransferase / 0.694
3ou6 SAMSAM-dependent methyltransferase / 0.693
4eqe KAAHistidine triad nucleotide-binding protein 1 3 0.691
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.689
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.688
5je4 SAHMethyl transferase / 0.688
1yf3 SAHDNA adenine methylase / 0.687
2qe6 SAMUncharacterized protein / 0.687
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.687
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.687
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.687
4xba 5GPAprataxin-like protein 3 0.682
3lcc SAHThiocyanate methyltransferase 1 / 0.681
5je3 SAHMethyl transferase / 0.681
3n1t 5GPPurine nucleoside phosphoramidase / 0.679
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.678
5je2 SAHMethyl transferase / 0.677
3fri SAH16S rRNA methylase / 0.672
4yuz S4MSpermidine synthase, putative / 0.670
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.668
3jyp NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.665
5epe SAHUncharacterized protein / 0.664
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.663
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.663
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.662
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.660
3grv ADNProbable ribosomal RNA small subunit methyltransferase A / 0.659
4yv2 S4MSpermidine synthase, putative / 0.659
1g1a NADdTDP-glucose 4,6-dehydratase / 0.658
3b89 5GP16S rRNA methylase / 0.657
3ec7 NADInositol 2-dehydrogenase / 0.655
5g3t FDAFlavin-dependent L-tryptophan oxidase VioA / 0.654
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.653
2xyr SFGReplicase polyprotein 1ab 2.1.1 0.652
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.652
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.652
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.650
4htf SAMtRNA 5-carboxymethoxyuridine methyltransferase / 0.650
5bp7 SAHSAM-dependent methyltransferase / 0.650