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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
2pt6 S4M Spermidine synthase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2pt6 S4MSpermidine synthase / 1.109
4yv1 S4MSpermidine synthase, putative / 0.865
4yv2 S4MSpermidine synthase, putative / 0.859
2o07 MTASpermidine synthase 2.5.1.16 0.827
4yuz S4MSpermidine synthase, putative / 0.827
4yuv S4MSpermidine synthase, putative / 0.816
2o06 MTASpermidine synthase 2.5.1.16 0.800
4yv0 S4MSpermidine synthase, putative / 0.790
1jq3 AATPolyamine aminopropyltransferase / 0.765
3bwc SAMSpermidine synthase, putative / 0.765
1kr5 SAHProtein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77 0.723
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.718
3rw9 DSHSpermidine synthase 2.5.1.16 0.699
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.694
1nw5 SAMModification methylase RsrI 2.1.1.72 0.692
4yac NAIC alpha-dehydrogenase / 0.692
1kia SAMGlycine N-methyltransferase 2.1.1.20 0.689
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.689
2hmv ADPKtr system potassium uptake protein A / 0.687
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.687
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.687
5je2 SAHMethyl transferase / 0.687
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.686
1y9d FADPyruvate oxidase 1.2.3.3 0.685
3fpf MTAUncharacterized protein / 0.684
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.680
1bdb NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase / 0.678
5bxy SAHPutative RNA methylase family UPF0020 / 0.675
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.674
3mj4 FADUDP-galactopyranose mutase / 0.670
2q28 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.669
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.666
2hun NAD336aa long hypothetical dTDP-glucose 4,6-dehydratase / 0.663
4tm1 FDAKtzI / 0.663
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.662
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.661
2hnk SAHSAM-dependent O-methyltransferase / 0.660
3ad9 FADSubunit beta of sarcosine oxidase / 0.660
3rfx NADUronate dehydrogenase / 0.660
1nbi SAMGlycine N-methyltransferase 2.1.1.20 0.656
1zmd FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.656
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.655
2eq6 FADDihydrolipoyl dehydrogenase / 0.655
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.655
3ou6 SAMSAM-dependent methyltransferase / 0.655
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.654
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.654
4kwc SAHMethyltransferase domain family / 0.653
4gf5 SAHCalS11 / 0.652
2bi8 FADUDP-galactopyranose mutase 5.4.99.9 0.651
3pb3 SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.651
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.651
3cmc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.650