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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
3s3t ATP Universal stress protein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3s3t ATPUniversal stress protein / 1.213
1mjh ATPUniversal stress protein MJ0577 / 0.961
3ab8 ATPUncharacterized protein / 0.890
3hgm ATPTRAP-T-associated universal stress protein TeaD / 0.878
2z08 ATPUniversal stress protein family / 0.792
4r2l ATPUniversal stress protein F / 0.761
3cis ATPUniversal stress protein Rv2623 / 0.725
3ncq ATPNitrogen regulatory protein P-II (GlnB-2) / 0.712
2pck SAHDiphthine synthase / 0.689
2dsg SAHDiphthine synthase / 0.688
2dsh SAHDiphthine synthase / 0.688
2dxv SAHDiphthine synthase / 0.688
2e08 SAHDiphthine synthase / 0.688
2egl SAHDiphthine synthase / 0.688
2ek3 SAHDiphthine synthase / 0.688
2dv4 SAHDiphthine synthase / 0.686
5a7y SAHtRNA (adenine(9)-N1)-methyltransferase 2.1.1.218 0.686
2e4n SAHDiphthine synthase / 0.685
2ejj SAHDiphthine synthase / 0.685
2dxw SAHDiphthine synthase / 0.684
2e07 SAHDiphthine synthase / 0.684
2e15 SAHDiphthine synthase / 0.684
2e17 SAHDiphthine synthase / 0.684
2e7r SAHDiphthine synthase / 0.684
2ehl SAHDiphthine synthase / 0.684
2ek7 SAHDiphthine synthase / 0.684
2dxx SAHDiphthine synthase / 0.683
2eeq SAHDiphthine synthase / 0.683
2egb SAHDiphthine synthase / 0.683
2ele SAHDiphthine synthase / 0.683
2hut SAHDiphthine synthase / 0.683
2p6i SAHDiphthine synthase / 0.683
2p6l SAHDiphthine synthase / 0.683
2p9d SAHDiphthine synthase / 0.683
2dek SAHDiphthine synthase / 0.682
2egs SAHDiphthine synthase / 0.682
2el3 SAHDiphthine synthase / 0.682
2owk SAHDiphthine synthase / 0.682
2owu SAHDiphthine synthase / 0.682
2p6k SAHDiphthine synthase / 0.682
2en5 SAHDiphthine synthase / 0.679
2huv SAHDiphthine synthase / 0.679
2pb5 SAHDiphthine synthase / 0.679
2pcg SAHDiphthine synthase / 0.679
2pch SAHDiphthine synthase / 0.679
2e8r SAHDiphthine synthase / 0.678
2eka SAHDiphthine synthase / 0.678
2el0 SAHDiphthine synthase / 0.678
1vce SAHDiphthine synthase / 0.677
1wng SAHDiphthine synthase / 0.677
2emr SAHDiphthine synthase / 0.677
2huq SAHDiphthine synthase / 0.676
2p6d SAHDiphthine synthase / 0.676
3n0z 3ATAdenylate cyclase 2 / 0.676
3oii SAHRibosomal RNA small subunit methyltransferase NEP1 / 0.676
2e8h SAHDiphthine synthase / 0.675
2eh2 SAHDiphthine synthase / 0.675
2z6r SAHDiphthine synthase / 0.675
2e16 SAHDiphthine synthase / 0.674
2emu SAHDiphthine synthase / 0.674
2dv7 SAHDiphthine synthase / 0.672
2eni SAHDiphthine synthase / 0.672
2owg SAHDiphthine synthase / 0.672
2pci SAHDiphthine synthase / 0.672
2dv3 SAHDiphthine synthase / 0.670
2eh4 SAHDiphthine synthase / 0.670
2e8s SAHDiphthine synthase / 0.668
2ed5 SAHDiphthine synthase / 0.668
2ek4 SAHDiphthine synthase / 0.668
4to0 DTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.668
5ahw CMPUniversal stress protein family protein, putative / 0.668
3hiy UTPUncharacterized protein / 0.667
4fhp UTPTerminal uridylyltransferase cid1 / 0.666
2eh5 SAHDiphthine synthase / 0.665
2p2x SAHDiphthine synthase / 0.664
4u0o MTALipoyl synthase 2 / 0.664
3egt 722Farnesyl pyrophosphate synthase / 0.660
3sl2 ATPSensor histidine kinase WalK / 0.660
2hma SAMtRNA-specific 2-thiouridylase MnmA / 0.659
1xjj DGTVitamin B12-dependent ribonucleotide reductase / 0.655
2cx8 SAHRibosomal RNA small subunit methyltransferase E / 0.655
2egw SAHRibosomal RNA small subunit methyltransferase E 2.1.1.193 0.655
4fh5 UTPTerminal uridylyltransferase cid1 / 0.655
1mx0 ANPType 2 DNA topoisomerase 6 subunit B / 0.654
1kh2 ATPArgininosuccinate synthase / 0.653
3tso GNPRas-related protein Rab-25 / 0.653
2p5f SAHDiphthine synthase / 0.652
3zkb ANPDNA gyrase subunit B / 0.652
4fak SAMRibosomal RNA large subunit methyltransferase H / 0.652
1cjv DADAdenylate cyclase type 2 / 0.651
1cjv DADAdenylate cyclase type 5 / 0.651
1j1z ATPArgininosuccinate synthase / 0.651
4wuc ANPDNA gyrase subunit B / 0.650