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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
3h5n ATP MccB protein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3h5n ATPMccB protein / 1.142
3h9j APCMccB protein / 0.746
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.717
2bra FAD[F-actin]-methionine sulfoxide oxidase MICAL1 1.14.13 0.694
3wv8 ATPHmd co-occurring protein HcgE / 0.687
3lov FADProtoporphyrinogen oxidase / 0.683
1h2h NADL-aspartate dehydrogenase 1.4.1.21 0.679
4b67 FADL-ornithine N(5)-monooxygenase / 0.679
4e2x SAHMethyltransferase / 0.679
1rp0 AHZThiamine thiazole synthase, chloroplastic / 0.678
1u28 NADNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.678
4emw FADCoenzyme A disulfide reductase / 0.678
1f8g NADNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.677
3nlc FADUncharacterized protein / 0.676
1g1a NADdTDP-glucose 4,6-dehydratase / 0.674
5cku FADL-ornithine N(5)-monooxygenase / 0.674
4tm1 FDAKtzI / 0.673
2oo5 TXDNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.672
2yy7 NADL-threonine dehydrogenase / 0.672
4yuz S4MSpermidine synthase, putative / 0.670
4a99 FADTetX family tetracycline inactivation enzyme / 0.669
2cdu ADPNADH oxidase / 0.668
4tnq TTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.667
3nn6 FB06-hydroxy-L-nicotine oxidase / 0.666
2fsv NADNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.665
1j5p NADL-aspartate dehydrogenase 1.4.1.21 0.664
3lcc SAHThiocyanate methyltransferase 1 / 0.664
5g3s FDAFlavin-dependent L-tryptophan oxidase VioA / 0.663
4yr9 NADL-threonine 3-dehydrogenase, mitochondrial 1.1.1.103 0.662
3kkj FADRenalase / 0.661
4oa5 SAHO-methyltransferase family protein / 0.661
3ag6 PAJPantothenate synthetase / 0.660
3wv7 ADPHmd co-occurring protein HcgE / 0.659
4b63 FADL-ornithine N(5)-monooxygenase / 0.659
4tlx FDAKtzI / 0.659
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.659
2q0l FADThioredoxin reductase 1.8.1.9 0.658
2ylr FADPhenylacetone monooxygenase 1.14.13.92 0.658
2ylt FADPhenylacetone monooxygenase 1.14.13.92 0.658
2ylw FADPhenylacetone monooxygenase 1.14.13.92 0.658
3s5w FADL-ornithine N(5)-monooxygenase / 0.658
3sfd FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.658
4tnp DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.658
2dki FAD3-hydroxybenzoate 4-monooxygenase 1.14.13.23 0.657
2vou FAD2,6-dihydroxypyridine 3-monooxygenase 1.14.13.10 0.657
4d79 ATPtRNA threonylcarbamoyladenosine dehydratase 6.1 0.656
2plw SAMRibosomal RNA methyltransferase, putative / 0.655
4nzh FADL-ornithine N(5)-monooxygenase / 0.655
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.654
2jas DTPDeoxyguanosine kinase / 0.653
3ish FADThioredoxin reductase 1.8.1.9 0.653
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.653
2g5c NADPrephenate dehydrogenase / 0.652
3duw SAHO-methyltransferase, putative / 0.652
3l8k ADPDihydrolipoamide dehydrogenase (PdhD-3) / 0.652
4gcm FADThioredoxin reductase 1.8.1.9 0.652
1nbi SAMGlycine N-methyltransferase 2.1.1.20 0.651
3uov FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase 1.14.13.160 0.650
4bjz FADProbable salicylate monooxygenase / 0.650
4fk1 FADPutative thioredoxin reductase / 0.650