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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
4y9d NAI C alpha-dehydrogenase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4y9d NAIC alpha-dehydrogenase / 0.918
1u7t NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.724
1iy8 NADLevodione reductase / 0.721
1e3s NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.719
4yac NAIC alpha-dehydrogenase / 0.714
1e6w NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.712
2gdz NAD15-hydroxyprostaglandin dehydrogenase [NAD(+)] 1.1.1.141 0.709
2dkn NAI3-alpha-hydroxysteroid dehydrogenase / 0.708
2pzj NADPutative nucleotide sugar epimerase/ dehydratase / 0.706
3geg NADShort-chain dehydrogenase/reductase SDR / 0.706
2o23 NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.702
2q1t NADPutative nucleotide sugar epimerase/ dehydratase / 0.702
1e3w NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.701
3wv7 ADPHmd co-occurring protein HcgE / 0.698
2wsb NADGalactitol dehydrogenase / 0.697
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.695
1nai NADUDP-glucose 4-epimerase 5.1.3.2 0.694
4nbu NAI3-oxoacyl-(Acyl-carrier-protein) reductase / 0.694
3ruc NADUDP-N-acetylglucosamine 4-epimerase / 0.689
1bdb NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase / 0.688
2q1s NAIPutative nucleotide sugar epimerase/ dehydratase / 0.688
4yjd FADD-amino-acid oxidase 1.4.3.3 0.688
4wec NADShort chain dehydrogenase / 0.687
3ko8 NADNAD-dependent epimerase/dehydratase / 0.686
4dbz NDPPutative ketoacyl reductase 1.3.1 0.686
5jsf NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.686
1j5p NADL-aspartate dehydrogenase 1.4.1.21 0.685
1zem NADXylitol dehydrogenase / 0.683
2ztm NADD(-)-3-hydroxybutyrate dehydrogenase / 0.683
3w8f NAD3-hydroxybutyrate dehydrogenase / 0.681
2hms NAIKtr system potassium uptake protein A / 0.680
4k28 NADShikimate dehydrogenase family protein / 0.680
4yai NAIC alpha-dehydrogenase / 0.680
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.676
1yf3 SAHDNA adenine methylase / 0.676
2c31 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.676
1c0l FADD-amino-acid oxidase 1.4.3.3 0.675
4yr9 NADL-threonine 3-dehydrogenase, mitochondrial 1.1.1.103 0.673
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.673
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.672
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.671
3aw9 NADNAD-dependent epimerase/dehydratase / 0.671
1dhr NADDihydropteridine reductase 1.5.1.34 0.670
1u7t TDT3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.669
2d1y NADOxidoreductase, short-chain dehydrogenase/reductase family / 0.669
3abi NADUncharacterized protein / 0.669
5g3s FDAFlavin-dependent L-tryptophan oxidase VioA / 0.669
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.668
1kvr NADUDP-glucose 4-epimerase 5.1.3.2 0.667
3gvi ADPMalate dehydrogenase / 0.667
4xwz FADFructosyl amine:oxygen oxidoreductase / 0.666
2ome NADC-terminal-binding protein 2 / 0.664
4fn4 NADShort chain dehydrogenase / 0.664
5ig2 NADShort-chain dehydrogenase/reductase SDR / 0.664
1nah NADUDP-glucose 4-epimerase 5.1.3.2 0.663
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.663
3rfx NADUronate dehydrogenase / 0.662
3ru9 NADUDP-N-acetylglucosamine 4-epimerase / 0.662
1nff NAD3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase 1.1.1.53 0.661
2q28 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.661
1u1i NADMyo-inositol-1-phosphate synthase (Ino1) / 0.660
2b4q NAPRhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase 1.1.1.100 0.660
1nbh SAMGlycine N-methyltransferase 2.1.1.20 0.659
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.659
3pqf NADL-lactate dehydrogenase 1.1.1.27 0.659
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.658
1x7h NDPPutative ketoacyl reductase 1.3.1 0.658
2oxt SAMGenome polyprotein / 0.656
2q1u NADPutative nucleotide sugar epimerase/ dehydratase / 0.656
4wct FADFructosyl amine:oxygen oxidoreductase / 0.656
4yuz S4MSpermidine synthase, putative / 0.656
2g1p SAHDNA adenine methylase 2.1.1.72 0.655
1c0k FADD-amino-acid oxidase 1.4.3.3 0.654
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.654
3g5q FADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO / 0.654
2hsd NAD3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase 1.1.1.53 0.653
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.653
4rdi ATPtRNA threonylcarbamoyladenosine dehydratase 6.1 0.653
1sc6 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.652
2jib ADPOxalyl-CoA decarboxylase 4.1.1.8 0.652
4b67 FADL-ornithine N(5)-monooxygenase / 0.652
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.651
3cps NADGlyceraldehyde-3-phosphate dehydrogenase / 0.651
3wv8 ATPHmd co-occurring protein HcgE / 0.651
4b79 NADProbable short-chain dehydrogenase / 0.651
1uay ADNOxidoreductase / 0.650
3nn6 FB06-hydroxy-L-nicotine oxidase / 0.650
3uq9 TBNPutative adenosine kinase / 0.650
4dc1 NDPPutative ketoacyl reductase 1.3.1 0.650