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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
3jyp NAD Quinate/shikimate dehydrogenase (NAD(+))

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3jyp NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.971
3jyq NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.904
3jyo NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.893
4l4s NAIL-lactate dehydrogenase A chain 1.1.1.27 0.730
1lld NADL-lactate dehydrogenase 2 1.1.1.27 0.729
2g76 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.720
3wsw NADL-lactate dehydrogenase / 0.716
3n7u NADFormate dehydrogenase, chloroplastic/mitochondrial / 0.709
1il0 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.696
2fzw NADAlcohol dehydrogenase class-3 1.1.1.1 0.695
3wle NAD(R)-specific carbonyl reductase / 0.695
4k28 NADShikimate dehydrogenase family protein / 0.695
2dt5 NADRedox-sensing transcriptional repressor Rex / 0.693
4e5k NADPhosphonate dehydrogenase 1.20.1.1 0.693
1bdb NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase / 0.692
1f0y NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.691
1m75 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.691
2v7g NADUrocanate hydratase 4.2.1.49 0.689
3nt4 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.689
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.687
2vhv NAIAlanine dehydrogenase 1.4.1.1 0.686
1vi2 NADQuinate/shikimate dehydrogenase / 0.684
3adp NAILambda-crystallin 1.1.1.45 0.684
3d64 NADAdenosylhomocysteinase / 0.684
2dfv NADL-threonine 3-dehydrogenase / 0.683
2fn7 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.683
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.681
4dxh NAJAlcohol dehydrogenase E chain 1.1.1.1 0.680
2vhx NADAlanine dehydrogenase 1.4.1.1 0.678
3abi NADUncharacterized protein / 0.678
3wv7 ADPHmd co-occurring protein HcgE / 0.677
3x2e NAIAdenosylhomocysteinase / 0.675
4j49 NADUncharacterized protein / 0.675
1adc PADAlcohol dehydrogenase E chain 1.1.1.1 0.674
1pjc NADAlanine dehydrogenase / 0.674
4nzh FADL-ornithine N(5)-monooxygenase / 0.674
5je4 SAHMethyl transferase / 0.674
2p35 SAHTrans-aconitate 2-methyltransferase / 0.673
3tsc NADUncharacterized protein / 0.673
3wv8 ATPHmd co-occurring protein HcgE / 0.673
3nt2 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.672
3oet NADErythronate-4-phosphate dehydrogenase / 0.672
4nfs NAJAlcohol dehydrogenase E chain 1.1.1.1 0.672
4dl9 NADS-(hydroxymethyl)glutathione dehydrogenase / 0.671
1ma0 NADAlcohol dehydrogenase class-3 1.1.1.1 0.670
1mp0 NADAlcohol dehydrogenase class-3 1.1.1.1 0.670
1skm SAHModification methylase HhaI 2.1.1.37 0.670
3cbg SAHO-methyltransferase / 0.670
3ec7 NADInositol 2-dehydrogenase / 0.670
3nt2 NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.670
4c4o NADSADH / 0.670
4e5p NADPhosphonate dehydrogenase 1.20.1.1 0.670
1m76 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.669
1p1h NADInositol-3-phosphate synthase 5.5.1.4 0.669
3fpf MTAUncharacterized protein / 0.669
3mht SAHModification methylase HhaI 2.1.1.37 0.669
1ie3 NADMalate dehydrogenase / 0.668
4nd2 A3DLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.668
4okn NAIL-lactate dehydrogenase A chain 1.1.1.27 0.668
5cdt NAJAlcohol dehydrogenase E chain 1.1.1.1 0.668
5kcz NAJAlcohol dehydrogenase E chain 1.1.1.1 0.668
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.667
2nad NADFormate dehydrogenase / 0.667
4nfh NAJAlcohol dehydrogenase E chain 1.1.1.1 0.667
5kje NAJAlcohol dehydrogenase E chain 1.1.1.1 0.667
2qg4 NADUDP-glucose 6-dehydrogenase 1.1.1.22 0.666
2vhw NAIAlanine dehydrogenase 1.4.1.1 0.666
4jk3 NADUncharacterized protein / 0.666
1pdh FASp-hydroxybenzoate hydroxylase / 0.665
3qgz ADNHistidine triad nucleotide-binding protein 1 3 0.665
2fkn NADUrocanate hydratase 4.2.1.49 0.664
2ldb NADL-lactate dehydrogenase 1.1.1.27 0.664
3oq6 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.664
2fze APRAlcohol dehydrogenase class-3 1.1.1.1 0.663
4bk2 FADProbable salicylate monooxygenase / 0.663
4gl4 NAIAlcohol dehydrogenase class-3 / 0.663
1y56 ATPUncharacterized protein / 0.662
2ph5 NADHomospermidine synthase / 0.662
5ig2 NADShort-chain dehydrogenase/reductase SDR / 0.662
2gdz NAD15-hydroxyprostaglandin dehydrogenase [NAD(+)] 1.1.1.141 0.661
2ixb NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.661
1dxy NADD-2-hydroxyisocaproate dehydrogenase 1.1.1 0.660
4om8 NAD3-hydroxybutyryl-coA dehydrogenase / 0.660
2pa3 NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.659
4yac NAIC alpha-dehydrogenase / 0.659
2ep7 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.658
7mht SAHModification methylase HhaI 2.1.1.37 0.658
1kol NADGlutathione-independent formaldehyde dehydrogenase / 0.657
1y9d FADPyruvate oxidase 1.2.3.3 0.657
4w6z 8IDAlcohol dehydrogenase 1 1.1.1.1 0.656
4cpd NADAlcohol dehydrogenase / 0.655
2voj NADAlanine dehydrogenase 1.4.1.1 0.654
3x2f NAIAdenosylhomocysteinase / 0.654
4nec SAHPutative SAM-dependent methyltransferase / 0.654
1p1i NADInositol-3-phosphate synthase 5.5.1.4 0.653
2c7q SAHModification methylase HhaI 2.1.1.37 0.653
2hmv ADPKtr system potassium uptake protein A / 0.653
2pv7 NADT-protein 1.3.1.12 0.653
4nd4 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.653
5cds NAJAlcohol dehydrogenase E chain 1.1.1.1 0.653
9mht SAHModification methylase HhaI 2.1.1.37 0.653
2q1t NADPutative nucleotide sugar epimerase/ dehydratase / 0.652
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.652
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.652
3l4s NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.652
1cdo NADAlcohol dehydrogenase 1 1.1.1.1 0.651
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.651
2q1s NAIPutative nucleotide sugar epimerase/ dehydratase / 0.651
3ntq NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.651
4c04 SFGProtein arginine N-methyltransferase 6 / 0.651
4j4b NAIUncharacterized protein / 0.651
5g3s FDAFlavin-dependent L-tryptophan oxidase VioA / 0.651
1a71 NADAlcohol dehydrogenase E chain 1.1.1.1 0.650
1nq5 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.650
2ore SAHDNA adenine methylase 2.1.1.72 0.650
3uko NADAlcohol dehydrogenase class-3 / 0.650
4yuz S4MSpermidine synthase, putative / 0.650
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.650