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

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3jyo NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.960
3jyp NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.893
3jyq NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.866
4k28 NADShikimate dehydrogenase family protein / 0.781
1lld NADL-lactate dehydrogenase 2 1.1.1.27 0.746
2q3e NAIUDP-glucose 6-dehydrogenase 1.1.1.22 0.746
3wsw NADL-lactate dehydrogenase / 0.738
4l4s NAIL-lactate dehydrogenase A chain 1.1.1.27 0.735
4j43 NADUncharacterized protein / 0.731
1f8f NADBenzyl alcohol dehydrogenase / 0.728
3n7u NADFormate dehydrogenase, chloroplastic/mitochondrial / 0.724
1hyh NADL-2-hydroxyisocaproate dehydrogenase / 0.722
1pl6 NADSorbitol dehydrogenase 1.1.1.14 0.722
3d64 NADAdenosylhomocysteinase / 0.722
1il0 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.720
1mp0 NADAlcohol dehydrogenase class-3 1.1.1.1 0.719
1uxj NADMalate dehydrogenase / 0.717
2g76 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.717
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.714
3ec7 NADInositol 2-dehydrogenase / 0.710
1f0y NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.708
2dt5 NADRedox-sensing transcriptional repressor Rex / 0.708
2wsb NADGalactitol dehydrogenase / 0.705
1pl8 NADSorbitol dehydrogenase 1.1.1.14 0.703
1uxk NADMalate dehydrogenase / 0.702
2yy7 NADL-threonine dehydrogenase / 0.702
3adp NAILambda-crystallin 1.1.1.45 0.701
5cdt NAJAlcohol dehydrogenase E chain 1.1.1.1 0.701
5kj1 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.701
4e5k NADPhosphonate dehydrogenase 1.20.1.1 0.700
4jnk NAIL-lactate dehydrogenase A chain 1.1.1.27 0.700
1kol NADGlutathione-independent formaldehyde dehydrogenase / 0.698
1lde NADAlcohol dehydrogenase E chain 1.1.1.1 0.698
2ldb NADL-lactate dehydrogenase 1.1.1.27 0.698
1bdb NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase / 0.697
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.697
2o4c NADErythronate-4-phosphate dehydrogenase / 0.697
1ma0 NADAlcohol dehydrogenase class-3 1.1.1.1 0.696
2fzw NADAlcohol dehydrogenase class-3 1.1.1.1 0.696
2q1w NADPutative nucleotide sugar epimerase/ dehydratase / 0.696
4j49 NADUncharacterized protein / 0.696
1rp0 AHZThiamine thiazole synthase, chloroplastic / 0.695
2vhz NAIAlanine dehydrogenase 1.4.1.1 0.695
1ie3 NADMalate dehydrogenase / 0.692
1y56 FAD382aa long hypothetical sarcosine oxidase / 0.691
5kj6 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.691
1adc PADAlcohol dehydrogenase E chain 1.1.1.1 0.690
1e3s NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.690
1r37 NADNAD-dependent alcohol dehydrogenase 1.1.1.1 0.690
1zmd NAIDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.690
4dl9 NADS-(hydroxymethyl)glutathione dehydrogenase / 0.690
4jk3 NADUncharacterized protein / 0.690
1pjc NADAlanine dehydrogenase / 0.689
5g3t FDAFlavin-dependent L-tryptophan oxidase VioA / 0.689
2qg4 NADUDP-glucose 6-dehydrogenase 1.1.1.22 0.688
1sc6 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.687
3d4p NADL-lactate dehydrogenase 1 1.1.1.27 0.687
5kjc NAJAlcohol dehydrogenase E chain 1.1.1.1 0.687
1mgo NADAlcohol dehydrogenase E chain 1.1.1.1 0.686
2g5c NADPrephenate dehydrogenase / 0.686
3m6i NADL-arabinitol 4-dehydrogenase 1.1.1.12 0.686
4dwv NAJAlcohol dehydrogenase E chain 1.1.1.1 0.686
4xcx SAHSmall RNA 2'-O-methyltransferase / 0.686
5cdg NAJAlcohol dehydrogenase E chain 1.1.1.1 0.686
5kjf NAJAlcohol dehydrogenase E chain 1.1.1.1 0.686
1ib6 NADMalate dehydrogenase / 0.685
2gdz NAD15-hydroxyprostaglandin dehydrogenase [NAD(+)] 1.1.1.141 0.685
4dxh NAJAlcohol dehydrogenase E chain 1.1.1.1 0.685
4nfh NAJAlcohol dehydrogenase E chain 1.1.1.1 0.685
5kje NAJAlcohol dehydrogenase E chain 1.1.1.1 0.685
2vhx NADAlanine dehydrogenase 1.4.1.1 0.684
3oq6 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.683
5kcp NAJAlcohol dehydrogenase E chain 1.1.1.1 0.683
5kcz NAJAlcohol dehydrogenase E chain 1.1.1.1 0.683
2vhw NAIAlanine dehydrogenase 1.4.1.1 0.682
3nt2 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.682
4yai NAIC alpha-dehydrogenase / 0.682
5cds NAJAlcohol dehydrogenase E chain 1.1.1.1 0.682
1het NADAlcohol dehydrogenase E chain 1.1.1.1 0.681
4e5p NADPhosphonate dehydrogenase 1.20.1.1 0.681
3ruc NADUDP-N-acetylglucosamine 4-epimerase / 0.680
1ht0 NADAlcohol dehydrogenase 1C 1.1.1.1 0.679
1o6z NADMalate dehydrogenase / 0.679
2vhv NAIAlanine dehydrogenase 1.4.1.1 0.679
2x0i NAIMalate dehydrogenase / 0.679
4xq9 NADHomospermidine synthase 2.5.1.44 0.678
1m75 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.677
2q0l FADThioredoxin reductase 1.8.1.9 0.677
3nt4 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.677
4d03 FADPhenylacetone monooxygenase 1.14.13.92 0.677
4fwe FADLysine-specific histone demethylase 1B 1 0.676
4j4b NAIUncharacterized protein / 0.676
4ng5 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.676
1bw9 NADPhenylalanine dehydrogenase / 0.675
2gsd NADFormate dehydrogenase / 0.675
2nad NADFormate dehydrogenase / 0.675
2o23 NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.675
2oxi NADAlcohol dehydrogenase E chain 1.1.1.1 0.675
2ym1 FADPhenylacetone monooxygenase 1.14.13.92 0.675
3mj4 FADUDP-galactopyranose mutase / 0.675
4cpd NADAlcohol dehydrogenase / 0.675
2dfv NADL-threonine 3-dehydrogenase / 0.674
4j49 NAIUncharacterized protein / 0.674
1a71 NADAlcohol dehydrogenase E chain 1.1.1.1 0.673
1m76 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.673
1u3v NADAlcohol dehydrogenase 1B 1.1.1.1 0.673
1y56 ATPUncharacterized protein / 0.673
2hun NAD336aa long hypothetical dTDP-glucose 4,6-dehydratase / 0.673
3wv8 ATPHmd co-occurring protein HcgE / 0.673
4j2w FADKynurenine 3-monooxygenase / 0.673
2e37 NADL-lactate dehydrogenase / 0.672
4b69 FADL-ornithine N(5)-monooxygenase / 0.672
5lc1 NADL-threonine 3-dehydrogenase / 0.672
1guy NADMalate dehydrogenase / 0.671
1k0l FADp-hydroxybenzoate hydroxylase / 0.671
3pqf NADL-lactate dehydrogenase 1.1.1.27 0.671
3tri NAPPyrroline-5-carboxylate reductase / 0.671
1hf3 NADAlcohol dehydrogenase E chain 1.1.1.1 0.670
2npx NADNADH peroxidase 1.11.1.1 0.670
3hdy FADUDP-galactopyranose mutase / 0.670
3oc4 FADOxidoreductase, pyridine nucleotide-disulfide family / 0.670
1jnz FADAdenylylsulfate reductase, subunit A (AprA) / 0.669
1p1i NADInositol-3-phosphate synthase 5.5.1.4 0.669
1pdh FASp-hydroxybenzoate hydroxylase / 0.669
3ggp NADPrephenate dehydrogenase / 0.669
3nt2 NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.669
3x2f NAIAdenosylhomocysteinase / 0.669
4okn NAIL-lactate dehydrogenase A chain 1.1.1.27 0.669
2ore SAHDNA adenine methylase 2.1.1.72 0.668
1c1d NAIPhenylalanine dehydrogenase / 0.667
1la2 NADInositol-3-phosphate synthase 5.5.1.4 0.667
1yba NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.667
4gl4 NAIAlcohol dehydrogenase class-3 / 0.666
4xd2 NAIAlcohol dehydrogenase E chain 1.1.1.1 0.666
1axe NADAlcohol dehydrogenase E chain 1.1.1.1 0.665
1ky4 NADAdenosylhomocysteinase 3.3.1.1 0.665
1p1h NADInositol-3-phosphate synthase 5.5.1.4 0.665
1rsg FADPolyamine oxidase FMS1 / 0.665
1zem NADXylitol dehydrogenase / 0.665
4b65 FADL-ornithine N(5)-monooxygenase / 0.664
4xqc NADHomospermidine synthase 2.5.1.44 0.664
2ekl NADD-3-phosphoglycerate dehydrogenase / 0.663
2ohx NADAlcohol dehydrogenase E chain 1.1.1.1 0.663
1agn NADAlcohol dehydrogenase class 4 mu/sigma chain 1.1.1.1 0.662
1dss NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.662
2fze APRAlcohol dehydrogenase class-3 1.1.1.1 0.662
2rgj FADFlavin-containing monooxygenase / 0.662
3lov FADProtoporphyrinogen oxidase / 0.662
4l0q NADAlcohol dehydrogenase class-3 / 0.662
4ysh FADGlycine oxidase / 0.662
2jb1 FADL-amino acid oxidase / 0.661
4ejm NAPPutative zinc-binding dehydrogenase / 0.661
4yag NAIC alpha-dehydrogenase / 0.661
3oet NADErythronate-4-phosphate dehydrogenase / 0.660
4nfs NAJAlcohol dehydrogenase E chain 1.1.1.1 0.660
1xcb NADRedox-sensing transcriptional repressor Rex / 0.659
2c54 NADGDP-mannose 3,5-epimerase 5.1.3.18 0.659
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.659
3ru9 NADUDP-N-acetylglucosamine 4-epimerase / 0.659
1e3w NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.658
1e6w NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.658
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.658
4om8 NAD3-hydroxybutyryl-coA dehydrogenase / 0.658
4yac NAIC alpha-dehydrogenase / 0.658
3wv7 ADPHmd co-occurring protein HcgE / 0.657
1bws NDPGDP-L-fucose synthase / 0.656
1nw6 SFGModification methylase RsrI 2.1.1.72 0.656
3kb6 NADD-lactate dehydrogenase / 0.656
3m2t NADProbable dehydrogenase / 0.656
3ptz NADUDP-glucose 6-dehydrogenase 1.1.1.22 0.656
4c4o NADSADH / 0.656
1emd NADMalate dehydrogenase / 0.655
1h2h NADL-aspartate dehydrogenase 1.4.1.21 0.655
2ejv NADL-threonine 3-dehydrogenase / 0.655
1efk NADNAD-dependent malic enzyme, mitochondrial 1.1.1.38 0.654
2ph5 NADHomospermidine synthase / 0.654
3rua NADUDP-N-acetylglucosamine 4-epimerase / 0.654
1e3l NADAlcohol dehydrogenase 4 1.1.1.1 0.653
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.653
2pa3 NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.653
3cmc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.653
4ywj NAD4-hydroxy-tetrahydrodipicolinate reductase / 0.653
2vyv NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.652
3ruf NADUDP-N-acetylglucosamine 4-epimerase / 0.652
3sx2 NADUncharacterized protein / 0.652
3toz NADShikimate dehydrogenase (NADP(+)) / 0.652
4cr8 NADN-acylmannosamine 1-dehydrogenase 1.1.1.233 0.652
4rtk SAHDNA adenine methylase 2.1.1.72 0.652
1hld NADAlcohol dehydrogenase E chain 1.1.1.1 0.651
1i2b NADUDP-sulfoquinovose synthase, chloroplastic 3.13.1.1 0.651
4lsm NADGlyceraldehyde-3-phosphate dehydrogenase / 0.651
1geu NADGlutathione reductase 1.8.1.7 0.650
1i3l NADUDP-glucose 4-epimerase / 0.650
4a99 FADTetX family tetracycline inactivation enzyme / 0.650
4b67 FADL-ornithine N(5)-monooxygenase / 0.650
4gcm FADThioredoxin reductase 1.8.1.9 0.650
4u8k FDAUDP-galactopyranose mutase / 0.650
5env NADAlcohol dehydrogenase 1 1.1.1.1 0.650