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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
2ixb NAD Alpha-N-acetylgalactosaminidase 3.2.1.49

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2ixb NADAlpha-N-acetylgalactosaminidase 3.2.1.49 1.275
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 1.233
3oa2 NADUDP-N-acetyl-2-amino-2-deoxy-D-glucuronate oxidase / 0.894
1zh8 NAPUncharacterized protein / 0.840
5a02 NAPGlucose-fructose oxidoreductase / 0.834
1h6c NDPGlucose--fructose oxidoreductase 1.1.99.28 0.829
3q2k NAIProbable oxidoreductase / 0.826
1h6a NDPGlucose--fructose oxidoreductase 1.1.99.28 0.823
1h6d NDPGlucose--fructose oxidoreductase 1.1.99.28 0.819
1ryd NDPGlucose--fructose oxidoreductase 1.1.99.28 0.808
5a06 NDPGlucose-fructose oxidoreductase / 0.805
5a05 NDPGlucose-fructose oxidoreductase / 0.799
1evj NADGlucose--fructose oxidoreductase 1.1.99.28 0.795
5a03 NDPGlucose-fructose oxidoreductase / 0.790
1ofg NDPGlucose--fructose oxidoreductase 1.1.99.28 0.781
1h6b NDPGlucose--fructose oxidoreductase 1.1.99.28 0.780
5a04 NDPGlucose-fructose oxidoreductase / 0.779
3adp NAILambda-crystallin 1.1.1.45 0.762
3m2t NADProbable dehydrogenase / 0.754
3ec7 NADInositol 2-dehydrogenase / 0.742
3o9z NADLipopolysaccaride biosynthesis protein wbpB / 0.739
3nt2 NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.736
2gsd NADFormate dehydrogenase / 0.735
2vhz NAIAlanine dehydrogenase 1.4.1.1 0.730
5ein NAP[LysW]-L-2-aminoadipate 6-phosphate reductase / 0.730
1m76 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.728
2nad NADFormate dehydrogenase / 0.726
2pv7 NADT-protein 1.3.1.12 0.725
2vhw NAIAlanine dehydrogenase 1.4.1.1 0.724
4wct FADFructosyl amine:oxygen oxidoreductase / 0.719
4k9d NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.718
4xqc NADHomospermidine synthase 2.5.1.44 0.717
3dmt NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.715
4xq9 NADHomospermidine synthase 2.5.1.44 0.715
3wv8 ATPHmd co-occurring protein HcgE / 0.714
4xrg NADHomospermidine synthase 2.5.1.44 0.714
4l8v NAPInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.713
4tvb NADHomospermidine synthase 2.5.1.44 0.713
2vq3 NAPMetalloreductase STEAP3 / 0.711
1nvm NADAcetaldehyde dehydrogenase 1.2.1.10 0.709
2q3e NAIUDP-glucose 6-dehydrogenase 1.1.1.22 0.709
3f3s NADLambda-crystallin homolog / 0.709
1dss NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.708
3qv1 NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.706
1u8f NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.704
3n7u NADFormate dehydrogenase, chloroplastic/mitochondrial / 0.704
1kvr NADUDP-glucose 4-epimerase 5.1.3.2 0.699
2glx NDP1,5-anhydro-D-fructose reductase / 0.697
2f1k NAPPrephenate dehydrogenase / 0.696
3aw9 NADNAD-dependent epimerase/dehydratase / 0.696
3cea NADMyo-inositol 2-dehydrogenase-like (Promiscuous) / 0.695
2voj NADAlanine dehydrogenase 1.4.1.1 0.694
2dt5 NADRedox-sensing transcriptional repressor Rex / 0.693
2q1t NADPutative nucleotide sugar epimerase/ dehydratase / 0.693
1yjq NAP2-dehydropantoate 2-reductase 1.1.1.169 0.692
2wsb NADGalactitol dehydrogenase / 0.692
1f17 NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.691
1gd1 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.691
1r37 NADNAD-dependent alcohol dehydrogenase 1.1.1.1 0.691
3oet NADErythronate-4-phosphate dehydrogenase / 0.691
1bdb NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase / 0.690
1c1d NAIPhenylalanine dehydrogenase / 0.690
5jla NADPutative short-chain dehydrogenase/reductase / 0.690
3cmc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.689
3ko8 NADNAD-dependent epimerase/dehydratase / 0.689
1h2b NAJNAD-dependent alcohol dehydrogenase / 0.687
1vi2 NADQuinate/shikimate dehydrogenase / 0.686
1nah NADUDP-glucose 4-epimerase 5.1.3.2 0.685
3mvq NDPGlutamate dehydrogenase 1, mitochondrial 1.4.1.3 0.685
3x2f NAIAdenosylhomocysteinase / 0.685
4plp NADHomospermidine synthase 2.5.1.44 0.685
1pl8 NADSorbitol dehydrogenase 1.1.1.14 0.684
2h63 NAPBiliverdin reductase A 1.3.1.24 0.684
2pzj NADPutative nucleotide sugar epimerase/ dehydratase / 0.683
1ie3 NADMalate dehydrogenase / 0.682
1npd NADQuinate/shikimate dehydrogenase / 0.682
1vsv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.682
2yjz NAPMetalloreductase STEAP4 1.16.1 0.682
4xgi NADGlutamate dehydrogenase / 0.681
5bsg NAPPyrroline-5-carboxylate reductase / 0.681
4o59 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.680
3ru9 NADUDP-N-acetylglucosamine 4-epimerase / 0.679
5c7o NADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific 1.2.1.12 0.679
1e3w NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.677
4b8z NAPGDP-L-fucose synthase 1.1.1.271 0.677
1pjc NADAlanine dehydrogenase / 0.676
4xb2 NDP319aa long hypothetical homoserine dehydrogenase / 0.675
5eio NAP[LysW]-L-2-aminoadipate 6-phosphate reductase / 0.675
1wp4 NDP3-hydroxyisobutyrate dehydrogenase / 0.674
2g82 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.674
5bsf NADPyrroline-5-carboxylate reductase / 0.674
3ruc NADUDP-N-acetylglucosamine 4-epimerase / 0.673
1hdg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.672
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.671
2cvz NDP3-hydroxyisobutyrate dehydrogenase / 0.671
2czc NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.59 0.671
2d1y NADOxidoreductase, short-chain dehydrogenase/reductase family / 0.671
2fkn NADUrocanate hydratase 4.2.1.49 0.671
2ome NADC-terminal-binding protein 2 / 0.671
2q1u NADPutative nucleotide sugar epimerase/ dehydratase / 0.671
2vyv NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.671
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.671
1cer NADGlyceraldehyde-3-phosphate dehydrogenase / 0.670
4ej0 NAPADP-L-glycero-D-manno-heptose-6-epimerase / 0.670
3hja NADGlyceraldehyde-3-phosphate dehydrogenase / 0.669
1nai NADUDP-glucose 4-epimerase 5.1.3.2 0.668
3cif NADGlyceraldehyde-3-phosphate dehydrogenase / 0.668
3ket NADRedox-sensing transcriptional repressor Rex / 0.668
1lc3 NADBiliverdin reductase A 1.3.1.24 0.667
3b1j NADGlyceraldehyde-3-phosphate dehydrogenase / 0.667
3cps NADGlyceraldehyde-3-phosphate dehydrogenase / 0.667
1jn0 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.666
1nqo NADGlyceraldehyde-3-phosphate dehydrogenase / 0.666
4p8r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.666
1szj NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.663
3nt4 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.663
3ggp NADPrephenate dehydrogenase / 0.662
4m55 NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.662
3jyp NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.661
3v1y NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.661
4o63 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.660
1f0y NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.659
1nbo NADGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.659
1axe NADAlcohol dehydrogenase E chain 1.1.1.1 0.658
1nq5 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.658
2fze APRAlcohol dehydrogenase class-3 1.1.1.1 0.658
3kbo NDPGlyoxylate/hydroxypyruvate reductase A / 0.658
4b7x NAPProbable oxidoreductase / 0.658
5aq1 NDPGlucose-6-phosphate 1-dehydrogenase / 0.658
1yl7 NAI4-hydroxy-tetrahydrodipicolinate reductase / 0.657
2vhx NADAlanine dehydrogenase 1.4.1.1 0.657
3ou2 SAHSAM-dependent methyltransferase / 0.657
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.657
4z0p NDPNAD-dependent dehydrogenase / 0.657
1x7d NADPutative ornithine cyclodeaminase / 0.655
3ntq NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.655
3wmx NADNAD dependent epimerase/dehydratase / 0.655
4e5k NADPhosphonate dehydrogenase 1.20.1.1 0.655
1npt NADGlyceraldehyde-3-phosphate dehydrogenase / 0.654
2ohx NADAlcohol dehydrogenase E chain 1.1.1.1 0.654
3pym NADGlyceraldehyde-3-phosphate dehydrogenase 3 1.2.1.12 0.654
1j0x NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.653
1q0q NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase 1.1.1.267 0.653
2vhv NAIAlanine dehydrogenase 1.4.1.1 0.653
3t4e NADQuinate/shikimate dehydrogenase / 0.653
2y05 NAPProstaglandin reductase 1 / 0.652
3hwr NDP2-dehydropantoate 2-reductase / 0.652
3i6q NDPPutative leucoanthocyanidin reductase 1 / 0.652
3s55 NADPutative short-chain dehydrogenase/reductase / 0.652
4r2l ATPUniversal stress protein F / 0.652
2gdz NAD15-hydroxyprostaglandin dehydrogenase [NAD(+)] 1.1.1.141 0.651
3h3j NADL-lactate dehydrogenase 1 1.1.1.27 0.651
3sx2 NADUncharacterized protein / 0.651
4lsm NADGlyceraldehyde-3-phosphate dehydrogenase / 0.651
1m75 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.650
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.650
4gkv NADAlcohol dehydrogenase, propanol-preferring 1.1.1.1 0.650
4gmg NAPYersiniabactin biosynthetic protein YbtU / 0.650
4j49 NAIUncharacterized protein / 0.650
4yac NAIC alpha-dehydrogenase / 0.650