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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
2ixa NAD Alpha-N-acetylgalactosaminidase 3.2.1.49

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 1.340
2ixb NADAlpha-N-acetylgalactosaminidase 3.2.1.49 1.233
3oa2 NADUDP-N-acetyl-2-amino-2-deoxy-D-glucuronate oxidase / 0.912
5a02 NAPGlucose-fructose oxidoreductase / 0.846
1h6d NDPGlucose--fructose oxidoreductase 1.1.99.28 0.842
1h6c NDPGlucose--fructose oxidoreductase 1.1.99.28 0.823
1zh8 NAPUncharacterized protein / 0.822
5a04 NDPGlucose-fructose oxidoreductase / 0.816
1h6a NDPGlucose--fructose oxidoreductase 1.1.99.28 0.812
5a05 NDPGlucose-fructose oxidoreductase / 0.806
3o9z NADLipopolysaccaride biosynthesis protein wbpB / 0.799
1ryd NDPGlucose--fructose oxidoreductase 1.1.99.28 0.796
5a06 NDPGlucose-fructose oxidoreductase / 0.794
5a03 NDPGlucose-fructose oxidoreductase / 0.790
3q2k NAIProbable oxidoreductase / 0.772
1evj NADGlucose--fructose oxidoreductase 1.1.99.28 0.765
1h6b NDPGlucose--fructose oxidoreductase 1.1.99.28 0.755
3m2t NADProbable dehydrogenase / 0.749
2nad NADFormate dehydrogenase / 0.740
1f0y NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.739
3f3s NADLambda-crystallin homolog / 0.739
2vq3 NAPMetalloreductase STEAP3 / 0.738
3nt2 NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.735
1nqa NADGlyceraldehyde-3-phosphate dehydrogenase / 0.731
3adp NAILambda-crystallin 1.1.1.45 0.731
2pv7 NADT-protein 1.3.1.12 0.730
3dmt NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.729
1kvr NADUDP-glucose 4-epimerase 5.1.3.2 0.727
2glx NDP1,5-anhydro-D-fructose reductase / 0.726
1x7d NADPutative ornithine cyclodeaminase / 0.725
2gsd NADFormate dehydrogenase / 0.725
4k9d NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.725
2vhw NAIAlanine dehydrogenase 1.4.1.1 0.723
3ec7 NADInositol 2-dehydrogenase / 0.722
5jla NADPutative short-chain dehydrogenase/reductase / 0.720
1nvm NADAcetaldehyde dehydrogenase 1.2.1.10 0.718
1ofg NDPGlucose--fructose oxidoreductase 1.1.99.28 0.718
1cf2 NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.715
2v7g NADUrocanate hydratase 4.2.1.49 0.715
3cmc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.714
4xqc NADHomospermidine synthase 2.5.1.44 0.714
5ein NAP[LysW]-L-2-aminoadipate 6-phosphate reductase / 0.714
2dt5 NADRedox-sensing transcriptional repressor Rex / 0.712
3qv1 NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.712
3tri NAPPyrroline-5-carboxylate reductase / 0.712
2vyn NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.710
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.710
1npt NADGlyceraldehyde-3-phosphate dehydrogenase / 0.708
1u8f NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.705
3ggp NADPrephenate dehydrogenase / 0.705
4om8 NAD3-hydroxybutyryl-coA dehydrogenase / 0.705
1pjc NADAlanine dehydrogenase / 0.704
2q3e NAIUDP-glucose 6-dehydrogenase 1.1.1.22 0.704
4wct FADFructosyl amine:oxygen oxidoreductase / 0.704
2q1u NADPutative nucleotide sugar epimerase/ dehydratase / 0.703
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.702
2f1k NAPPrephenate dehydrogenase / 0.701
4xgi NADGlutamate dehydrogenase / 0.701
1gd1 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.700
1h2b NAJNAD-dependent alcohol dehydrogenase / 0.699
3cif NADGlyceraldehyde-3-phosphate dehydrogenase / 0.699
5c7o NADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific 1.2.1.12 0.699
2g82 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.697
3x2f NAIAdenosylhomocysteinase / 0.697
4gmg NAPYersiniabactin biosynthetic protein YbtU / 0.696
4xrg NADHomospermidine synthase 2.5.1.44 0.696
1nah NADUDP-glucose 4-epimerase 5.1.3.2 0.694
1nq5 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.694
4plp NADHomospermidine synthase 2.5.1.44 0.694
1vi2 NADQuinate/shikimate dehydrogenase / 0.692
3ikt NADRedox-sensing transcriptional repressor Rex / 0.692
1yjq NAP2-dehydropantoate 2-reductase 1.1.1.169 0.691
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.690
4p8r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.690
4tvb NADHomospermidine synthase 2.5.1.44 0.690
1nqo NADGlyceraldehyde-3-phosphate dehydrogenase / 0.689
3cea NADMyo-inositol 2-dehydrogenase-like (Promiscuous) / 0.689
4lsm NADGlyceraldehyde-3-phosphate dehydrogenase / 0.689
5bsg NAPPyrroline-5-carboxylate reductase / 0.689
1c1d NAIPhenylalanine dehydrogenase / 0.688
2vyv NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.688
3cps NADGlyceraldehyde-3-phosphate dehydrogenase / 0.688
4o59 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.688
1hdg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.687
1cer NADGlyceraldehyde-3-phosphate dehydrogenase / 0.686
1il0 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.686
3hja NADGlyceraldehyde-3-phosphate dehydrogenase / 0.684
4l8v NAPInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.684
4xq9 NADHomospermidine synthase 2.5.1.44 0.684
2d2i NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.683
2h63 NAPBiliverdin reductase A 1.3.1.24 0.682
3keo NADRedox-sensing transcriptional repressor Rex / 0.682
3ru9 NADUDP-N-acetylglucosamine 4-epimerase / 0.682
1jn0 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.681
1vsv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.681
3lvf NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.679
4gae NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic 1.1.1.267 0.679
4yac NAIC alpha-dehydrogenase / 0.679
2yjz NAPMetalloreductase STEAP4 1.16.1 0.678
3lu1 NADUDP-N-acetylglucosamine 4-epimerase / 0.678
3wfj NAD2-dehydropantoate 2-reductase / 0.678
4b8z NAPGDP-L-fucose synthase 1.1.1.271 0.678
1r37 NADNAD-dependent alcohol dehydrogenase 1.1.1.1 0.677
1f17 NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.676
3v1y NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.676
1m75 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.675
1wp4 NDP3-hydroxyisobutyrate dehydrogenase / 0.675
3pym NADGlyceraldehyde-3-phosphate dehydrogenase 3 1.2.1.12 0.675
3tnl NADShikimate dehydrogenase (NADP(+)) / 0.675
1axe NADAlcohol dehydrogenase E chain 1.1.1.1 0.674
2voj NADAlanine dehydrogenase 1.4.1.1 0.674
4xb2 NDP319aa long hypothetical homoserine dehydrogenase / 0.674
1nbo NADGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.673
2cvz NDP3-hydroxyisobutyrate dehydrogenase / 0.673
4b7x NAPProbable oxidoreductase / 0.673
3pef NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.672
5aq1 NDPGlucose-6-phosphate 1-dehydrogenase / 0.672
2pzj NADPutative nucleotide sugar epimerase/ dehydratase / 0.671
2vhv NAIAlanine dehydrogenase 1.4.1.1 0.671
3nt4 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.671
1yl7 NAI4-hydroxy-tetrahydrodipicolinate reductase / 0.669
3ket NADRedox-sensing transcriptional repressor Rex / 0.669
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.668
1lld NADL-lactate dehydrogenase 2 1.1.1.27 0.668
2d1y NADOxidoreductase, short-chain dehydrogenase/reductase family / 0.667
2ibt NEAModification methylase TaqI 2.1.1.72 0.667
3b1j NADGlyceraldehyde-3-phosphate dehydrogenase / 0.667
3rua NADUDP-N-acetylglucosamine 4-epimerase / 0.667
3wmx NADNAD dependent epimerase/dehydratase / 0.667
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.666
2fkn NADUrocanate hydratase 4.2.1.49 0.666
5bsf NADPyrroline-5-carboxylate reductase / 0.666
1lc3 NADBiliverdin reductase A 1.3.1.24 0.665
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.665
7mht SAHModification methylase HhaI 2.1.1.37 0.665
1n2s NAIdTDP-4-dehydrorhamnose reductase 1.1.1.133 0.664
2c29 NAPDihydroflavonol 4-reductase / 0.664
2dvm NAD439aa long hypothetical malate oxidoreductase (NAD) [malic enzyme] / 0.664
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.663
1npd NADQuinate/shikimate dehydrogenase / 0.663
2b4r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.663
2c7q SAHModification methylase HhaI 2.1.1.37 0.663
1hyh NADL-2-hydroxyisocaproate dehydrogenase / 0.662
3h3j NADL-lactate dehydrogenase 1 1.1.1.27 0.662
3l4s NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.662
4wji NAPPutative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase / 0.662
4xd2 NAIAlcohol dehydrogenase E chain 1.1.1.1 0.661
2j3k NAPNADPH-dependent oxidoreductase 2-alkenal reductase 1.3.1.74 0.660
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.660
4jk3 NADUncharacterized protein / 0.660
5lc1 NADL-threonine 3-dehydrogenase / 0.660
9mht SAHModification methylase HhaI 2.1.1.37 0.660
1orr NADCDP-paratose 2-epimerase / 0.659
2dph NADFormaldehyde dismutase / 0.659
3jyo NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.659
3sxp NADADP-L-glycero-D-mannoheptose-6-epimerase / 0.659
4e5m NAPPhosphonate dehydrogenase 1.20.1.1 0.659
5kj6 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.659
1m76 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.658
1o6z NADMalate dehydrogenase / 0.658
2ahr NAPPyrroline-5-carboxylate reductase / 0.658
3k2b NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.658
1het NADAlcohol dehydrogenase E chain 1.1.1.1 0.657
3kbo NDPGlyoxylate/hydroxypyruvate reductase A / 0.657
3wsw NADL-lactate dehydrogenase / 0.657
4o63 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.657
1sc6 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.656
1xq6 NAPUncharacterized protein At5g02240 / 0.656
2y05 NAPProstaglandin reductase 1 / 0.656
4ebf NADPhosphonate dehydrogenase 1.20.1.1 0.656
4z0p NDPNAD-dependent dehydrogenase / 0.656
1nyt NAPShikimate dehydrogenase (NADP(+)) / 0.655
1rye NDPGlucose--fructose oxidoreductase 1.1.99.28 0.655
2c54 NADGDP-mannose 3,5-epimerase 5.1.3.18 0.655
2fze APRAlcohol dehydrogenase class-3 1.1.1.1 0.655
2i9p NAD3-hydroxyisobutyrate dehydrogenase, mitochondrial 1.1.1.31 0.655
2jkv NAP6-phosphogluconate dehydrogenase, decarboxylating 1.1.1.44 0.655
3abi NADUncharacterized protein / 0.655
3oet NADErythronate-4-phosphate dehydrogenase / 0.655
3pdu NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.655
1xse NDPCorticosteroid 11-beta-dehydrogenase isozyme 1 1.1.1.146 0.654
2q1t NADPutative nucleotide sugar epimerase/ dehydratase / 0.654
5a1t NAIL-lactate dehydrogenase / 0.654
5bp9 SAHPutative methyltransferase protein / 0.654
1t2a GDPGDP-mannose 4,6 dehydratase 4.2.1.47 0.653
1wzi NDPMalate dehydrogenase / 0.653
3mvq NDPGlutamate dehydrogenase 1, mitochondrial 1.4.1.3 0.653
3sx2 NADUncharacterized protein / 0.653
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.653
1f8f NADBenzyl alcohol dehydrogenase / 0.652
2czc NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.59 0.652
4o0l NDPNADPH-dependent 3-quinuclidinone reductase / 0.652
2yxl SFG450aa long hypothetical fmu protein / 0.651
3toz NADShikimate dehydrogenase (NADP(+)) / 0.651
3zu2 NAIEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.651
2g76 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.650
3ntq NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.650
4imp NDPPolyketide synthase extender modules 3-4 / 0.650
4j49 NAIUncharacterized protein / 0.650