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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
2gdz NAD 15-hydroxyprostaglandin dehydrogenase [NAD(+)] 1.1.1.141

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity
Align
2gdz NAD15-hydroxyprostaglandin dehydrogenase [NAD(+)] 1.1.1.141 1.249
2wsb NADGalactitol dehydrogenase / 1.056
3sx2 NADUncharacterized protein / 1.017
5ig2 NADShort-chain dehydrogenase/reductase SDR / 1.003
5js6 NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 1.001
5jsf NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 1.001
1geg NADDiacetyl reductase [(S)-acetoin forming] 1.1.1.304 0.992
3wds NADNADH-dependent quinuclidinone reductase / 0.970
3a28 NADL-2,3-butanediol dehydrogenase 1.1.1.76 0.968
2o23 NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.956
5jla NADPutative short-chain dehydrogenase/reductase / 0.949
1bdb NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase / 0.936
3p19 NDPPutative blue fluorescent protein / 0.932
3s55 NADPutative short-chain dehydrogenase/reductase / 0.932
4nbt NAD3-oxoacyl-[acyl-carrier-protein] reductase / 0.930
4yag NAIC alpha-dehydrogenase / 0.929
1e3s NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.925
2dkn NAI3-alpha-hydroxysteroid dehydrogenase / 0.921
1e3w NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.915
1e6w NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.915
1xg5 NAPDehydrogenase/reductase SDR family member 11 / 0.909
2jah NDPClavaldehyde dehydrogenase / 0.908
1nff NAD3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase 1.1.1.53 0.907
2q2v NADBeta-D-hydroxybutyrate dehydrogenase / 0.904
3ruc NADUDP-N-acetylglucosamine 4-epimerase / 0.902
3pgx NADUncharacterized NAD-dependent oxidoreductase MAP_4146 / 0.900
3w8e NAD3-hydroxybutyrate dehydrogenase / 0.898
4fn4 NADShort chain dehydrogenase / 0.887
3w8f NAD3-hydroxybutyrate dehydrogenase / 0.881
3o26 NDPSalutaridine reductase / 0.877
3rku NAPNADP-dependent 3-hydroxy acid dehydrogenase / 0.877
1x7h NDPPutative ketoacyl reductase 1.3.1 0.876
1edo NAP3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic 1.1.1.100 0.873
3l77 NJPShort-chain alcohol dehydrogenase / 0.870
4kwh NAPReductase homolog / 0.869
3qrw NDPPutative ketoacyl reductase 1.3.1 0.867
4dc0 NDPPutative ketoacyl reductase 1.3.1 0.867
1cyd NDPCarbonyl reductase [NADPH] 2 1.1.1.184 0.863
4b79 NADProbable short-chain dehydrogenase / 0.862
3tn7 NJPShort-chain alcohol dehydrogenase / 0.861
2ag5 NAD3-hydroxybutyrate dehydrogenase type 2 / 0.860
4z3d NDPCarbonyl reductase [NADPH] 1 1.1.1.184 0.859
4bmv NAPShort-chain dehydrogenase / 0.858
2bd0 NAPSepiapterin reductase / 0.857
3nug NADPyridoxal 4-dehydrogenase 1.1.1.107 0.850
3geg NADShort-chain dehydrogenase/reductase SDR / 0.847
2ztl NADD(-)-3-hydroxybutyrate dehydrogenase / 0.846
1u7t TDT3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.845
3ai2 NDPNADPH-sorbose reductase / 0.845
1pr9 NAPL-xylulose reductase 1.1.1.10 0.844
3tsc NADUncharacterized protein / 0.843
4dbz NDPPutative ketoacyl reductase 1.3.1 0.842
1vl8 NAPOxidoreductase, short chain dehydrogenase/reductase family / 0.841
4yai NAIC alpha-dehydrogenase / 0.840
2ztm NADD(-)-3-hydroxybutyrate dehydrogenase / 0.838
3ak4 NADNADH-dependent quinuclidinone reductase / 0.838
3w8d NAD3-hydroxybutyrate dehydrogenase / 0.838
3bhi NAPCarbonyl reductase [NADPH] 1 1.1.1.184 0.835
3ai3 NDPNADPH-sorbose reductase / 0.829
4gh5 NADShort-chain dehydrogenase/reductase SDR / 0.828
1x7g NAPPutative ketoacyl reductase 1.3.1 0.825
3rj5 NADAlcohol dehydrogenase 1.1.1.1 0.825
1w4z NAPPutative ketoacyl reductase 1.3.1 0.824
4fj2 NAP17beta-hydroxysteroid dehydrogenase / 0.824
4iqg NAPShort-chain dehydrogenase/reductase SDR / 0.823
1n5d NDPCarbonyl reductase [NADPH] 1 / 0.822
3o4r NAPDehydrogenase/reductase SDR family member 4 1.1.1.184 0.818
2y99 NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase 1.3.1.56 0.817
3vdq NAD3-hydroxybutyrate dehydrogenase / 0.816
2d1y NADOxidoreductase, short-chain dehydrogenase/reductase family / 0.815
2ztv NADD(-)-3-hydroxybutyrate dehydrogenase / 0.815
4fj1 NAP17beta-hydroxysteroid dehydrogenase / 0.813
3rj9 NADAlcohol dehydrogenase 1.1.1.1 0.812
3d3w NAPL-xylulose reductase 1.1.1.10 0.809
1ae1 NAPTropinone reductase 1 / 0.807
5b1y NDP3-oxoacyl-[acyl-carrier-protein] reductase / 0.806
2c29 NAPDihydroflavonol 4-reductase / 0.804
4o0l NDPNADPH-dependent 3-quinuclidinone reductase / 0.803
3r3s NADPutative oxidoreductase / 0.800
1oaa NAPSepiapterin reductase 1.1.1.153 0.799
4qec NAPElxO / 0.798
1iy8 NADLevodione reductase / 0.797
1h5q NAPNADP-dependent mannitol dehydrogenase 1.1.1.138 0.795
4m87 NADEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.795
4j7u NAPSepiapterin reductase 1.1.1.153 0.793
4zju NADEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.793
2q2q NADBeta-D-hydroxybutyrate dehydrogenase / 0.792
4nbu NAI3-oxoacyl-(Acyl-carrier-protein) reductase / 0.792
5idw NAPShort-chain dehydrogenase/reductase SDR / 0.792
4rf2 NAPNADPH dependent R-specific alcohol dehydrogenase / 0.787
3ru9 NADUDP-N-acetylglucosamine 4-epimerase / 0.786
4wec NADShort chain dehydrogenase / 0.782
1g0n NDPTetrahydroxynaphthalene reductase 1.1.1.252 0.781
4hwk NAPSepiapterin reductase 1.1.1.153 0.778
3qwf NAP17beta-hydroxysteroid dehydrogenase / 0.776
2dte NAIGlucose 1-dehydrogenase related protein / 0.775
3uic NADEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.775
2bgm NAJSecoisolariciresinol dehydrogenase 1.1.1.331 0.772
2nnl NAPDihydroflavonol 4-reductase 1.1.1.219 0.772
1xse NDPCorticosteroid 11-beta-dehydrogenase isozyme 1 1.1.1.146 0.771
1ipe NDPTropinone reductase 2 1.1.1.236 0.769
1i2b NADUDP-sulfoquinovose synthase, chloroplastic 3.13.1.1 0.768
2h9i EADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.768
4yac NAIC alpha-dehydrogenase / 0.767
5cpb NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.767
2ewm NAD(S)-1-Phenylethanol dehydrogenase 1.1.1.311 0.766
1mg5 NAIAlcohol dehydrogenase 1.1.1.1 0.765
3wmx NADNAD dependent epimerase/dehydratase / 0.765
1ek5 NADUDP-glucose 4-epimerase / 0.764
1fdu NAPEstradiol 17-beta-dehydrogenase 1 1.1.1.62 0.764
4fj0 NAP17beta-hydroxysteroid dehydrogenase / 0.763
1u7t NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.762
2yut NAPPutative short-chain oxidoreductase / 0.759
4egb NADdTDP-glucose 4,6-dehydratase / 0.758
2ztu NADD(-)-3-hydroxybutyrate dehydrogenase / 0.756
4u7w NDPMxaA / 0.756
1sny NAPLD36273p / 0.755
3ruh NADUDP-N-acetylglucosamine 4-epimerase / 0.755
2ntj P1HEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.754
4twr NADNAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase / 0.751
5lc1 NADL-threonine 3-dehydrogenase / 0.750
3gy0 NAPNAD(P)-dependent oxidoreductase / 0.749
1eny NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.748
3uce NDPDehydrogenase / 0.748
2q1w NADPutative nucleotide sugar epimerase/ dehydratase / 0.746
2wdz NADGalactitol dehydrogenase / 0.745
1kvr NADUDP-glucose 4-epimerase 5.1.3.2 0.744
2p5y NADUDP-glucose 4-epimerase / 0.744
2aqh NAIEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.743
2c59 NADGDP-mannose 3,5-epimerase 5.1.3.18 0.743
3iah NAPPutative oxoacyl-(Acyl carrier protein) reductase / 0.743
4pvd NDPNADPH-dependent methylglyoxal reductase GRE2 / 0.743
2idz ZIDEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.742
4j7x NAPSepiapterin reductase 1.1.1.153 0.742
4o1m NADEnoyl-acyl carrier reductase / 0.740
1b16 NAQAlcohol dehydrogenase 1.1.1.1 0.739
3sj7 NDP3-oxoacyl-(Acyl-carrier-protein) reductase, putative / 0.739
3ru7 NADUDP-N-acetylglucosamine 4-epimerase / 0.737
4dc1 NDPPutative ketoacyl reductase 1.3.1 0.737
5jyd NADShort chain dehydrogenase / 0.737
1xkq NDPUncharacterized protein / 0.736
4bqp NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.736
4is3 NAD3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 1.17.98.1 0.735
1rwb NADGlucose 1-dehydrogenase 1.1.1.47 0.734
3lqf NADGalactitol dehydrogenase / 0.733
4i5e NAPAlclohol dehydrogenase/short-chain dehydrogenase / 0.733
1i3l NADUDP-glucose 4-epimerase / 0.732
3bmo NAPPteridine reductase / 0.732
2q1t NADPutative nucleotide sugar epimerase/ dehydratase / 0.731
3lu1 NADUDP-N-acetylglucosamine 4-epimerase / 0.731
4oxy NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.731
4nbw NADShort-chain dehydrogenase/reductase SDR / 0.729
3aw9 NADNAD-dependent epimerase/dehydratase / 0.726
3mje NDPAmphB / 0.725
2aqk NAIEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.724
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.724
1qyv NAPEstradiol 17-beta-dehydrogenase 1 1.1.1.62 0.723
1zem NADXylitol dehydrogenase / 0.723
1b15 NAEAlcohol dehydrogenase 1.1.1.1 0.721
1gee NADGlucose 1-dehydrogenase 1.1.1.47 0.721
3ndr NADPyridoxal 4-dehydrogenase 1.1.1.107 0.721
1vrw NAIEnoyl-ACP reductase / 0.718
2b4q NAPRhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase 1.1.1.100 0.716
2hrb NAPCarbonyl reductase [NADPH] 3 1.1.1.184 0.716
2ydx NAPMethionine adenosyltransferase 2 subunit beta / 0.716
4dre NAIEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.716
2ie0 ZIDEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.715
4b8z NAPGDP-L-fucose synthase 1.1.1.271 0.715
4hxy NDPPlm1 / 0.713
2nv6 ZIDEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.712
3sju NDPKeto reductase / 0.712
1enz NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.710
4lis NADUDP-glucose 4-epimerase (Eurofung) / 0.710
4hp8 NAP2-deoxy-D-gluconate 3-dehydrogenase / 0.709
4y9d NAIC alpha-dehydrogenase / 0.709
2b35 NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.708
5d2e NAPMlnE / 0.707
1b2l NDCAlcohol dehydrogenase 1.1.1.1 0.706
1gco NADGlucose 1-dehydrogenase 1.1.1.47 0.705
3oey NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.705
2dt5 NADRedox-sensing transcriptional repressor Rex / 0.704
2hmv ADPKtr system potassium uptake protein A / 0.704
3icp NADNAD-dependent epimerase/dehydratase / 0.704
3aut NAIGlucose 1-dehydrogenase 4 1.1.1.47 0.703
3tox NAPPutative oxidoreductase / 0.703
4k6f NAPPutative Acetoacetyl-CoA reductase / 0.701
2ieb ZIDEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.700
3ijr NADOxidoreductase, short chain dehydrogenase/reductase family / 0.700
4dqu NAIEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.700
5koi NADEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.700
3uxy NADShort-chain dehydrogenase/reductase SDR / 0.699
4fw8 NAI3-oxoacyl-(Acyl-carrier-protein) reductase / 0.699
2aqi NAIEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.698
2b37 NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.698
3ehe NADUDP-glucose 4-epimerase (GalE-1) / 0.696
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.695
3pef NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.694
3rua NADUDP-N-acetylglucosamine 4-epimerase / 0.694
1rkx NADCDP-D-glucose-4,6-dehydratase / 0.693
2yy7 NADL-threonine dehydrogenase / 0.693
4m55 NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.693
2p5u NADUDP-glucose 4-epimerase / 0.692
2ekp NAD2-deoxy-D-gluconate 3-dehydrogenase / 0.691
3oa2 NADUDP-N-acetyl-2-amino-2-deoxy-D-glucuronate oxidase / 0.691
3of2 NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.691
3sxp NADADP-L-glycero-D-mannoheptose-6-epimerase / 0.691
3rue NADUDP-N-acetylglucosamine 4-epimerase / 0.690
2nq8 ZIDEnoyl-ACP reductase / 0.688
2y05 NAPProstaglandin reductase 1 / 0.687
3ruf NADUDP-N-acetylglucosamine 4-epimerase / 0.687
4bgi NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.687
4eue NAITrans-2-enoyl-CoA reductase [NADH] / 0.687
5hws NAP2-dehydropantoate 2-reductase / 0.687
5jy1 NADPutative short-chain dehydrogenase/reductase / 0.687
1orr NADCDP-paratose 2-epimerase / 0.686
2zat NAPDehydrogenase/reductase SDR family member 4 1.1.1.184 0.686
2hun NAD336aa long hypothetical dTDP-glucose 4,6-dehydratase / 0.685
2wyv NADEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.685
3jyo NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.685
4imp NDPPolyketide synthase extender modules 3-4 / 0.685
4qed NAPElxO / 0.685
4trn NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.685
1nai NADUDP-glucose 4-epimerase 5.1.3.2 0.683
1g6k NADGlucose 1-dehydrogenase 1.1.1.47 0.682
2hsd NAD3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase 1.1.1.53 0.682
3o03 NAPDehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) / 0.682
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.682
2c54 NADGDP-mannose 3,5-epimerase 5.1.3.18 0.680
3rud NADUDP-N-acetylglucosamine 4-epimerase / 0.680
4gll NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.679
2gn8 NAPUDP-N-acetylglucosamine 4,6-dehydratase (inverting) 4.2.1.115 0.678
3g49 NAPCorticosteroid 11-beta-dehydrogenase isozyme 1 1.1.1.146 0.678
3ajr NADNDP-sugar epimerase / 0.677
2ggs NDPdTDP-4-dehydrorhamnose reductase / 0.675
3ec7 NADInositol 2-dehydrogenase / 0.675
1nah NADUDP-glucose 4-epimerase 5.1.3.2 0.674
2c7q SAHModification methylase HhaI 2.1.1.37 0.674
2ntv P1HEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.674
3oew NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.674
4b4o NDPEpimerase family protein SDR39U1 / 0.674
2b69 NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.673
3rfx NADUronate dehydrogenase / 0.673
1kc1 NDPdTDP-4-dehydrorhamnose reductase 1.1.1.133 0.672
3ko8 NADNAD-dependent epimerase/dehydratase / 0.672
3tri NAPPyrroline-5-carboxylate reductase / 0.671
4ej0 NAPADP-L-glycero-D-manno-heptose-6-epimerase / 0.671
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.670
4bms NAPAlclohol dehydrogenase/short-chain dehydrogenase / 0.670
2q1u NADPutative nucleotide sugar epimerase/ dehydratase / 0.669
1p1h NADInositol-3-phosphate synthase 5.5.1.4 0.668
2aq8 NAIEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.668
4bkq NAIEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.666
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.665
3wsw NADL-lactate dehydrogenase / 0.665
7mht SAHModification methylase HhaI 2.1.1.37 0.665
1g1a NADdTDP-glucose 4,6-dehydratase / 0.663
1n2s NAIdTDP-4-dehydrorhamnose reductase 1.1.1.133 0.663
2q1s NAIPutative nucleotide sugar epimerase/ dehydratase / 0.663
3a9w NADNDP-sugar epimerase / 0.661
3jyp NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.661
4clo NAPPteridine reductase / 0.661
2o06 MTASpermidine synthase 2.5.1.16 0.660
3h3j NADL-lactate dehydrogenase 1 1.1.1.27 0.658
4okn NAIL-lactate dehydrogenase A chain 1.1.1.27 0.657
5a05 NDPGlucose-fructose oxidoreductase / 0.657
2bfo NDPPteridine reductase 1 1.5.1.33 0.656
3pqf NADL-lactate dehydrogenase 1.1.1.27 0.656
4ek9 EP4Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.656
2g76 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.655
3t7s SAMUncharacterized protein / 0.655
1h6d NDPGlucose--fructose oxidoreductase 1.1.99.28 0.654
4lk3 NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.654
2bgl NAJSecoisolariciresinol dehydrogenase 1.1.1.331 0.653
2yw9 NAPEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.653
1j5p NADL-aspartate dehydrogenase 1.4.1.21 0.652
1uay ADNOxidoreductase / 0.652
1wzi NDPMalate dehydrogenase / 0.652
2ep7 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.652
2ldb NADL-lactate dehydrogenase 1.1.1.27 0.652
4c7k NAPCorticosteroid 11-beta-dehydrogenase isozyme 1 1.1.1.146 0.652
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.651
2g82 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.651
2ixb NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.651
1o6z NADMalate dehydrogenase / 0.650
1zmc NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.650
4yr9 NADL-threonine 3-dehydrogenase, mitochondrial 1.1.1.103 0.650