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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
3vdq NAD 3-hydroxybutyrate dehydrogenase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity
Align
3vdq NAD3-hydroxybutyrate dehydrogenase / 1.113
2ztl NADD(-)-3-hydroxybutyrate dehydrogenase / 1.013
3w8f NAD3-hydroxybutyrate dehydrogenase / 0.986
3w8e NAD3-hydroxybutyrate dehydrogenase / 0.983
2q2v NADBeta-D-hydroxybutyrate dehydrogenase / 0.970
3w8d NAD3-hydroxybutyrate dehydrogenase / 0.965
2ztm NADD(-)-3-hydroxybutyrate dehydrogenase / 0.960
4rf2 NAPNADPH dependent R-specific alcohol dehydrogenase / 0.924
1x7h NDPPutative ketoacyl reductase 1.3.1 0.914
5js6 NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.904
5jsf NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.896
2ztv NADD(-)-3-hydroxybutyrate dehydrogenase / 0.894
1x7g NAPPutative ketoacyl reductase 1.3.1 0.891
3wds NADNADH-dependent quinuclidinone reductase / 0.888
3rj5 NADAlcohol dehydrogenase 1.1.1.1 0.883
3p19 NDPPutative blue fluorescent protein / 0.878
4b79 NADProbable short-chain dehydrogenase / 0.871
2q2q NADBeta-D-hydroxybutyrate dehydrogenase / 0.864
1edo NAP3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic 1.1.1.100 0.863
4z3d NDPCarbonyl reductase [NADPH] 1 1.1.1.184 0.862
2dte NAIGlucose 1-dehydrogenase related protein / 0.858
3qrw NDPPutative ketoacyl reductase 1.3.1 0.856
4dc1 NDPPutative ketoacyl reductase 1.3.1 0.853
3pgx NADUncharacterized NAD-dependent oxidoreductase MAP_4146 / 0.852
3ak4 NADNADH-dependent quinuclidinone reductase / 0.850
4gh5 NADShort-chain dehydrogenase/reductase SDR / 0.847
4fj2 NAP17beta-hydroxysteroid dehydrogenase / 0.844
3ai3 NDPNADPH-sorbose reductase / 0.843
2wsb NADGalactitol dehydrogenase / 0.837
2d1y NADOxidoreductase, short-chain dehydrogenase/reductase family / 0.836
4dbz NDPPutative ketoacyl reductase 1.3.1 0.835
3geg NADShort-chain dehydrogenase/reductase SDR / 0.833
4pvd NDPNADPH-dependent methylglyoxal reductase GRE2 / 0.832
3nug NADPyridoxal 4-dehydrogenase 1.1.1.107 0.825
2jah NDPClavaldehyde dehydrogenase / 0.820
4c7k NAPCorticosteroid 11-beta-dehydrogenase isozyme 1 1.1.1.146 0.820
4zju NADEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.820
1xg5 NAPDehydrogenase/reductase SDR family member 11 / 0.819
4fn4 NADShort chain dehydrogenase / 0.819
2gdz NAD15-hydroxyprostaglandin dehydrogenase [NAD(+)] 1.1.1.141 0.816
3sju NDPKeto reductase / 0.816
1n5d NDPCarbonyl reductase [NADPH] 1 / 0.815
2ztu NADD(-)-3-hydroxybutyrate dehydrogenase / 0.815
3ai2 NDPNADPH-sorbose reductase / 0.814
3rj9 NADAlcohol dehydrogenase 1.1.1.1 0.814
1h5q NAPNADP-dependent mannitol dehydrogenase 1.1.1.138 0.813
2zat NAPDehydrogenase/reductase SDR family member 4 1.1.1.184 0.812
1cyd NDPCarbonyl reductase [NADPH] 2 1.1.1.184 0.809
3o4r NAPDehydrogenase/reductase SDR family member 4 1.1.1.184 0.809
3r3s NADPutative oxidoreductase / 0.809
2dkn NAI3-alpha-hydroxysteroid dehydrogenase / 0.808
5jla NADPutative short-chain dehydrogenase/reductase / 0.808
3tn7 NJPShort-chain alcohol dehydrogenase / 0.806
1w4z NAPPutative ketoacyl reductase 1.3.1 0.805
2ekp NAD2-deoxy-D-gluconate 3-dehydrogenase / 0.805
3o26 NDPSalutaridine reductase / 0.804
3qwf NAP17beta-hydroxysteroid dehydrogenase / 0.803
4j7x NAPSepiapterin reductase 1.1.1.153 0.801
2rbe NDPCorticosteroid 11-beta-dehydrogenase isozyme 1 1.1.1.146 0.800
5ig2 NADShort-chain dehydrogenase/reductase SDR / 0.799
4dc0 NDPPutative ketoacyl reductase 1.3.1 0.798
1ipe NDPTropinone reductase 2 1.1.1.236 0.796
4is3 NAD3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 1.17.98.1 0.792
4kwh NAPReductase homolog / 0.789
2ag5 NAD3-hydroxybutyrate dehydrogenase type 2 / 0.788
3tsc NADUncharacterized protein / 0.788
3bhi NAPCarbonyl reductase [NADPH] 1 1.1.1.184 0.786
4bmv NAPShort-chain dehydrogenase / 0.784
4fj1 NAP17beta-hydroxysteroid dehydrogenase / 0.783
4dmm NAP3-oxoacyl-[acyl-carrier-protein] reductase / 0.782
1oaa NAPSepiapterin reductase 1.1.1.153 0.778
1ae1 NAPTropinone reductase 1 / 0.777
4yag NAIC alpha-dehydrogenase / 0.775
1bdb NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase / 0.772
2q1t NADPutative nucleotide sugar epimerase/ dehydratase / 0.772
3a28 NADL-2,3-butanediol dehydrogenase 1.1.1.76 0.772
1vl8 NAPOxidoreductase, short chain dehydrogenase/reductase family / 0.766
1g0n NDPTetrahydroxynaphthalene reductase 1.1.1.252 0.765
1geg NADDiacetyl reductase [(S)-acetoin forming] 1.1.1.304 0.764
1xse NDPCorticosteroid 11-beta-dehydrogenase isozyme 1 1.1.1.146 0.763
1e6w NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.762
4hwk NAPSepiapterin reductase 1.1.1.153 0.762
5idw NAPShort-chain dehydrogenase/reductase SDR / 0.762
3of2 NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.761
5jyd NADShort chain dehydrogenase / 0.761
3oey NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.760
1b16 NAQAlcohol dehydrogenase 1.1.1.1 0.758
1sny NAPLD36273p / 0.757
3ijr NADOxidoreductase, short chain dehydrogenase/reductase family / 0.757
2yy7 NADL-threonine dehydrogenase / 0.756
4m87 NADEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.755
4hp8 NAP2-deoxy-D-gluconate 3-dehydrogenase / 0.754
4trn NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.754
1rwb NADGlucose 1-dehydrogenase 1.1.1.47 0.753
1pr9 NAPL-xylulose reductase 1.1.1.10 0.751
4k6f NAPPutative Acetoacetyl-CoA reductase / 0.751
2wdz NADGalactitol dehydrogenase / 0.750
3oew NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.748
1nfr NAD3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase 1.1.1.53 0.747
2ntj P1HEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.745
4yai NAIC alpha-dehydrogenase / 0.745
2wyv NADEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.744
3d3w NAPL-xylulose reductase 1.1.1.10 0.743
3sx2 NADUncharacterized protein / 0.743
1e3s NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.742
4bii NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.742
4dre NAIEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.742
3gy0 NAPNAD(P)-dependent oxidoreductase / 0.741
3l77 NJPShort-chain alcohol dehydrogenase / 0.741
3iah NAPPutative oxoacyl-(Acyl carrier protein) reductase / 0.740
4nbt NAD3-oxoacyl-[acyl-carrier-protein] reductase / 0.740
1gee NADGlucose 1-dehydrogenase 1.1.1.47 0.739
2c29 NAPDihydroflavonol 4-reductase / 0.739
2nnl NAPDihydroflavonol 4-reductase 1.1.1.219 0.739
3s55 NADPutative short-chain dehydrogenase/reductase / 0.739
2b4q NAPRhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase 1.1.1.100 0.737
4cql NADEstradiol 17-beta-dehydrogenase 8 1.1.1.62 0.736
5cpb NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.733
4o0l NDPNADPH-dependent 3-quinuclidinone reductase / 0.732
3ndr NADPyridoxal 4-dehydrogenase 1.1.1.107 0.730
4qec NAPElxO / 0.730
1eny NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.726
2b35 NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.726
1gco NADGlucose 1-dehydrogenase 1.1.1.47 0.725
1qyv NAPEstradiol 17-beta-dehydrogenase 1 1.1.1.62 0.724
1zem NADXylitol dehydrogenase / 0.724
2idz ZIDEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.724
2o23 NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.723
1i2b NADUDP-sulfoquinovose synthase, chloroplastic 3.13.1.1 0.721
2q1w NADPutative nucleotide sugar epimerase/ dehydratase / 0.721
1i3l NADUDP-glucose 4-epimerase / 0.720
3tox NAPPutative oxidoreductase / 0.720
4wec NADShort chain dehydrogenase / 0.720
1ek5 NADUDP-glucose 4-epimerase / 0.719
2b37 NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.718
3h4v NAPPteridine reductase 1 1.5.1.33 0.718
3sj7 NDP3-oxoacyl-(Acyl-carrier-protein) reductase, putative / 0.718
2bd0 NAPSepiapterin reductase / 0.717
3uic NADEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.717
4nbu NAI3-oxoacyl-(Acyl-carrier-protein) reductase / 0.717
2ieb ZIDEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.716
3aw9 NADNAD-dependent epimerase/dehydratase / 0.716
4qed NAPElxO / 0.715
2aqh NAIEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.713
2h9i EADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.713
2c59 NADGDP-mannose 3,5-epimerase 5.1.3.18 0.711
4o1m NADEnoyl-acyl carrier reductase / 0.711
4dti NAIEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.710
4oxy NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.710
5jy1 NADPutative short-chain dehydrogenase/reductase / 0.709
1fdu NAPEstradiol 17-beta-dehydrogenase 1 1.1.1.62 0.708
3pdu NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.708
3bmo NAPPteridine reductase / 0.707
2pzj NADPutative nucleotide sugar epimerase/ dehydratase / 0.706
5bt9 NAP3-oxoacyl-(Acyl-carrier-protein) reductase / 0.705
3lqf NADGalactitol dehydrogenase / 0.704
4j7u NAPSepiapterin reductase 1.1.1.153 0.703
4lis NADUDP-glucose 4-epimerase (Eurofung) / 0.703
1w73 NAP2,4-dienoyl-CoA reductase, mitochondrial 1.3.1.34 0.702
2aq8 NAIEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.702
4fj0 NAP17beta-hydroxysteroid dehydrogenase / 0.702
1b15 NAEAlcohol dehydrogenase 1.1.1.1 0.701
4clo NAPPteridine reductase / 0.701
3pef NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.700
1sby NADAlcohol dehydrogenase 1.1.1.1 0.698
3uce NDPDehydrogenase / 0.698
1mg5 NAIAlcohol dehydrogenase 1.1.1.1 0.697
1u7t TDT3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.697
4u7w NDPMxaA / 0.697
5koi NADEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.697
1enz NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.696
1nff NAD3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase 1.1.1.53 0.696
5d2e NAPMlnE / 0.696
2bfo NDPPteridine reductase 1 1.5.1.33 0.695
4bms NAPAlclohol dehydrogenase/short-chain dehydrogenase / 0.695
2nv6 ZIDEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.694
2y99 NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase 1.3.1.56 0.694
2hun NAD336aa long hypothetical dTDP-glucose 4,6-dehydratase / 0.693
3o03 NAPDehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) / 0.693
4bqp NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.692
4fw8 NAI3-oxoacyl-(Acyl-carrier-protein) reductase / 0.692
1b14 NADAlcohol dehydrogenase 1.1.1.1 0.691
3aut NAIGlucose 1-dehydrogenase 4 1.1.1.47 0.690
2p5y NADUDP-glucose 4-epimerase / 0.689
2b69 NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.687
3ru7 NADUDP-N-acetylglucosamine 4-epimerase / 0.687
4bgi NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.687
4dqu NAIEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.687
3mje NDPAmphB / 0.686
2ntv P1HEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.685
1g6k NADGlucose 1-dehydrogenase 1.1.1.47 0.684
1iy8 NADLevodione reductase / 0.683
3ko8 NADNAD-dependent epimerase/dehydratase / 0.683
3a4v NADNDP-sugar epimerase / 0.682
4nbw NADShort-chain dehydrogenase/reductase SDR / 0.680
2yw9 NAPEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.679
1e3w NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.678
3f1k NAPUncharacterized oxidoreductase YciK 1 0.678
3icp NADNAD-dependent epimerase/dehydratase / 0.676
2aqk NAIEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.675
1i36 NAPConserved protein / 0.673
3g49 NAPCorticosteroid 11-beta-dehydrogenase isozyme 1 1.1.1.146 0.673
1w8d NAP2,4-dienoyl-CoA reductase, mitochondrial 1.3.1.34 0.672
4eue NAITrans-2-enoyl-CoA reductase [NADH] / 0.671
3sxp NADADP-L-glycero-D-mannoheptose-6-epimerase / 0.670
4hbg NDP3-oxoacyl-[acyl-carrier-protein] reductase 1.1.1.100 0.670
4n5n NAPAcetoacetyl-CoA reductase 1.1.1.36 0.670
5b1y NDP3-oxoacyl-[acyl-carrier-protein] reductase / 0.670
1fk8 NAD3-alpha-hydroxysteroid dehydrogenase/carbonyl reductase 1.1.1.50 0.669
3rua NADUDP-N-acetylglucosamine 4-epimerase / 0.669
1nai NADUDP-glucose 4-epimerase 5.1.3.2 0.667
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.666
2pr2 DG1Enoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.666
2b36 NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.665
2bgl NAJSecoisolariciresinol dehydrogenase 1.1.1.331 0.665
3zu2 NAIEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.665
1g1a NADdTDP-glucose 4,6-dehydratase / 0.664
2ie0 ZIDEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.664
2jkv NAP6-phosphogluconate dehydrogenase, decarboxylating 1.1.1.44 0.664
1bxk NADdTDP-glucose 4,6-dehydratase 2 / 0.663
4hxy NDPPlm1 / 0.662
4idg NADPutative UDP-glucose 4-epimerase / 0.662
4xgi NADGlutamate dehydrogenase / 0.662
1b2l NDCAlcohol dehydrogenase 1.1.1.1 0.661
3a9w NADNDP-sugar epimerase / 0.661
5hws NAP2-dehydropantoate 2-reductase / 0.661
2aqi NAIEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.660
3phj DHKShikimate dehydrogenase (NADP(+)) / 0.660
4yr9 NADL-threonine 3-dehydrogenase, mitochondrial 1.1.1.103 0.660
1u7t NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.657
2c54 NADGDP-mannose 3,5-epimerase 5.1.3.18 0.657
4egb NADdTDP-glucose 4,6-dehydratase / 0.657
3abi NADUncharacterized protein / 0.656
3ruh NADUDP-N-acetylglucosamine 4-epimerase / 0.656
5lc1 NADL-threonine 3-dehydrogenase / 0.656
3a1n NADNDP-sugar epimerase / 0.655
1lsj NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.654
2rcy NAPPyrroline-5-carboxylate reductase / 0.653
3ehe NADUDP-glucose 4-epimerase (GalE-1) / 0.653
1xkq NDPUncharacterized protein / 0.652
4ej0 NAPADP-L-glycero-D-manno-heptose-6-epimerase / 0.652
1a71 NADAlcohol dehydrogenase E chain 1.1.1.1 0.650
4ng5 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.650
4xrg NADHomospermidine synthase 2.5.1.44 0.650