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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
3w8e NAD 3-hydroxybutyrate dehydrogenase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity
Align
3w8e NAD3-hydroxybutyrate dehydrogenase / 1.206
2ztl NADD(-)-3-hydroxybutyrate dehydrogenase / 1.109
3w8d NAD3-hydroxybutyrate dehydrogenase / 1.094
3w8f NAD3-hydroxybutyrate dehydrogenase / 1.093
2q2v NADBeta-D-hydroxybutyrate dehydrogenase / 1.058
2ztv NADD(-)-3-hydroxybutyrate dehydrogenase / 0.998
3vdq NAD3-hydroxybutyrate dehydrogenase / 0.983
2dte NAIGlucose 1-dehydrogenase related protein / 0.970
2ztm NADD(-)-3-hydroxybutyrate dehydrogenase / 0.968
1edo NAP3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic 1.1.1.100 0.947
3p19 NDPPutative blue fluorescent protein / 0.944
3wds NADNADH-dependent quinuclidinone reductase / 0.942
4dc0 NDPPutative ketoacyl reductase 1.3.1 0.940
5jsf NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.927
1x7h NDPPutative ketoacyl reductase 1.3.1 0.925
4b79 NADProbable short-chain dehydrogenase / 0.923
3nug NADPyridoxal 4-dehydrogenase 1.1.1.107 0.912
2wsb NADGalactitol dehydrogenase / 0.911
3qrw NDPPutative ketoacyl reductase 1.3.1 0.909
3ai3 NDPNADPH-sorbose reductase / 0.907
2gdz NAD15-hydroxyprostaglandin dehydrogenase [NAD(+)] 1.1.1.141 0.898
4bmv NAPShort-chain dehydrogenase / 0.897
5jla NADPutative short-chain dehydrogenase/reductase / 0.893
1x7g NAPPutative ketoacyl reductase 1.3.1 0.892
2q2q NADBeta-D-hydroxybutyrate dehydrogenase / 0.892
4iqg NAPShort-chain dehydrogenase/reductase SDR / 0.887
3pgx NADUncharacterized NAD-dependent oxidoreductase MAP_4146 / 0.883
2ekp NAD2-deoxy-D-gluconate 3-dehydrogenase / 0.881
5js6 NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.879
5ig2 NADShort-chain dehydrogenase/reductase SDR / 0.876
3ai2 NDPNADPH-sorbose reductase / 0.874
4dbz NDPPutative ketoacyl reductase 1.3.1 0.873
2jah NDPClavaldehyde dehydrogenase / 0.870
4fj2 NAP17beta-hydroxysteroid dehydrogenase / 0.868
1h5q NAPNADP-dependent mannitol dehydrogenase 1.1.1.138 0.863
2dkn NAI3-alpha-hydroxysteroid dehydrogenase / 0.863
3a28 NADL-2,3-butanediol dehydrogenase 1.1.1.76 0.863
3ak4 NADNADH-dependent quinuclidinone reductase / 0.862
4fj1 NAP17beta-hydroxysteroid dehydrogenase / 0.862
1ae1 NAPTropinone reductase 1 / 0.861
2ztu NADD(-)-3-hydroxybutyrate dehydrogenase / 0.861
3bhi NAPCarbonyl reductase [NADPH] 1 1.1.1.184 0.861
3rj5 NADAlcohol dehydrogenase 1.1.1.1 0.856
4kwh NAPReductase homolog / 0.856
1bdb NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase / 0.853
2b4q NAPRhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase 1.1.1.100 0.852
1xg5 NAPDehydrogenase/reductase SDR family member 11 / 0.851
3rj9 NADAlcohol dehydrogenase 1.1.1.1 0.850
3qwf NAP17beta-hydroxysteroid dehydrogenase / 0.849
1xse NDPCorticosteroid 11-beta-dehydrogenase isozyme 1 1.1.1.146 0.848
1cyd NDPCarbonyl reductase [NADPH] 2 1.1.1.184 0.847
4rf2 NAPNADPH dependent R-specific alcohol dehydrogenase / 0.847
4z3d NDPCarbonyl reductase [NADPH] 1 1.1.1.184 0.846
1geg NADDiacetyl reductase [(S)-acetoin forming] 1.1.1.304 0.845
2o23 NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.842
3rku NAPNADP-dependent 3-hydroxy acid dehydrogenase / 0.842
4pvd NDPNADPH-dependent methylglyoxal reductase GRE2 / 0.840
4j7u NAPSepiapterin reductase 1.1.1.153 0.837
2d1y NADOxidoreductase, short-chain dehydrogenase/reductase family / 0.836
4dc1 NDPPutative ketoacyl reductase 1.3.1 0.833
2rbe NDPCorticosteroid 11-beta-dehydrogenase isozyme 1 1.1.1.146 0.831
4gh5 NADShort-chain dehydrogenase/reductase SDR / 0.831
3l77 NJPShort-chain alcohol dehydrogenase / 0.829
3o26 NDPSalutaridine reductase / 0.828
4hwk NAPSepiapterin reductase 1.1.1.153 0.827
4yai NAIC alpha-dehydrogenase / 0.827
2zat NAPDehydrogenase/reductase SDR family member 4 1.1.1.184 0.821
3sx2 NADUncharacterized protein / 0.820
1oaa NAPSepiapterin reductase 1.1.1.153 0.818
3tn7 NJPShort-chain alcohol dehydrogenase / 0.817
4fn4 NADShort chain dehydrogenase / 0.817
4wec NADShort chain dehydrogenase / 0.816
3geg NADShort-chain dehydrogenase/reductase SDR / 0.810
4c7k NAPCorticosteroid 11-beta-dehydrogenase isozyme 1 1.1.1.146 0.808
4fj0 NAP17beta-hydroxysteroid dehydrogenase / 0.807
3s55 NADPutative short-chain dehydrogenase/reductase / 0.806
1mg5 NAIAlcohol dehydrogenase 1.1.1.1 0.805
3iah NAPPutative oxoacyl-(Acyl carrier protein) reductase / 0.805
1e3s NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.804
4j7x NAPSepiapterin reductase 1.1.1.153 0.802
1n5d NDPCarbonyl reductase [NADPH] 1 / 0.801
1rwb NADGlucose 1-dehydrogenase 1.1.1.47 0.801
1g0n NDPTetrahydroxynaphthalene reductase 1.1.1.252 0.799
4zju NADEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.799
4hp8 NAP2-deoxy-D-gluconate 3-dehydrogenase / 0.796
1w4z NAPPutative ketoacyl reductase 1.3.1 0.794
2y99 NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase 1.3.1.56 0.794
4nbt NAD3-oxoacyl-[acyl-carrier-protein] reductase / 0.794
2ag5 NAD3-hydroxybutyrate dehydrogenase type 2 / 0.792
3ijr NADOxidoreductase, short chain dehydrogenase/reductase family / 0.791
4k6f NAPPutative Acetoacetyl-CoA reductase / 0.790
3gy0 NAPNAD(P)-dependent oxidoreductase / 0.788
2yy7 NADL-threonine dehydrogenase / 0.787
3tsc NADUncharacterized protein / 0.780
4yag NAIC alpha-dehydrogenase / 0.780
5idw NAPShort-chain dehydrogenase/reductase SDR / 0.780
1nfr NAD3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase 1.1.1.53 0.777
2c29 NAPDihydroflavonol 4-reductase / 0.777
3r3s NADPutative oxidoreductase / 0.777
2p5y NADUDP-glucose 4-epimerase / 0.775
4o0l NDPNADPH-dependent 3-quinuclidinone reductase / 0.774
1ipe NDPTropinone reductase 2 1.1.1.236 0.773
1zem NADXylitol dehydrogenase / 0.771
2bgm NAJSecoisolariciresinol dehydrogenase 1.1.1.331 0.771
2ntj P1HEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.771
1i2b NADUDP-sulfoquinovose synthase, chloroplastic 3.13.1.1 0.767
2bd0 NAPSepiapterin reductase / 0.765
2ieb ZIDEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.764
3d3w NAPL-xylulose reductase 1.1.1.10 0.764
4u7w NDPMxaA / 0.764
2wyv NADEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.763
3mje NDPAmphB / 0.763
1b16 NAQAlcohol dehydrogenase 1.1.1.1 0.761
2idz ZIDEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.761
3oew NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.759
4nbu NAI3-oxoacyl-(Acyl-carrier-protein) reductase / 0.759
4dmm NAP3-oxoacyl-[acyl-carrier-protein] reductase / 0.758
1kvr NADUDP-glucose 4-epimerase 5.1.3.2 0.757
1vl8 NAPOxidoreductase, short chain dehydrogenase/reductase family / 0.757
4m87 NADEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.757
4qec NAPElxO / 0.757
1pr9 NAPL-xylulose reductase 1.1.1.10 0.756
2c59 NADGDP-mannose 3,5-epimerase 5.1.3.18 0.755
4is3 NAD3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 1.17.98.1 0.755
4trn NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.754
1sny NAPLD36273p / 0.753
4nbw NADShort-chain dehydrogenase/reductase SDR / 0.751
2nnl NAPDihydroflavonol 4-reductase 1.1.1.219 0.750
1fdu NAPEstradiol 17-beta-dehydrogenase 1 1.1.1.62 0.749
1u7t TDT3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.749
1eny NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.748
1gco NADGlucose 1-dehydrogenase 1.1.1.47 0.748
1gee NADGlucose 1-dehydrogenase 1.1.1.47 0.748
2p5u NADUDP-glucose 4-epimerase / 0.747
1qyv NAPEstradiol 17-beta-dehydrogenase 1 1.1.1.62 0.746
1u7t NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.746
3uic NADEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.746
3g49 NAPCorticosteroid 11-beta-dehydrogenase isozyme 1 1.1.1.146 0.744
3of2 NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.744
4eue NAITrans-2-enoyl-CoA reductase [NADH] / 0.744
3aw9 NADNAD-dependent epimerase/dehydratase / 0.743
4qed NAPElxO / 0.742
1xkq NDPUncharacterized protein / 0.741
2nv6 ZIDEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.741
2aq8 NAIEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.739
5jyd NADShort chain dehydrogenase / 0.739
1nff NAD3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase 1.1.1.53 0.738
4fw8 NAI3-oxoacyl-(Acyl-carrier-protein) reductase / 0.738
2h9i EADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.735
2aqh NAIEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.733
3oey NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.732
5cpb NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.731
2q1w NADPutative nucleotide sugar epimerase/ dehydratase / 0.729
2b35 NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.728
3lu1 NADUDP-N-acetylglucosamine 4-epimerase / 0.728
3a9w NADNDP-sugar epimerase / 0.727
3h4v NAPPteridine reductase 1 1.5.1.33 0.726
4bms NAPAlclohol dehydrogenase/short-chain dehydrogenase / 0.726
1e6w NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.725
4lis NADUDP-glucose 4-epimerase (Eurofung) / 0.725
3ndr NADPyridoxal 4-dehydrogenase 1.1.1.107 0.724
4dti NAIEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.724
3ruh NADUDP-N-acetylglucosamine 4-epimerase / 0.722
3ruc NADUDP-N-acetylglucosamine 4-epimerase / 0.721
4twr NADNAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase / 0.720
5jy1 NADPutative short-chain dehydrogenase/reductase / 0.720
1enz NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.719
3ru7 NADUDP-N-acetylglucosamine 4-epimerase / 0.719
4bqp NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.719
2hrb NAPCarbonyl reductase [NADPH] 3 1.1.1.184 0.716
4ej0 NAPADP-L-glycero-D-manno-heptose-6-epimerase / 0.716
5d2e NAPMlnE / 0.716
3tox NAPPutative oxidoreductase / 0.714
5koi NADEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.713
1i36 NAPConserved protein / 0.712
3bmo NAPPteridine reductase / 0.710
3wmx NADNAD dependent epimerase/dehydratase / 0.710
4o1m NADEnoyl-acyl carrier reductase / 0.710
5b1y NDP3-oxoacyl-[acyl-carrier-protein] reductase / 0.710
1e3w NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.709
1b14 NADAlcohol dehydrogenase 1.1.1.1 0.708
3a4v NADNDP-sugar epimerase / 0.708
3ko8 NADNAD-dependent epimerase/dehydratase / 0.708
3sj7 NDP3-oxoacyl-(Acyl-carrier-protein) reductase, putative / 0.708
2ie0 ZIDEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.705
3ajr NADNDP-sugar epimerase / 0.705
1rkx NADCDP-D-glucose-4,6-dehydratase / 0.704
2aqi NAIEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.704
3aut NAIGlucose 1-dehydrogenase 4 1.1.1.47 0.704
4dre NAIEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.703
1b2l NDCAlcohol dehydrogenase 1.1.1.1 0.701
2ydx NAPMethionine adenosyltransferase 2 subunit beta / 0.701
4bii NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.701
2wdz NADGalactitol dehydrogenase / 0.700
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.700
3o03 NAPDehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) / 0.699
3pdu NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.697
3pef NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.696
3sju NDPKeto reductase / 0.696
2c20 NADUDP-glucose 4-epimerase / 0.694
4fc7 NAPPeroxisomal 2,4-dienoyl-CoA reductase 1.3.1.34 0.693
2bfo NDPPteridine reductase 1 1.5.1.33 0.691
4egb NADdTDP-glucose 4,6-dehydratase / 0.690
2pr2 DG1Enoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.689
3lqf NADGalactitol dehydrogenase / 0.689
4b4o NDPEpimerase family protein SDR39U1 / 0.689
2q1t NADPutative nucleotide sugar epimerase/ dehydratase / 0.688
4oxy NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.687
1g6k NADGlucose 1-dehydrogenase 1.1.1.47 0.686
2nq8 ZIDEnoyl-ACP reductase / 0.684
4hxy NDPPlm1 / 0.683
2b69 NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.682
4bkq NAIEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.682
4xrg NADHomospermidine synthase 2.5.1.44 0.680
4eso NAPPutative oxidoreductase / 0.679
2ntv P1HEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.678
4xqc NADHomospermidine synthase 2.5.1.44 0.678
4xq9 NADHomospermidine synthase 2.5.1.44 0.677
2rcy NAPPyrroline-5-carboxylate reductase / 0.676
3abi NADUncharacterized protein / 0.676
4cql NADEstradiol 17-beta-dehydrogenase 8 1.1.1.62 0.676
4tvb NADHomospermidine synthase 2.5.1.44 0.676
1i3l NADUDP-glucose 4-epimerase / 0.675
1iy8 NADLevodione reductase / 0.675
2yw9 NAPEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.675
4bgi NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.675
4idg NADPutative UDP-glucose 4-epimerase / 0.674
2aqk NAIEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.673
3ru9 NADUDP-N-acetylglucosamine 4-epimerase / 0.673
3uxy NADShort-chain dehydrogenase/reductase SDR / 0.673
2pzj NADPutative nucleotide sugar epimerase/ dehydratase / 0.672
3d4p NADL-lactate dehydrogenase 1 1.1.1.27 0.672
4gll NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.672
4n5n NAPAcetoacetyl-CoA reductase 1.1.1.36 0.671
1b15 NAEAlcohol dehydrogenase 1.1.1.1 0.670
1wzi NDPMalate dehydrogenase / 0.670
1nah NADUDP-glucose 4-epimerase 5.1.3.2 0.669
3icp NADNAD-dependent epimerase/dehydratase / 0.669
2ggs NDPdTDP-4-dehydrorhamnose reductase / 0.668
2gv8 NDPThiol-specific monooxygenase 1.14.13 0.667
2hsd NAD3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase 1.1.1.53 0.667
1w73 NAP2,4-dienoyl-CoA reductase, mitochondrial 1.3.1.34 0.666
3rua NADUDP-N-acetylglucosamine 4-epimerase / 0.666
1nvm NADAcetaldehyde dehydrogenase 1.2.1.10 0.665
3a1n NADNDP-sugar epimerase / 0.665
1sby NADAlcohol dehydrogenase 1.1.1.1 0.664
1lsj NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.663
3zu2 NAIEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.663
5hws NAP2-dehydropantoate 2-reductase / 0.663
2x0r NADMalate dehydrogenase / 0.662
5kjc NAJAlcohol dehydrogenase E chain 1.1.1.1 0.661
3ruf NADUDP-N-acetylglucosamine 4-epimerase / 0.660
3sxp NADADP-L-glycero-D-mannoheptose-6-epimerase / 0.660
1r37 NADNAD-dependent alcohol dehydrogenase 1.1.1.1 0.658
3rue NADUDP-N-acetylglucosamine 4-epimerase / 0.658
3dtt NAPNADP oxidoreductase, coenzyme F420-dependent / 0.657
4y0k NAPAntE / 0.657
1dir NADDihydropteridine reductase 1.5.1.34 0.656
4i5e NAPAlclohol dehydrogenase/short-chain dehydrogenase / 0.656
5kcp NAJAlcohol dehydrogenase E chain 1.1.1.1 0.656
1fk8 NAD3-alpha-hydroxysteroid dehydrogenase/carbonyl reductase 1.1.1.50 0.655
1pzg A3DLactate dehydrogenase / 0.655
2b37 NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.655
4y1b NAPAntE / 0.655
1f0y NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.654
2a94 AP0L-lactate dehydrogenase 1.1.1.27 0.654
1n2s NAIdTDP-4-dehydrorhamnose reductase 1.1.1.133 0.653
1w8d NAP2,4-dienoyl-CoA reductase, mitochondrial 1.3.1.34 0.652
1hdz NADAlcohol dehydrogenase 1B 1.1.1.1 0.650
2bgl NAJSecoisolariciresinol dehydrogenase 1.1.1.331 0.650
3ehe NADUDP-glucose 4-epimerase (GalE-1) / 0.650
3zw9 NADPeroxisomal bifunctional enzyme 1.1.1.35 0.650
4mdh NADMalate dehydrogenase, cytoplasmic 1.1.1.37 0.650