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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
3w8f NAD 3-hydroxybutyrate dehydrogenase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity
Align
3w8f NAD3-hydroxybutyrate dehydrogenase / 1.236
3w8d NAD3-hydroxybutyrate dehydrogenase / 1.229
2ztl NADD(-)-3-hydroxybutyrate dehydrogenase / 1.124
2q2v NADBeta-D-hydroxybutyrate dehydrogenase / 1.116
2ztm NADD(-)-3-hydroxybutyrate dehydrogenase / 1.111
3w8e NAD3-hydroxybutyrate dehydrogenase / 1.093
1x7h NDPPutative ketoacyl reductase 1.3.1 1.018
2ztv NADD(-)-3-hydroxybutyrate dehydrogenase / 1.008
4b79 NADProbable short-chain dehydrogenase / 0.995
3p19 NDPPutative blue fluorescent protein / 0.986
3vdq NAD3-hydroxybutyrate dehydrogenase / 0.986
1edo NAP3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic 1.1.1.100 0.967
4dc0 NDPPutative ketoacyl reductase 1.3.1 0.945
2wsb NADGalactitol dehydrogenase / 0.944
3wds NADNADH-dependent quinuclidinone reductase / 0.944
5jsf NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.936
4kwh NAPReductase homolog / 0.932
3ak4 NADNADH-dependent quinuclidinone reductase / 0.931
3qrw NDPPutative ketoacyl reductase 1.3.1 0.931
5js6 NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.929
4dbz NDPPutative ketoacyl reductase 1.3.1 0.923
2o23 NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.921
2dte NAIGlucose 1-dehydrogenase related protein / 0.920
4dc1 NDPPutative ketoacyl reductase 1.3.1 0.919
2q2q NADBeta-D-hydroxybutyrate dehydrogenase / 0.914
1oaa NAPSepiapterin reductase 1.1.1.153 0.910
2jah NDPClavaldehyde dehydrogenase / 0.910
4fn4 NADShort chain dehydrogenase / 0.909
3bhi NAPCarbonyl reductase [NADPH] 1 1.1.1.184 0.907
5ig2 NADShort-chain dehydrogenase/reductase SDR / 0.902
1pr9 NAPL-xylulose reductase 1.1.1.10 0.897
2dkn NAI3-alpha-hydroxysteroid dehydrogenase / 0.897
1x7g NAPPutative ketoacyl reductase 1.3.1 0.894
3ai3 NDPNADPH-sorbose reductase / 0.890
3o26 NDPSalutaridine reductase / 0.889
2gdz NAD15-hydroxyprostaglandin dehydrogenase [NAD(+)] 1.1.1.141 0.881
5jla NADPutative short-chain dehydrogenase/reductase / 0.881
4z3d NDPCarbonyl reductase [NADPH] 1 1.1.1.184 0.877
1ae1 NAPTropinone reductase 1 / 0.874
3pgx NADUncharacterized NAD-dependent oxidoreductase MAP_4146 / 0.873
4yag NAIC alpha-dehydrogenase / 0.873
1e6w NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.871
3ai2 NDPNADPH-sorbose reductase / 0.871
4rf2 NAPNADPH dependent R-specific alcohol dehydrogenase / 0.869
1n5d NDPCarbonyl reductase [NADPH] 1 / 0.867
3rj5 NADAlcohol dehydrogenase 1.1.1.1 0.867
1geg NADDiacetyl reductase [(S)-acetoin forming] 1.1.1.304 0.865
1w4z NAPPutative ketoacyl reductase 1.3.1 0.865
3rku NAPNADP-dependent 3-hydroxy acid dehydrogenase / 0.865
4fj1 NAP17beta-hydroxysteroid dehydrogenase / 0.861
1bdb NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase / 0.856
1e3w NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.856
4bmv NAPShort-chain dehydrogenase / 0.856
4fj2 NAP17beta-hydroxysteroid dehydrogenase / 0.856
1h5q NAPNADP-dependent mannitol dehydrogenase 1.1.1.138 0.854
3d3w NAPL-xylulose reductase 1.1.1.10 0.852
3nug NADPyridoxal 4-dehydrogenase 1.1.1.107 0.851
3l77 NJPShort-chain alcohol dehydrogenase / 0.849
4j7u NAPSepiapterin reductase 1.1.1.153 0.849
4fj0 NAP17beta-hydroxysteroid dehydrogenase / 0.847
4j7x NAPSepiapterin reductase 1.1.1.153 0.847
2c29 NAPDihydroflavonol 4-reductase / 0.846
2ekp NAD2-deoxy-D-gluconate 3-dehydrogenase / 0.843
3rj9 NADAlcohol dehydrogenase 1.1.1.1 0.843
4o0l NDPNADPH-dependent 3-quinuclidinone reductase / 0.842
4is3 NAD3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 1.17.98.1 0.841
1ipe NDPTropinone reductase 2 1.1.1.236 0.840
3a28 NADL-2,3-butanediol dehydrogenase 1.1.1.76 0.840
2b4q NAPRhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase 1.1.1.100 0.838
3qwf NAP17beta-hydroxysteroid dehydrogenase / 0.832
3tsc NADUncharacterized protein / 0.832
1xkq NDPUncharacterized protein / 0.831
2d1y NADOxidoreductase, short-chain dehydrogenase/reductase family / 0.831
3r3s NADPutative oxidoreductase / 0.827
3iah NAPPutative oxoacyl-(Acyl carrier protein) reductase / 0.826
3s55 NADPutative short-chain dehydrogenase/reductase / 0.826
3tn7 NJPShort-chain alcohol dehydrogenase / 0.825
4dmm NAP3-oxoacyl-[acyl-carrier-protein] reductase / 0.825
3uce NDPDehydrogenase / 0.823
3geg NADShort-chain dehydrogenase/reductase SDR / 0.822
4gh5 NADShort-chain dehydrogenase/reductase SDR / 0.821
2ztu NADD(-)-3-hydroxybutyrate dehydrogenase / 0.819
1e3s NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.818
1xse NDPCorticosteroid 11-beta-dehydrogenase isozyme 1 1.1.1.146 0.817
2ag5 NAD3-hydroxybutyrate dehydrogenase type 2 / 0.816
4qec NAPElxO / 0.813
4yai NAIC alpha-dehydrogenase / 0.813
1cyd NDPCarbonyl reductase [NADPH] 2 1.1.1.184 0.811
1gee NADGlucose 1-dehydrogenase 1.1.1.47 0.811
1vl8 NAPOxidoreductase, short chain dehydrogenase/reductase family / 0.811
2bd0 NAPSepiapterin reductase / 0.811
1u7t TDT3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.809
1xg5 NAPDehydrogenase/reductase SDR family member 11 / 0.805
4nbt NAD3-oxoacyl-[acyl-carrier-protein] reductase / 0.804
3o4r NAPDehydrogenase/reductase SDR family member 4 1.1.1.184 0.803
2zat NAPDehydrogenase/reductase SDR family member 4 1.1.1.184 0.802
2idz ZIDEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.801
2rbe NDPCorticosteroid 11-beta-dehydrogenase isozyme 1 1.1.1.146 0.799
3gy0 NAPNAD(P)-dependent oxidoreductase / 0.798
4m87 NADEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.798
1fdu NAPEstradiol 17-beta-dehydrogenase 1 1.1.1.62 0.797
1g0n NDPTetrahydroxynaphthalene reductase 1.1.1.252 0.793
2nnl NAPDihydroflavonol 4-reductase 1.1.1.219 0.792
2yut NAPPutative short-chain oxidoreductase / 0.791
2p5y NADUDP-glucose 4-epimerase / 0.790
2yy7 NADL-threonine dehydrogenase / 0.790
4qed NAPElxO / 0.790
2ieb ZIDEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.789
1rwb NADGlucose 1-dehydrogenase 1.1.1.47 0.787
1gco NADGlucose 1-dehydrogenase 1.1.1.47 0.786
4hp8 NAP2-deoxy-D-gluconate 3-dehydrogenase / 0.786
1mg5 NAIAlcohol dehydrogenase 1.1.1.1 0.784
4iqg NAPShort-chain dehydrogenase/reductase SDR / 0.783
2wdz NADGalactitol dehydrogenase / 0.779
1qyv NAPEstradiol 17-beta-dehydrogenase 1 1.1.1.62 0.777
3sx2 NADUncharacterized protein / 0.774
3uic NADEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.773
1zem NADXylitol dehydrogenase / 0.772
3ruc NADUDP-N-acetylglucosamine 4-epimerase / 0.772
4hwk NAPSepiapterin reductase 1.1.1.153 0.772
4k6f NAPPutative Acetoacetyl-CoA reductase / 0.770
4zju NADEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.770
4pvd NDPNADPH-dependent methylglyoxal reductase GRE2 / 0.769
3mje NDPAmphB / 0.766
3o03 NAPDehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) / 0.765
4wec NADShort chain dehydrogenase / 0.765
4c7k NAPCorticosteroid 11-beta-dehydrogenase isozyme 1 1.1.1.146 0.758
3ndr NADPyridoxal 4-dehydrogenase 1.1.1.107 0.754
2q1w NADPutative nucleotide sugar epimerase/ dehydratase / 0.753
3g49 NAPCorticosteroid 11-beta-dehydrogenase isozyme 1 1.1.1.146 0.753
2c59 NADGDP-mannose 3,5-epimerase 5.1.3.18 0.752
4bms NAPAlclohol dehydrogenase/short-chain dehydrogenase / 0.752
4i5e NAPAlclohol dehydrogenase/short-chain dehydrogenase / 0.752
1sny NAPLD36273p / 0.751
2bgm NAJSecoisolariciresinol dehydrogenase 1.1.1.331 0.751
1nff NAD3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase 1.1.1.53 0.746
3aw9 NADNAD-dependent epimerase/dehydratase / 0.746
2q1t NADPutative nucleotide sugar epimerase/ dehydratase / 0.745
4u7w NDPMxaA / 0.745
3ko8 NADNAD-dependent epimerase/dehydratase / 0.743
4oxy NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.743
4trn NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.742
2ntj P1HEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.740
2wyv NADEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.740
4o1m NADEnoyl-acyl carrier reductase / 0.739
5jyd NADShort chain dehydrogenase / 0.738
5koi NADEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.738
3aut NAIGlucose 1-dehydrogenase 4 1.1.1.47 0.737
3h4v NAPPteridine reductase 1 1.5.1.33 0.737
3of2 NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.737
4eue NAITrans-2-enoyl-CoA reductase [NADH] / 0.737
2hrb NAPCarbonyl reductase [NADPH] 3 1.1.1.184 0.736
2p5u NADUDP-glucose 4-epimerase / 0.735
2ie0 ZIDEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.734
4eso NAPPutative oxidoreductase / 0.734
3icp NADNAD-dependent epimerase/dehydratase / 0.732
1kvr NADUDP-glucose 4-epimerase 5.1.3.2 0.730
2y99 NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase 1.3.1.56 0.730
4nbu NAI3-oxoacyl-(Acyl-carrier-protein) reductase / 0.730
3bmo NAPPteridine reductase / 0.729
3ijr NADOxidoreductase, short chain dehydrogenase/reductase family / 0.729
3sju NDPKeto reductase / 0.729
5b1y NDP3-oxoacyl-[acyl-carrier-protein] reductase / 0.726
2aqk NAIEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.725
3a4v NADNDP-sugar epimerase / 0.725
3ru7 NADUDP-N-acetylglucosamine 4-epimerase / 0.725
2aqi NAIEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.723
4fc7 NAPPeroxisomal 2,4-dienoyl-CoA reductase 1.3.1.34 0.721
5idw NAPShort-chain dehydrogenase/reductase SDR / 0.721
2h9i EADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.720
4lis NADUDP-glucose 4-epimerase (Eurofung) / 0.720
1i2b NADUDP-sulfoquinovose synthase, chloroplastic 3.13.1.1 0.719
2b35 NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.719
3oew NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.719
1g6k NADGlucose 1-dehydrogenase 1.1.1.47 0.717
1u7t NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.717
4hxy NDPPlm1 / 0.717
3oey NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.716
3tox NAPPutative oxidoreductase / 0.716
4cql NADEstradiol 17-beta-dehydrogenase 8 1.1.1.62 0.716
1eny NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.715
4dre NAIEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.711
2nv6 ZIDEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.710
3u4c NDPNADPH-dependent reductase BacG / 0.710
3ruh NADUDP-N-acetylglucosamine 4-epimerase / 0.709
4nbw NADShort-chain dehydrogenase/reductase SDR / 0.709
2b37 NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.708
3pef NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.708
5d2e NAPMlnE / 0.706
1b15 NAEAlcohol dehydrogenase 1.1.1.1 0.705
1b14 NADAlcohol dehydrogenase 1.1.1.1 0.704
1enz NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.702
4bii NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.701
1vrw NAIEnoyl-ACP reductase / 0.700
4b8z NAPGDP-L-fucose synthase 1.1.1.271 0.700
2hun NAD336aa long hypothetical dTDP-glucose 4,6-dehydratase / 0.698
3sxp NADADP-L-glycero-D-mannoheptose-6-epimerase / 0.698
4ej0 NAPADP-L-glycero-D-manno-heptose-6-epimerase / 0.698
1b2l NDCAlcohol dehydrogenase 1.1.1.1 0.696
5cpb NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.696
1fk8 NAD3-alpha-hydroxysteroid dehydrogenase/carbonyl reductase 1.1.1.50 0.694
3a9w NADNDP-sugar epimerase / 0.694
1sby NADAlcohol dehydrogenase 1.1.1.1 0.693
4fw8 NAI3-oxoacyl-(Acyl-carrier-protein) reductase / 0.693
1nfr NAD3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase 1.1.1.53 0.692
1rkx NADCDP-D-glucose-4,6-dehydratase / 0.691
1w8d NAP2,4-dienoyl-CoA reductase, mitochondrial 1.3.1.34 0.691
2rcy NAPPyrroline-5-carboxylate reductase / 0.691
3wmx NADNAD dependent epimerase/dehydratase / 0.691
1w73 NAP2,4-dienoyl-CoA reductase, mitochondrial 1.3.1.34 0.690
2hsd NAD3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase 1.1.1.53 0.690
3lu1 NADUDP-N-acetylglucosamine 4-epimerase / 0.690
3sj7 NDP3-oxoacyl-(Acyl-carrier-protein) reductase, putative / 0.690
2ntv P1HEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.688
4bkq NAIEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.687
4tqg NDPPutative dTDP-d-glucose 4 6-dehydratase / 0.686
2pzj NADPutative nucleotide sugar epimerase/ dehydratase / 0.684
1ek5 NADUDP-glucose 4-epimerase / 0.683
3ru9 NADUDP-N-acetylglucosamine 4-epimerase / 0.683
3ruf NADUDP-N-acetylglucosamine 4-epimerase / 0.682
3zu2 NAIEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.682
4bgi NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.682
1iy8 NADLevodione reductase / 0.681
2aqh NAIEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.681
2x86 NAPADP-L-glycero-D-manno-heptose-6-epimerase / 0.681
4y9d NAIC alpha-dehydrogenase / 0.681
3au8 NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic 1.1.1.267 0.680
4xgi NADGlutamate dehydrogenase / 0.680
4b8w NAPGDP-L-fucose synthase 1.1.1.271 0.679
4imp NDPPolyketide synthase extender modules 3-4 / 0.678
1wnt NAPL-xylulose reductase 1.1.1.10 0.676
2aq8 NAIEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.676
5lc1 NADL-threonine 3-dehydrogenase / 0.676
3ras NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase / 0.675
2ggs NDPdTDP-4-dehydrorhamnose reductase / 0.673
1hld NADAlcohol dehydrogenase E chain 1.1.1.1 0.671
2cvz NDP3-hydroxyisobutyrate dehydrogenase / 0.671
3w6u NAP6-phosphogluconate dehydrogenase, NAD-binding protein / 0.671
4hbg NDP3-oxoacyl-[acyl-carrier-protein] reductase 1.1.1.100 0.671
4yac NAIC alpha-dehydrogenase / 0.671
2nq8 ZIDEnoyl-ACP reductase / 0.670
4dqu NAIEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.670
3lqf NADGalactitol dehydrogenase / 0.669
4egb NADdTDP-glucose 4,6-dehydratase / 0.669
1i3l NADUDP-glucose 4-epimerase / 0.668
3hwr NDP2-dehydropantoate 2-reductase / 0.667
4wji NAPPutative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase / 0.666
2yw9 NAPEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.665
3rua NADUDP-N-acetylglucosamine 4-epimerase / 0.665
2dph NADFormaldehyde dismutase / 0.664
3f1k NAPUncharacterized oxidoreductase YciK 1 0.663
3uxy NADShort-chain dehydrogenase/reductase SDR / 0.663
5hws NAP2-dehydropantoate 2-reductase / 0.663
3rud NADUDP-N-acetylglucosamine 4-epimerase / 0.662
4twr NADNAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase / 0.661
3ehe NADUDP-glucose 4-epimerase (GalE-1) / 0.660
1q0q NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase 1.1.1.267 0.659
2gn8 NAPUDP-N-acetylglucosamine 4,6-dehydratase (inverting) 4.2.1.115 0.658
4ng5 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.658
1yqd NAPSinapyl alcohol dehydrogenase / 0.657
4bqp NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.657
2jkv NAP6-phosphogluconate dehydrogenase, decarboxylating 1.1.1.44 0.656
3pdu NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.656
2vhv NAIAlanine dehydrogenase 1.4.1.1 0.655
4xb2 NDP319aa long hypothetical homoserine dehydrogenase / 0.655
1wp4 NDP3-hydroxyisobutyrate dehydrogenase / 0.653
1wzi NDPMalate dehydrogenase / 0.653
4dti NAIEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.653
3ggp NADPrephenate dehydrogenase / 0.652
3two NDPMannitol dehydrogenase / 0.652
4idg NADPutative UDP-glucose 4-epimerase / 0.652
1bws NDPGDP-L-fucose synthase / 0.651
4nfh NAJAlcohol dehydrogenase E chain 1.1.1.1 0.651
2bfo NDPPteridine reductase 1 1.5.1.33 0.650
3ajr NADNDP-sugar epimerase / 0.650
4tvb NADHomospermidine synthase 2.5.1.44 0.650