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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
1rkx NAD CDP-D-glucose-4,6-dehydratase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1rkx NADCDP-D-glucose-4,6-dehydratase / 1.216
3ruf NADUDP-N-acetylglucosamine 4-epimerase / 0.917
3rua NADUDP-N-acetylglucosamine 4-epimerase / 0.901
2p5y NADUDP-glucose 4-epimerase / 0.891
2c29 NAPDihydroflavonol 4-reductase / 0.888
4hxy NDPPlm1 / 0.888
3rud NADUDP-N-acetylglucosamine 4-epimerase / 0.885
3icp NADNAD-dependent epimerase/dehydratase / 0.884
3lu1 NADUDP-N-acetylglucosamine 4-epimerase / 0.869
3ru9 NADUDP-N-acetylglucosamine 4-epimerase / 0.868
2c59 NADGDP-mannose 3,5-epimerase 5.1.3.18 0.860
2nnl NAPDihydroflavonol 4-reductase 1.1.1.219 0.847
3mje NDPAmphB / 0.847
5d2e NAPMlnE / 0.842
3ehe NADUDP-glucose 4-epimerase (GalE-1) / 0.841
3iah NAPPutative oxoacyl-(Acyl carrier protein) reductase / 0.836
4gll NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.831
4ej0 NAPADP-L-glycero-D-manno-heptose-6-epimerase / 0.829
3nug NADPyridoxal 4-dehydrogenase 1.1.1.107 0.823
2q1t NADPutative nucleotide sugar epimerase/ dehydratase / 0.820
1zem NADXylitol dehydrogenase / 0.818
4z3d NDPCarbonyl reductase [NADPH] 1 1.1.1.184 0.816
3ko8 NADNAD-dependent epimerase/dehydratase / 0.813
4hp8 NAP2-deoxy-D-gluconate 3-dehydrogenase / 0.812
1kvr NADUDP-glucose 4-epimerase 5.1.3.2 0.810
1wvg APRCDP-glucose 4,6-dehydratase 4.2.1.45 0.807
1n7h NDPGDP-mannose 4,6 dehydratase 2 4.2.1.47 0.806
3ndr NADPyridoxal 4-dehydrogenase 1.1.1.107 0.805
2o23 NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.804
3ruc NADUDP-N-acetylglucosamine 4-epimerase / 0.801
2q1u NADPutative nucleotide sugar epimerase/ dehydratase / 0.797
3sxp NADADP-L-glycero-D-mannoheptose-6-epimerase / 0.796
4o0l NDPNADPH-dependent 3-quinuclidinone reductase / 0.794
4u7w NDPMxaA / 0.794
1t2a NDPGDP-mannose 4,6 dehydratase 4.2.1.47 0.793
1n7g NDPGDP-mannose 4,6 dehydratase 2 4.2.1.47 0.792
2c54 NADGDP-mannose 3,5-epimerase 5.1.3.18 0.791
2b69 NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.789
1eq2 NAPADP-L-glycero-D-manno-heptose-6-epimerase / 0.788
4dmm NAP3-oxoacyl-[acyl-carrier-protein] reductase / 0.788
2q1s NAIPutative nucleotide sugar epimerase/ dehydratase / 0.787
3gy0 NAPNAD(P)-dependent oxidoreductase / 0.785
3pgx NADUncharacterized NAD-dependent oxidoreductase MAP_4146 / 0.784
1sny NAPLD36273p / 0.783
4idg NADPutative UDP-glucose 4-epimerase / 0.783
1nah NADUDP-glucose 4-epimerase 5.1.3.2 0.782
1i3l NADUDP-glucose 4-epimerase / 0.781
4qec NAPElxO / 0.780
3ru7 NADUDP-N-acetylglucosamine 4-epimerase / 0.777
4lk3 NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.777
1e6w NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.776
2gn8 NAPUDP-N-acetylglucosamine 4,6-dehydratase (inverting) 4.2.1.115 0.774
4pvd NDPNADPH-dependent methylglyoxal reductase GRE2 / 0.774
1vl8 NAPOxidoreductase, short chain dehydrogenase/reductase family / 0.769
1g6k NADGlucose 1-dehydrogenase 1.1.1.47 0.766
2pzj NADPutative nucleotide sugar epimerase/ dehydratase / 0.766
1e3s NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.765
4id9 NADPutative UDP-glucose 4-epimerase / 0.763
2q1w NADPutative nucleotide sugar epimerase/ dehydratase / 0.761
3o26 NDPSalutaridine reductase / 0.761
3ak4 NADNADH-dependent quinuclidinone reductase / 0.760
3rj5 NADAlcohol dehydrogenase 1.1.1.1 0.760
4fc7 NAPPeroxisomal 2,4-dienoyl-CoA reductase 1.3.1.34 0.760
4k6f NAPPutative Acetoacetyl-CoA reductase / 0.760
2x86 NAPADP-L-glycero-D-manno-heptose-6-epimerase / 0.758
1e3w NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.757
3aw9 NADNAD-dependent epimerase/dehydratase / 0.757
1edo NAP3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic 1.1.1.100 0.756
3bhi NAPCarbonyl reductase [NADPH] 1 1.1.1.184 0.756
2yut NAPPutative short-chain oxidoreductase / 0.755
3ruh NADUDP-N-acetylglucosamine 4-epimerase / 0.755
1gee NADGlucose 1-dehydrogenase 1.1.1.47 0.752
4twr NADNAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase / 0.749
1gco NADGlucose 1-dehydrogenase 1.1.1.47 0.748
4gh5 NADShort-chain dehydrogenase/reductase SDR / 0.748
3tsc NADUncharacterized protein / 0.747
1geg NADDiacetyl reductase [(S)-acetoin forming] 1.1.1.304 0.746
1i2b NADUDP-sulfoquinovose synthase, chloroplastic 3.13.1.1 0.745
2ggs NDPdTDP-4-dehydrorhamnose reductase / 0.744
1w8d NAP2,4-dienoyl-CoA reductase, mitochondrial 1.3.1.34 0.742
2d1y NADOxidoreductase, short-chain dehydrogenase/reductase family / 0.742
1orr NADCDP-paratose 2-epimerase / 0.740
3a28 NADL-2,3-butanediol dehydrogenase 1.1.1.76 0.740
3uxy NADShort-chain dehydrogenase/reductase SDR / 0.740
3sx2 NADUncharacterized protein / 0.739
1mg5 NAIAlcohol dehydrogenase 1.1.1.1 0.738
2yy7 NADL-threonine dehydrogenase / 0.738
2hun NAD336aa long hypothetical dTDP-glucose 4,6-dehydratase / 0.737
3d3w NAPL-xylulose reductase 1.1.1.10 0.736
3rj9 NADAlcohol dehydrogenase 1.1.1.1 0.736
4fn4 NADShort chain dehydrogenase / 0.736
4b79 NADProbable short-chain dehydrogenase / 0.735
3s55 NADPutative short-chain dehydrogenase/reductase / 0.733
2jah NDPClavaldehyde dehydrogenase / 0.732
3tox NAPPutative oxidoreductase / 0.732
3of2 NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.731
3r3s NADPutative oxidoreductase / 0.731
3wmx NADNAD dependent epimerase/dehydratase / 0.731
5ig2 NADShort-chain dehydrogenase/reductase SDR / 0.731
2p5u NADUDP-glucose 4-epimerase / 0.729
5jyd NADShort chain dehydrogenase / 0.729
1sby NADAlcohol dehydrogenase 1.1.1.1 0.728
4dc0 NDPPutative ketoacyl reductase 1.3.1 0.727
1rpn NDPGDP-mannose 4,6-dehydratase / 0.726
2bgm NAJSecoisolariciresinol dehydrogenase 1.1.1.331 0.726
4b8z NAPGDP-L-fucose synthase 1.1.1.271 0.725
2dkn NAI3-alpha-hydroxysteroid dehydrogenase / 0.724
1u7t NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.723
4wec NADShort chain dehydrogenase / 0.722
2q2v NADBeta-D-hydroxybutyrate dehydrogenase / 0.721
4yag NAIC alpha-dehydrogenase / 0.721
1nff NAD3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase 1.1.1.53 0.719
1g1a NADdTDP-glucose 4,6-dehydratase / 0.718
2z1m NDPGDP-mannose 4,6-dehydratase / 0.718
3rfx NADUronate dehydrogenase / 0.718
4c7k NAPCorticosteroid 11-beta-dehydrogenase isozyme 1 1.1.1.146 0.718
5js6 NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.718
3wds NADNADH-dependent quinuclidinone reductase / 0.717
5jsf NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.717
3oey NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.716
4nbu NAI3-oxoacyl-(Acyl-carrier-protein) reductase / 0.716
1n5d NDPCarbonyl reductase [NADPH] 1 / 0.715
3qwf NAP17beta-hydroxysteroid dehydrogenase / 0.715
4imp NDPPolyketide synthase extender modules 3-4 / 0.715
1kc1 NDPdTDP-4-dehydrorhamnose reductase 1.1.1.133 0.714
2b37 NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.714
3rue NADUDP-N-acetylglucosamine 4-epimerase / 0.714
4fj2 NAP17beta-hydroxysteroid dehydrogenase / 0.714
5jla NADPutative short-chain dehydrogenase/reductase / 0.714
1fk8 NAD3-alpha-hydroxysteroid dehydrogenase/carbonyl reductase 1.1.1.50 0.712
4tqg NDPPutative dTDP-d-glucose 4 6-dehydratase / 0.711
2ztm NADD(-)-3-hydroxybutyrate dehydrogenase / 0.710
4cql NADEstradiol 17-beta-dehydrogenase 8 1.1.1.62 0.709
3ajr NADNDP-sugar epimerase / 0.707
4i5e NAPAlclohol dehydrogenase/short-chain dehydrogenase / 0.707
1g0n NDPTetrahydroxynaphthalene reductase 1.1.1.252 0.706
1pr9 NAPL-xylulose reductase 1.1.1.10 0.706
2x6t NAPADP-L-glycero-D-manno-heptose-6-epimerase / 0.705
3w8e NAD3-hydroxybutyrate dehydrogenase / 0.704
2pk3 A2RGDP-6-deoxy-D-mannose reductase / 0.703
3sj7 NDP3-oxoacyl-(Acyl-carrier-protein) reductase, putative / 0.703
3uce NDPDehydrogenase / 0.703
1w73 NAP2,4-dienoyl-CoA reductase, mitochondrial 1.3.1.34 0.702
3qrw NDPPutative ketoacyl reductase 1.3.1 0.701
2aqk NAIEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.700
2bd0 NAPSepiapterin reductase / 0.700
3p19 NDPPutative blue fluorescent protein / 0.700
3a9w NADNDP-sugar epimerase / 0.699
3tn7 NJPShort-chain alcohol dehydrogenase / 0.699
4oxy NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.699
4b4o NDPEpimerase family protein SDR39U1 / 0.698
3aut NAIGlucose 1-dehydrogenase 4 1.1.1.47 0.696
4hwk NAPSepiapterin reductase 1.1.1.153 0.696
1ipe NDPTropinone reductase 2 1.1.1.236 0.693
2gdz NAD15-hydroxyprostaglandin dehydrogenase [NAD(+)] 1.1.1.141 0.693
4bms NAPAlclohol dehydrogenase/short-chain dehydrogenase / 0.693
3a4v NADNDP-sugar epimerase / 0.692
5cpb NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.692
1b15 NAEAlcohol dehydrogenase 1.1.1.1 0.691
1rwb NADGlucose 1-dehydrogenase 1.1.1.47 0.691
3orf NADDihydropteridine reductase 1.5.1.34 0.691
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.691
3w8f NAD3-hydroxybutyrate dehydrogenase / 0.691
4e5y NDPGDP-L-fucose synthase 1.1.1.271 0.691
1x7h NDPPutative ketoacyl reductase 1.3.1 0.690
1bdb NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase / 0.689
2ztl NADD(-)-3-hydroxybutyrate dehydrogenase / 0.689
4egb NADdTDP-glucose 4,6-dehydratase / 0.687
1xg5 NAPDehydrogenase/reductase SDR family member 11 / 0.686
4cr8 NADN-acylmannosamine 1-dehydrogenase 1.1.1.233 0.685
4yr9 NADL-threonine 3-dehydrogenase, mitochondrial 1.1.1.103 0.685
2aqh NAIEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.684
3o4r NAPDehydrogenase/reductase SDR family member 4 1.1.1.184 0.684
1n2s NAIdTDP-4-dehydrorhamnose reductase 1.1.1.133 0.683
3ai3 NDPNADPH-sorbose reductase / 0.683
1b2l NDCAlcohol dehydrogenase 1.1.1.1 0.682
2zat NAPDehydrogenase/reductase SDR family member 4 1.1.1.184 0.682
4bmv NAPShort-chain dehydrogenase / 0.682
3f1k NAPUncharacterized oxidoreductase YciK 1 0.678
3oew NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.678
2rbe NDPCorticosteroid 11-beta-dehydrogenase isozyme 1 1.1.1.146 0.677
1iy8 NADLevodione reductase / 0.676
2q2q NADBeta-D-hydroxybutyrate dehydrogenase / 0.676
3sju NDPKeto reductase / 0.676
4yai NAIC alpha-dehydrogenase / 0.676
1cyd NDPCarbonyl reductase [NADPH] 2 1.1.1.184 0.675
3w8d NAD3-hydroxybutyrate dehydrogenase / 0.675
2ydx NAPMethionine adenosyltransferase 2 subunit beta / 0.674
3a1n NADNDP-sugar epimerase / 0.674
3oa2 NADUDP-N-acetyl-2-amino-2-deoxy-D-glucuronate oxidase / 0.674
2y99 NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase 1.3.1.56 0.673
4iqg NAPShort-chain dehydrogenase/reductase SDR / 0.673
4m55 NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.673
3o03 NAPDehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) / 0.671
2ntv P1HEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.669
5idw NAPShort-chain dehydrogenase/reductase SDR / 0.668
1fdu NAPEstradiol 17-beta-dehydrogenase 1 1.1.1.62 0.667
2wsb NADGalactitol dehydrogenase / 0.667
3h4v NAPPteridine reductase 1 1.5.1.33 0.667
4hbg NDP3-oxoacyl-[acyl-carrier-protein] reductase 1.1.1.100 0.667
2idz ZIDEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.665
2aq8 NAIEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.664
4dre NAIEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.664
5bt9 NAP3-oxoacyl-(Acyl-carrier-protein) reductase / 0.664
2ztu NADD(-)-3-hydroxybutyrate dehydrogenase / 0.662
4bv9 NDPKetimine reductase mu-crystallin 1.5.1.25 0.662
1qr6 NADNAD-dependent malic enzyme, mitochondrial 1.1.1.38 0.661
4xcv NDPProbable hydroxyacid dehydrogenase protein / 0.661
1bxk NADdTDP-glucose 4,6-dehydratase 2 / 0.660
1p44 NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.660
2c20 NADUDP-glucose 4-epimerase / 0.660
3geg NADShort-chain dehydrogenase/reductase SDR / 0.660
1j5p NADL-aspartate dehydrogenase 1.4.1.21 0.659
1ae1 NAPTropinone reductase 1 / 0.656
1eny NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.656
2wyv NADEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.656
3ai2 NDPNADPH-sorbose reductase / 0.656
3kbo NDPGlyoxylate/hydroxypyruvate reductase A / 0.656
4rf2 NAPNADPH dependent R-specific alcohol dehydrogenase / 0.656
5jy1 NADPutative short-chain dehydrogenase/reductase / 0.656
2wdz NADGalactitol dehydrogenase / 0.655
4zju NADEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.655
2ekp NAD2-deoxy-D-gluconate 3-dehydrogenase / 0.653
1h6b NDPGlucose--fructose oxidoreductase 1.1.99.28 0.652
1zh8 NAPUncharacterized protein / 0.652
2b35 NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.652
3ijr NADOxidoreductase, short chain dehydrogenase/reductase family / 0.652
4dbz NDPPutative ketoacyl reductase 1.3.1 0.652
4dti NAIEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.652
5a03 NDPGlucose-fructose oxidoreductase / 0.652
2ieb ZIDEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.651
1xse NDPCorticosteroid 11-beta-dehydrogenase isozyme 1 1.1.1.146 0.650
4trn NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.650
5a05 NDPGlucose-fructose oxidoreductase / 0.650
5lc1 NADL-threonine 3-dehydrogenase / 0.650