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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
3rua NAD UDP-N-acetylglucosamine 4-epimerase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity
Align
3rua NADUDP-N-acetylglucosamine 4-epimerase / 1.230
3ruf NADUDP-N-acetylglucosamine 4-epimerase / 1.221
3ru9 NADUDP-N-acetylglucosamine 4-epimerase / 1.166
3ruc NADUDP-N-acetylglucosamine 4-epimerase / 1.142
3rud NADUDP-N-acetylglucosamine 4-epimerase / 1.102
3lu1 NADUDP-N-acetylglucosamine 4-epimerase / 1.092
3ru7 NADUDP-N-acetylglucosamine 4-epimerase / 1.064
3ruh NADUDP-N-acetylglucosamine 4-epimerase / 1.046
2p5y NADUDP-glucose 4-epimerase / 1.026
2q1w NADPutative nucleotide sugar epimerase/ dehydratase / 1.006
2b69 NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.974
2q1t NADPutative nucleotide sugar epimerase/ dehydratase / 0.963
1i3l NADUDP-glucose 4-epimerase / 0.961
3ko8 NADNAD-dependent epimerase/dehydratase / 0.958
3sxp NADADP-L-glycero-D-mannoheptose-6-epimerase / 0.948
1kvr NADUDP-glucose 4-epimerase 5.1.3.2 0.944
4gll NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.941
2c59 NADGDP-mannose 3,5-epimerase 5.1.3.18 0.939
1orr NADCDP-paratose 2-epimerase / 0.931
2q1u NADPutative nucleotide sugar epimerase/ dehydratase / 0.930
1nah NADUDP-glucose 4-epimerase 5.1.3.2 0.924
3icp NADNAD-dependent epimerase/dehydratase / 0.922
3aw9 NADNAD-dependent epimerase/dehydratase / 0.921
3ehe NADUDP-glucose 4-epimerase (GalE-1) / 0.910
3s55 NADPutative short-chain dehydrogenase/reductase / 0.908
3pgx NADUncharacterized NAD-dependent oxidoreductase MAP_4146 / 0.906
2pzj NADPutative nucleotide sugar epimerase/ dehydratase / 0.904
1rkx NADCDP-D-glucose-4,6-dehydratase / 0.901
4ej0 NAPADP-L-glycero-D-manno-heptose-6-epimerase / 0.899
2q1s NAIPutative nucleotide sugar epimerase/ dehydratase / 0.897
4twr NADNAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase / 0.878
2d1y NADOxidoreductase, short-chain dehydrogenase/reductase family / 0.872
1e6w NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.866
3rue NADUDP-N-acetylglucosamine 4-epimerase / 0.866
4lk3 NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.861
1zem NADXylitol dehydrogenase / 0.852
1e3w NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.850
2o23 NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.849
2c54 NADGDP-mannose 3,5-epimerase 5.1.3.18 0.847
2p5u NADUDP-glucose 4-epimerase / 0.841
4nbt NAD3-oxoacyl-[acyl-carrier-protein] reductase / 0.841
3sx2 NADUncharacterized protein / 0.838
3tsc NADUncharacterized protein / 0.838
3nug NADPyridoxal 4-dehydrogenase 1.1.1.107 0.836
5d2e NAPMlnE / 0.832
2wsb NADGalactitol dehydrogenase / 0.825
1e3s NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.823
4lis NADUDP-glucose 4-epimerase (Eurofung) / 0.821
2hun NAD336aa long hypothetical dTDP-glucose 4,6-dehydratase / 0.813
2x6t NAPADP-L-glycero-D-manno-heptose-6-epimerase / 0.809
4qec NAPElxO / 0.808
2wdz NADGalactitol dehydrogenase / 0.805
2x86 NAPADP-L-glycero-D-manno-heptose-6-epimerase / 0.803
4hxy NDPPlm1 / 0.801
1eq2 NAPADP-L-glycero-D-manno-heptose-6-epimerase / 0.798
1n7h NDPGDP-mannose 4,6 dehydratase 2 4.2.1.47 0.791
1geg NADDiacetyl reductase [(S)-acetoin forming] 1.1.1.304 0.788
2c29 NAPDihydroflavonol 4-reductase / 0.787
2dkn NAI3-alpha-hydroxysteroid dehydrogenase / 0.787
1g1a NADdTDP-glucose 4,6-dehydratase / 0.785
4m55 NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.785
1nff NAD3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase 1.1.1.53 0.784
1i2b NADUDP-sulfoquinovose synthase, chloroplastic 3.13.1.1 0.782
2nnl NAPDihydroflavonol 4-reductase 1.1.1.219 0.781
1u7t NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.780
1rpn NDPGDP-mannose 4,6-dehydratase / 0.779
2gn8 NAPUDP-N-acetylglucosamine 4,6-dehydratase (inverting) 4.2.1.115 0.779
3ndr NADPyridoxal 4-dehydrogenase 1.1.1.107 0.772
1nfr NAD3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase 1.1.1.53 0.770
3wds NADNADH-dependent quinuclidinone reductase / 0.770
4z3d NDPCarbonyl reductase [NADPH] 1 1.1.1.184 0.770
1t2a NDPGDP-mannose 4,6 dehydratase 4.2.1.47 0.769
1bdb NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase / 0.767
4gh5 NADShort-chain dehydrogenase/reductase SDR / 0.764
4qed NAPElxO / 0.763
2z1m NDPGDP-mannose 4,6-dehydratase / 0.759
4idg NADPutative UDP-glucose 4-epimerase / 0.759
1rwb NADGlucose 1-dehydrogenase 1.1.1.47 0.758
4dmm NAP3-oxoacyl-[acyl-carrier-protein] reductase / 0.757
4u7w NDPMxaA / 0.756
1gco NADGlucose 1-dehydrogenase 1.1.1.47 0.755
1gee NADGlucose 1-dehydrogenase 1.1.1.47 0.755
3mje NDPAmphB / 0.755
4egb NADdTDP-glucose 4,6-dehydratase / 0.753
3iah NAPPutative oxoacyl-(Acyl carrier protein) reductase / 0.750
1vl8 NAPOxidoreductase, short chain dehydrogenase/reductase family / 0.747
2bgm NAJSecoisolariciresinol dehydrogenase 1.1.1.331 0.746
3p19 NDPPutative blue fluorescent protein / 0.746
4nbu NAI3-oxoacyl-(Acyl-carrier-protein) reductase / 0.746
1n5d NDPCarbonyl reductase [NADPH] 1 / 0.745
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.744
1g6k NADGlucose 1-dehydrogenase 1.1.1.47 0.742
4hp8 NAP2-deoxy-D-gluconate 3-dehydrogenase / 0.742
1g0n NDPTetrahydroxynaphthalene reductase 1.1.1.252 0.741
3gy0 NAPNAD(P)-dependent oxidoreductase / 0.740
5ig2 NADShort-chain dehydrogenase/reductase SDR / 0.739
5idw NAPShort-chain dehydrogenase/reductase SDR / 0.737
1iy8 NADLevodione reductase / 0.736
3ai2 NDPNADPH-sorbose reductase / 0.736
1u7t TDT3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.735
3g49 NAPCorticosteroid 11-beta-dehydrogenase isozyme 1 1.1.1.146 0.733
3sj7 NDP3-oxoacyl-(Acyl-carrier-protein) reductase, putative / 0.733
4is3 NAD3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 1.17.98.1 0.733
5jsf NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.731
1edo NAP3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic 1.1.1.100 0.730
1pr9 NAPL-xylulose reductase 1.1.1.10 0.729
2wyv NADEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.729
3a28 NADL-2,3-butanediol dehydrogenase 1.1.1.76 0.729
3d3w NAPL-xylulose reductase 1.1.1.10 0.729
4nbw NADShort-chain dehydrogenase/reductase SDR / 0.729
4wec NADShort chain dehydrogenase / 0.728
4o0l NDPNADPH-dependent 3-quinuclidinone reductase / 0.726
1n7g NDPGDP-mannose 4,6 dehydratase 2 4.2.1.47 0.725
3rku NAPNADP-dependent 3-hydroxy acid dehydrogenase / 0.725
4dc0 NDPPutative ketoacyl reductase 1.3.1 0.725
4yag NAIC alpha-dehydrogenase / 0.725
4kwh NAPReductase homolog / 0.723
4k6f NAPPutative Acetoacetyl-CoA reductase / 0.720
3sju NDPKeto reductase / 0.719
3tox NAPPutative oxidoreductase / 0.719
4iqg NAPShort-chain dehydrogenase/reductase SDR / 0.719
5jy1 NADPutative short-chain dehydrogenase/reductase / 0.719
1b2l NDCAlcohol dehydrogenase 1.1.1.1 0.718
2c20 NADUDP-glucose 4-epimerase / 0.718
5js6 NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.718
2hmv ADPKtr system potassium uptake protein A / 0.717
2z95 NDPGDP-mannose 4,6-dehydratase / 0.717
4pvd NDPNADPH-dependent methylglyoxal reductase GRE2 / 0.717
2dte NAIGlucose 1-dehydrogenase related protein / 0.716
4b79 NADProbable short-chain dehydrogenase / 0.716
3rj9 NADAlcohol dehydrogenase 1.1.1.1 0.715
4fc7 NAPPeroxisomal 2,4-dienoyl-CoA reductase 1.3.1.34 0.715
4fj1 NAP17beta-hydroxysteroid dehydrogenase / 0.713
4j7x NAPSepiapterin reductase 1.1.1.153 0.713
2jah NDPClavaldehyde dehydrogenase / 0.711
3rj5 NADAlcohol dehydrogenase 1.1.1.1 0.711
1nai NADUDP-glucose 4-epimerase 5.1.3.2 0.710
4dbz NDPPutative ketoacyl reductase 1.3.1 0.710
4yai NAIC alpha-dehydrogenase / 0.710
2hrb NAPCarbonyl reductase [NADPH] 3 1.1.1.184 0.709
3wmx NADNAD dependent epimerase/dehydratase / 0.709
1bxk NADdTDP-glucose 4,6-dehydratase 2 / 0.707
1oaa NAPSepiapterin reductase 1.1.1.153 0.706
1sny NAPLD36273p / 0.706
4bms NAPAlclohol dehydrogenase/short-chain dehydrogenase / 0.706
4j7u NAPSepiapterin reductase 1.1.1.153 0.706
1x7h NDPPutative ketoacyl reductase 1.3.1 0.705
3a4v NADNDP-sugar epimerase / 0.705
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.704
5lc1 NADL-threonine 3-dehydrogenase / 0.704
4b4o NDPEpimerase family protein SDR39U1 / 0.703
2yw9 NAPEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.702
3o26 NDPSalutaridine reductase / 0.702
2bd0 NAPSepiapterin reductase / 0.701
3orf NADDihydropteridine reductase 1.5.1.34 0.701
4i5e NAPAlclohol dehydrogenase/short-chain dehydrogenase / 0.701
1w73 NAP2,4-dienoyl-CoA reductase, mitochondrial 1.3.1.34 0.700
4hwk NAPSepiapterin reductase 1.1.1.153 0.700
2yy7 NADL-threonine dehydrogenase / 0.699
1x7g NAPPutative ketoacyl reductase 1.3.1 0.698
3tn7 NJPShort-chain alcohol dehydrogenase / 0.697
1b16 NAQAlcohol dehydrogenase 1.1.1.1 0.696
1eg2 MTAModification methylase RsrI 2.1.1.72 0.696
3ak4 NADNADH-dependent quinuclidinone reductase / 0.696
3q9t FAYUncharacterized protein / 0.696
4cql NADEstradiol 17-beta-dehydrogenase 8 1.1.1.62 0.696
1fk8 NAD3-alpha-hydroxysteroid dehydrogenase/carbonyl reductase 1.1.1.50 0.695
1kc1 NDPdTDP-4-dehydrorhamnose reductase 1.1.1.133 0.695
2dt5 NADRedox-sensing transcriptional repressor Rex / 0.695
3ajr NADNDP-sugar epimerase / 0.695
3qrw NDPPutative ketoacyl reductase 1.3.1 0.695
2gdz NAD15-hydroxyprostaglandin dehydrogenase [NAD(+)] 1.1.1.141 0.694
3a9w NADNDP-sugar epimerase / 0.694
4b8z NAPGDP-L-fucose synthase 1.1.1.271 0.694
4dc1 NDPPutative ketoacyl reductase 1.3.1 0.693
4l4x NDPAmphI / 0.692
3ijr NADOxidoreductase, short chain dehydrogenase/reductase family / 0.691
5bt9 NAP3-oxoacyl-(Acyl-carrier-protein) reductase / 0.691
1w8d NAP2,4-dienoyl-CoA reductase, mitochondrial 1.3.1.34 0.690
3bhi NAPCarbonyl reductase [NADPH] 1 1.1.1.184 0.690
3geg NADShort-chain dehydrogenase/reductase SDR / 0.690
4id9 NADPutative UDP-glucose 4-epimerase / 0.690
3ai3 NDPNADPH-sorbose reductase / 0.689
1mg5 NAIAlcohol dehydrogenase 1.1.1.1 0.688
2q2v NADBeta-D-hydroxybutyrate dehydrogenase / 0.688
3qv1 NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.687
4yuz S4MSpermidine synthase, putative / 0.687
1fdu NAPEstradiol 17-beta-dehydrogenase 1 1.1.1.62 0.686
1ipe NDPTropinone reductase 2 1.1.1.236 0.686
2ztl NADD(-)-3-hydroxybutyrate dehydrogenase / 0.686
4imp NDPPolyketide synthase extender modules 3-4 / 0.685
1sby NADAlcohol dehydrogenase 1.1.1.1 0.683
2yut NAPPutative short-chain oxidoreductase / 0.683
1p1h NADInositol-3-phosphate synthase 5.5.1.4 0.682
2rbe NDPCorticosteroid 11-beta-dehydrogenase isozyme 1 1.1.1.146 0.682
3rfx NADUronate dehydrogenase / 0.682
4tqg NDPPutative dTDP-d-glucose 4 6-dehydratase / 0.682
1xse NDPCorticosteroid 11-beta-dehydrogenase isozyme 1 1.1.1.146 0.681
2uyh SAHModification methylase HhaI 2.1.1.37 0.681
2zat NAPDehydrogenase/reductase SDR family member 4 1.1.1.184 0.680
4e5y NDPGDP-L-fucose synthase 1.1.1.271 0.680
2ztv NADD(-)-3-hydroxybutyrate dehydrogenase / 0.679
3uxy NADShort-chain dehydrogenase/reductase SDR / 0.679
2ag5 NAD3-hydroxybutyrate dehydrogenase type 2 / 0.678
3aut NAIGlucose 1-dehydrogenase 4 1.1.1.47 0.678
7mht SAHModification methylase HhaI 2.1.1.37 0.678
2aa3 AP0L-lactate dehydrogenase / 0.677
4zju NADEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.677
1wy7 SAHUncharacterized protein / 0.675
3w8d NAD3-hydroxybutyrate dehydrogenase / 0.675
1h5q NAPNADP-dependent mannitol dehydrogenase 1.1.1.138 0.674
3l77 NJPShort-chain alcohol dehydrogenase / 0.674
5jla NADPutative short-chain dehydrogenase/reductase / 0.674
1b15 NAEAlcohol dehydrogenase 1.1.1.1 0.673
1uay ADNOxidoreductase / 0.673
2ztm NADD(-)-3-hydroxybutyrate dehydrogenase / 0.672
4m87 NADEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.672
5jyd NADShort chain dehydrogenase / 0.671
2ekp NAD2-deoxy-D-gluconate 3-dehydrogenase / 0.670
3h4v NAPPteridine reductase 1 1.5.1.33 0.670
3o03 NAPDehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) / 0.669
3vdq NAD3-hydroxybutyrate dehydrogenase / 0.669
4o1m NADEnoyl-acyl carrier reductase / 0.669
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.668
4clo NAPPteridine reductase / 0.668
1n2s NAIdTDP-4-dehydrorhamnose reductase 1.1.1.133 0.667
2hsd NAD3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase 1.1.1.53 0.667
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.667
1cyd NDPCarbonyl reductase [NADPH] 2 1.1.1.184 0.666
3w8e NAD3-hydroxybutyrate dehydrogenase / 0.666
1w4z NAPPutative ketoacyl reductase 1.3.1 0.665
2ztu NADD(-)-3-hydroxybutyrate dehydrogenase / 0.665
3w8f NAD3-hydroxybutyrate dehydrogenase / 0.665
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.665
2p35 SAHTrans-aconitate 2-methyltransferase / 0.664
3qvt NAIMyo-inositol-1-phosphate synthase (Ino1) / 0.664
3wsw NADL-lactate dehydrogenase / 0.664
1qyx NAPEstradiol 17-beta-dehydrogenase 1 1.1.1.62 0.663
3f1k NAPUncharacterized oxidoreductase YciK 1 0.663
3r3s NADPutative oxidoreductase / 0.663
4yac NAIC alpha-dehydrogenase / 0.663
5a05 NDPGlucose-fructose oxidoreductase / 0.662
1dir NADDihydropteridine reductase 1.5.1.34 0.661
3o4r NAPDehydrogenase/reductase SDR family member 4 1.1.1.184 0.661
1ie3 NADMalate dehydrogenase / 0.659
4ek9 EP4Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.659
4xqc NADHomospermidine synthase 2.5.1.44 0.659
4c7k NAPCorticosteroid 11-beta-dehydrogenase isozyme 1 1.1.1.146 0.658
1bw9 NADPhenylalanine dehydrogenase / 0.657
2ih2 NEAModification methylase TaqI 2.1.1.72 0.657
2y99 NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase 1.3.1.56 0.657
1xq6 NAPUncharacterized protein At5g02240 / 0.656
1z7e ATPBifunctional polymyxin resistance protein ArnA / 0.656
2o4c NADErythronate-4-phosphate dehydrogenase / 0.656
2g82 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.655
1b14 NADAlcohol dehydrogenase 1.1.1.1 0.654
1f8f NADBenzyl alcohol dehydrogenase / 0.654
1zh8 NAPUncharacterized protein / 0.654
3jyo NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.654
1dhr NADDihydropteridine reductase 1.5.1.34 0.653
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.653
4yr9 NADL-threonine 3-dehydrogenase, mitochondrial 1.1.1.103 0.653
2yxl SFG450aa long hypothetical fmu protein / 0.652
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.651
1yba NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.650
2b35 NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.650