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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
1nai NAD UDP-glucose 4-epimerase 5.1.3.2

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1nai NADUDP-glucose 4-epimerase 5.1.3.2 1.333
1nah NADUDP-glucose 4-epimerase 5.1.3.2 1.059
1kvr NADUDP-glucose 4-epimerase 5.1.3.2 0.984
1ek5 NADUDP-glucose 4-epimerase / 0.958
2q1t NADPutative nucleotide sugar epimerase/ dehydratase / 0.879
4gll NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.868
3ruc NADUDP-N-acetylglucosamine 4-epimerase / 0.822
2pzj NADPutative nucleotide sugar epimerase/ dehydratase / 0.817
4twr NADNAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase / 0.814
2q1u NADPutative nucleotide sugar epimerase/ dehydratase / 0.806
2p5u NADUDP-glucose 4-epimerase / 0.795
1i3l NADUDP-glucose 4-epimerase / 0.780
5ig2 NADShort-chain dehydrogenase/reductase SDR / 0.779
3aw9 NADNAD-dependent epimerase/dehydratase / 0.777
3sx2 NADUncharacterized protein / 0.774
3s55 NADPutative short-chain dehydrogenase/reductase / 0.766
3lu1 NADUDP-N-acetylglucosamine 4-epimerase / 0.763
3pgx NADUncharacterized NAD-dependent oxidoreductase MAP_4146 / 0.759
4lis NADUDP-glucose 4-epimerase (Eurofung) / 0.754
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.753
1iy8 NADLevodione reductase / 0.752
2p5y NADUDP-glucose 4-epimerase / 0.748
2c20 NADUDP-glucose 4-epimerase / 0.746
4yac NAIC alpha-dehydrogenase / 0.744
1orr NADCDP-paratose 2-epimerase / 0.743
4i5e NAPAlclohol dehydrogenase/short-chain dehydrogenase / 0.740
1vl8 NAPOxidoreductase, short chain dehydrogenase/reductase family / 0.738
4gh5 NADShort-chain dehydrogenase/reductase SDR / 0.738
1rsg FADPolyamine oxidase FMS1 / 0.736
2q1s NAIPutative nucleotide sugar epimerase/ dehydratase / 0.736
1e6w NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.735
1nff NAD3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase 1.1.1.53 0.735
4fn4 NADShort chain dehydrogenase / 0.735
1e3w NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.734
3geg NADShort-chain dehydrogenase/reductase SDR / 0.731
5js6 NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.731
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.726
1e3s NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.724
3ko8 NADNAD-dependent epimerase/dehydratase / 0.724
4m55 NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.724
4yai NAIC alpha-dehydrogenase / 0.724
4ej0 NAPADP-L-glycero-D-manno-heptose-6-epimerase / 0.723
1i2b NADUDP-sulfoquinovose synthase, chloroplastic 3.13.1.1 0.720
2c59 NADGDP-mannose 3,5-epimerase 5.1.3.18 0.720
2jah NDPClavaldehyde dehydrogenase / 0.719
3l77 NJPShort-chain alcohol dehydrogenase / 0.719
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.719
1xg5 NAPDehydrogenase/reductase SDR family member 11 / 0.717
2bgm NAJSecoisolariciresinol dehydrogenase 1.1.1.331 0.715
3tsc NADUncharacterized protein / 0.713
3a1n NADNDP-sugar epimerase / 0.710
3rua NADUDP-N-acetylglucosamine 4-epimerase / 0.710
4uy6 SAHHistidine N-alpha-methyltransferase / 0.710
1oaa NAPSepiapterin reductase 1.1.1.153 0.709
4j7x NAPSepiapterin reductase 1.1.1.153 0.708
1geg NADDiacetyl reductase [(S)-acetoin forming] 1.1.1.304 0.707
3bhi NAPCarbonyl reductase [NADPH] 1 1.1.1.184 0.707
4yuv S4MSpermidine synthase, putative / 0.707
1p1h NADInositol-3-phosphate synthase 5.5.1.4 0.706
2x6t NAPADP-L-glycero-D-manno-heptose-6-epimerase / 0.705
3a4v NADNDP-sugar epimerase / 0.705
3ehe NADUDP-glucose 4-epimerase (GalE-1) / 0.705
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.704
1la2 NADInositol-3-phosphate synthase 5.5.1.4 0.703
2b69 NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.703
3ruh NADUDP-N-acetylglucosamine 4-epimerase / 0.703
2ewm NAD(S)-1-Phenylethanol dehydrogenase 1.1.1.311 0.701
3mje NDPAmphB / 0.701
2c29 NAPDihydroflavonol 4-reductase / 0.700
3rku NAPNADP-dependent 3-hydroxy acid dehydrogenase / 0.700
2gn8 NAPUDP-N-acetylglucosamine 4,6-dehydratase (inverting) 4.2.1.115 0.699
2c31 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.698
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.698
4wec NADShort chain dehydrogenase / 0.697
2gsd NADFormate dehydrogenase / 0.695
2nad NADFormate dehydrogenase / 0.695
3wds NADNADH-dependent quinuclidinone reductase / 0.695
3o4r NAPDehydrogenase/reductase SDR family member 4 1.1.1.184 0.694
4y9d NAIC alpha-dehydrogenase / 0.694
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.693
2wdz NADGalactitol dehydrogenase / 0.693
3rj5 NADAlcohol dehydrogenase 1.1.1.1 0.693
3iah NAPPutative oxoacyl-(Acyl carrier protein) reductase / 0.692
1nfr NAD3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase 1.1.1.53 0.691
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.691
3a9w NADNDP-sugar epimerase / 0.691
3oa2 NADUDP-N-acetyl-2-amino-2-deoxy-D-glucuronate oxidase / 0.691
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.691
2bry FAD[F-actin]-methionine sulfoxide oxidase MICAL1 1.14.13 0.690
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.689
2jib ADPOxalyl-CoA decarboxylase 4.1.1.8 0.689
2q2q NADBeta-D-hydroxybutyrate dehydrogenase / 0.689
4b79 NADProbable short-chain dehydrogenase / 0.689
1n5d NDPCarbonyl reductase [NADPH] 1 / 0.688
1g1a NADdTDP-glucose 4,6-dehydratase / 0.687
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.687
5jla NADPutative short-chain dehydrogenase/reductase / 0.687
2ji7 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.686
4lk3 NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.686
4k28 NADShikimate dehydrogenase family protein / 0.685
1bw9 NADPhenylalanine dehydrogenase / 0.684
3ssm SAHMycinamicin VI 2''-O-methyltransferase / 0.684
4b4o NDPEpimerase family protein SDR39U1 / 0.684
2gdz NAD15-hydroxyprostaglandin dehydrogenase [NAD(+)] 1.1.1.141 0.683
3icp NADNAD-dependent epimerase/dehydratase / 0.683
3qvt NAIMyo-inositol-1-phosphate synthase (Ino1) / 0.683
4z3d NDPCarbonyl reductase [NADPH] 1 1.1.1.184 0.683
3ru9 NADUDP-N-acetylglucosamine 4-epimerase / 0.682
2q1w NADPutative nucleotide sugar epimerase/ dehydratase / 0.679
3rud NADUDP-N-acetylglucosamine 4-epimerase / 0.679
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.678
2y99 NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase 1.3.1.56 0.678
3d3w NAPL-xylulose reductase 1.1.1.10 0.678
3nt2 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.678
2o23 NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.677
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.675
1ae1 NAPTropinone reductase 1 / 0.674
2dkn NAI3-alpha-hydroxysteroid dehydrogenase / 0.674
5jsf NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.674
2x86 NAPADP-L-glycero-D-manno-heptose-6-epimerase / 0.673
3o03 NAPDehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) / 0.673
1b14 NADAlcohol dehydrogenase 1.1.1.1 0.672
1d2h SAHGlycine N-methyltransferase 2.1.1.20 0.672
1wy7 SAHUncharacterized protein / 0.672
2q28 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.672
3ru7 NADUDP-N-acetylglucosamine 4-epimerase / 0.672
2bgl NAJSecoisolariciresinol dehydrogenase 1.1.1.331 0.671
3a28 NADL-2,3-butanediol dehydrogenase 1.1.1.76 0.671
4qec NAPElxO / 0.671
3ruf NADUDP-N-acetylglucosamine 4-epimerase / 0.670
5lc1 NADL-threonine 3-dehydrogenase / 0.670
1zmc NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.669
2dc1 NADProbable L-aspartate dehydrogenase / 0.669
4idg NADPutative UDP-glucose 4-epimerase / 0.669
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.669
2ixb NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.668
2ji6 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.668
4nbu NAI3-oxoacyl-(Acyl-carrier-protein) reductase / 0.668
4yuz S4MSpermidine synthase, putative / 0.668
5a06 NDPGlucose-fructose oxidoreductase / 0.668
2wsb NADGalactitol dehydrogenase / 0.667
3vdq NAD3-hydroxybutyrate dehydrogenase / 0.667
2f8l SAMLmo1582 protein / 0.665
3qwf NAP17beta-hydroxysteroid dehydrogenase / 0.665
2c54 NADGDP-mannose 3,5-epimerase 5.1.3.18 0.664
4b8z NAPGDP-L-fucose synthase 1.1.1.271 0.664
4yr9 NADL-threonine 3-dehydrogenase, mitochondrial 1.1.1.103 0.664
3tn7 NJPShort-chain alcohol dehydrogenase / 0.663
4bmv NAPShort-chain dehydrogenase / 0.663
3sxp NADADP-L-glycero-D-mannoheptose-6-epimerase / 0.662
1pr9 NAPL-xylulose reductase 1.1.1.10 0.661
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.661
4hxy NDPPlm1 / 0.661
2pk3 A2RGDP-6-deoxy-D-mannose reductase / 0.660
4egb NADdTDP-glucose 4,6-dehydratase / 0.660
1hku NADC-terminal-binding protein 1 1.1.1 0.659
1mg5 NAIAlcohol dehydrogenase 1.1.1.1 0.659
1zem NADXylitol dehydrogenase / 0.659
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.659
3uxy NADShort-chain dehydrogenase/reductase SDR / 0.659
4cr8 NADN-acylmannosamine 1-dehydrogenase 1.1.1.233 0.659
5bxy SAHPutative RNA methylase family UPF0020 / 0.659
5epe SAHUncharacterized protein / 0.659
2o06 MTASpermidine synthase 2.5.1.16 0.658
3w8d NAD3-hydroxybutyrate dehydrogenase / 0.658
1wnt NAPL-xylulose reductase 1.1.1.10 0.657
2vna NAPProstaglandin reductase 2 1.3.1.48 0.657
2y05 NAPProstaglandin reductase 1 / 0.657
4cql NADEstradiol 17-beta-dehydrogenase 8 1.1.1.62 0.657
4dbz NDPPutative ketoacyl reductase 1.3.1 0.657
4hb9 FADUncharacterized protein / 0.657
4j49 NADUncharacterized protein / 0.657
4j49 NAIUncharacterized protein / 0.657
1edo NAP3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic 1.1.1.100 0.656
4nbw NADShort-chain dehydrogenase/reductase SDR / 0.656
5d2e NAPMlnE / 0.656
5idw NAPShort-chain dehydrogenase/reductase SDR / 0.656
2aa3 AP0L-lactate dehydrogenase / 0.655
4dc1 NDPPutative ketoacyl reductase 1.3.1 0.655
4yag NAIC alpha-dehydrogenase / 0.655
1khh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.654
1u7t TDT3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.654
1x7h NDPPutative ketoacyl reductase 1.3.1 0.654
3lqf NADGalactitol dehydrogenase / 0.654
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.653
3lzw FADFerredoxin--NADP reductase 2 1.18.1.2 0.653
3oet NADErythronate-4-phosphate dehydrogenase / 0.653
3rfx NADUronate dehydrogenase / 0.652
1nbo NADGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.650
4plp NADHomospermidine synthase 2.5.1.44 0.650