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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
4yr9 NAD L-threonine 3-dehydrogenase, mitochondrial 1.1.1.103

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4yr9 NADL-threonine 3-dehydrogenase, mitochondrial 1.1.1.103 1.199
2yy7 NADL-threonine dehydrogenase / 0.865
5lc1 NADL-threonine 3-dehydrogenase / 0.837
3wmx NADNAD dependent epimerase/dehydratase / 0.809
1g1a NADdTDP-glucose 4,6-dehydratase / 0.805
2wdz NADGalactitol dehydrogenase / 0.753
1bxk NADdTDP-glucose 4,6-dehydratase 2 / 0.750
1n5d NDPCarbonyl reductase [NADPH] 1 / 0.747
3a4v NADNDP-sugar epimerase / 0.744
2c59 NADGDP-mannose 3,5-epimerase 5.1.3.18 0.735
5jy1 NADPutative short-chain dehydrogenase/reductase / 0.725
2nnl NAPDihydroflavonol 4-reductase 1.1.1.219 0.713
2hun NAD336aa long hypothetical dTDP-glucose 4,6-dehydratase / 0.711
4c7k NAPCorticosteroid 11-beta-dehydrogenase isozyme 1 1.1.1.146 0.711
4lis NADUDP-glucose 4-epimerase (Eurofung) / 0.710
2p5y NADUDP-glucose 4-epimerase / 0.708
3aw9 NADNAD-dependent epimerase/dehydratase / 0.708
4cr8 NADN-acylmannosamine 1-dehydrogenase 1.1.1.233 0.708
2d1y NADOxidoreductase, short-chain dehydrogenase/reductase family / 0.705
1cyd NDPCarbonyl reductase [NADPH] 2 1.1.1.184 0.704
1pr9 NAPL-xylulose reductase 1.1.1.10 0.703
2c54 NADGDP-mannose 3,5-epimerase 5.1.3.18 0.703
2oo5 TXDNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.700
3nug NADPyridoxal 4-dehydrogenase 1.1.1.107 0.700
2c29 NAPDihydroflavonol 4-reductase / 0.697
1geg NADDiacetyl reductase [(S)-acetoin forming] 1.1.1.304 0.696
2q1t NADPutative nucleotide sugar epimerase/ dehydratase / 0.696
4j7x NAPSepiapterin reductase 1.1.1.153 0.695
1f8g NADNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.693
1oaa NAPSepiapterin reductase 1.1.1.153 0.693
1x15 NADNAD(P) transhydrogenase subunit alpha 1.6.1.2 0.692
1xse NDPCorticosteroid 11-beta-dehydrogenase isozyme 1 1.1.1.146 0.692
3sx2 NADUncharacterized protein / 0.692
1w73 NAP2,4-dienoyl-CoA reductase, mitochondrial 1.3.1.34 0.690
2c20 NADUDP-glucose 4-epimerase / 0.690
2hmv ADPKtr system potassium uptake protein A / 0.690
2hrb NAPCarbonyl reductase [NADPH] 3 1.1.1.184 0.690
2wsb NADGalactitol dehydrogenase / 0.689
1u28 NADNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.687
2q1w NADPutative nucleotide sugar epimerase/ dehydratase / 0.687
3a9w NADNDP-sugar epimerase / 0.687
4l4x NDPAmphI / 0.687
2p5u NADUDP-glucose 4-epimerase / 0.686
1rkx NADCDP-D-glucose-4,6-dehydratase / 0.685
2fsv NADNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.685
3rfx NADUronate dehydrogenase / 0.685
4u7w NDPMxaA / 0.685
3ehe NADUDP-glucose 4-epimerase (GalE-1) / 0.684
4b8z NAPGDP-L-fucose synthase 1.1.1.271 0.683
3ndr NADPyridoxal 4-dehydrogenase 1.1.1.107 0.682
1dxy NADD-2-hydroxyisocaproate dehydrogenase 1.1.1 0.679
1n7g NDPGDP-mannose 4,6 dehydratase 2 4.2.1.47 0.679
2pk3 A2RGDP-6-deoxy-D-mannose reductase / 0.679
3d3w NAPL-xylulose reductase 1.1.1.10 0.678
4gh5 NADShort-chain dehydrogenase/reductase SDR / 0.678
4fn4 NADShort chain dehydrogenase / 0.677
1nah NADUDP-glucose 4-epimerase 5.1.3.2 0.676
1zmd NAIDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.676
2g76 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.676
4hxy NDPPlm1 / 0.676
3l8k ADPDihydrolipoamide dehydrogenase (PdhD-3) / 0.675
4tvb NADHomospermidine synthase 2.5.1.44 0.675
4xrg NADHomospermidine synthase 2.5.1.44 0.675
3bmo NAPPteridine reductase / 0.674
1ek5 NADUDP-glucose 4-epimerase / 0.673
3a1n NADNDP-sugar epimerase / 0.673
3icp NADNAD-dependent epimerase/dehydratase / 0.673
4ej0 NAPADP-L-glycero-D-manno-heptose-6-epimerase / 0.673
4fj2 NAP17beta-hydroxysteroid dehydrogenase / 0.673
4twr NADNAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase / 0.673
4xq9 NADHomospermidine synthase 2.5.1.44 0.673
4xqc NADHomospermidine synthase 2.5.1.44 0.673
4y9d NAIC alpha-dehydrogenase / 0.673
3ajr NADNDP-sugar epimerase / 0.672
5js6 NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.671
1eq2 NAPADP-L-glycero-D-manno-heptose-6-epimerase / 0.670
2q1s NAIPutative nucleotide sugar epimerase/ dehydratase / 0.670
3adp NAILambda-crystallin 1.1.1.45 0.670
3lu1 NADUDP-N-acetylglucosamine 4-epimerase / 0.670
4z3d NDPCarbonyl reductase [NADPH] 1 1.1.1.184 0.670
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.669
1zem NADXylitol dehydrogenase / 0.668
3oew NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.668
1i2b NADUDP-sulfoquinovose synthase, chloroplastic 3.13.1.1 0.667
1uay ADNOxidoreductase / 0.667
2oor NADNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.667
3gy0 NAPNAD(P)-dependent oxidoreductase / 0.667
4dc1 NDPPutative ketoacyl reductase 1.3.1 0.666
4j4b NAIUncharacterized protein / 0.666
1e3s NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.665
1lsj NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.665
2bfo NDPPteridine reductase 1 1.5.1.33 0.665
5mdh NADMalate dehydrogenase, cytoplasmic 1.1.1.37 0.665
1bdb NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase / 0.664
1nai NADUDP-glucose 4-epimerase 5.1.3.2 0.664
2bgl NAJSecoisolariciresinol dehydrogenase 1.1.1.331 0.663
3iah NAPPutative oxoacyl-(Acyl carrier protein) reductase / 0.663
3o03 NAPDehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) / 0.663
2ji7 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.662
2x0i NAIMalate dehydrogenase / 0.662
3h5n ATPMccB protein / 0.662
3ikt NADRedox-sensing transcriptional repressor Rex / 0.662
3rud NADUDP-N-acetylglucosamine 4-epimerase / 0.662
3wv7 ADPHmd co-occurring protein HcgE / 0.662
1nff NAD3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase 1.1.1.53 0.661
2b69 NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.661
4clo NAPPteridine reductase / 0.661
4cql NADEstradiol 17-beta-dehydrogenase 8 1.1.1.62 0.661
4fj0 NAP17beta-hydroxysteroid dehydrogenase / 0.661
4kwh NAPReductase homolog / 0.661
4lk3 NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.661
1f17 NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.660
1j5p NADL-aspartate dehydrogenase 1.4.1.21 0.660
1wwk NAD307aa long hypothetical phosphoglycerate dehydrogenase / 0.660
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.660
3ruh NADUDP-N-acetylglucosamine 4-epimerase / 0.660
3vdq NAD3-hydroxybutyrate dehydrogenase / 0.660
1kol NADGlutathione-independent formaldehyde dehydrogenase / 0.659
2ggs NDPdTDP-4-dehydrorhamnose reductase / 0.659
2hdh NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.659
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.659
3h2s NDPPutative NADH-flavin reductase / 0.659
5ig2 NADShort-chain dehydrogenase/reductase SDR / 0.659
3fri SAH16S rRNA methylase / 0.658
3tsc NADUncharacterized protein / 0.658
1nfr NAD3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase 1.1.1.53 0.657
4gll NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.657
1w4z NAPPutative ketoacyl reductase 1.3.1 0.656
3ru9 NADUDP-N-acetylglucosamine 4-epimerase / 0.656
3ru7 NADUDP-N-acetylglucosamine 4-epimerase / 0.655
4nbt NAD3-oxoacyl-[acyl-carrier-protein] reductase / 0.655
3mht SAHModification methylase HhaI 2.1.1.37 0.654
3sj7 NDP3-oxoacyl-(Acyl-carrier-protein) reductase, putative / 0.654
1wnt NAPL-xylulose reductase 1.1.1.10 0.653
2rgj FADFlavin-containing monooxygenase / 0.653
3g49 NAPCorticosteroid 11-beta-dehydrogenase isozyme 1 1.1.1.146 0.653
3rua NADUDP-N-acetylglucosamine 4-epimerase / 0.653
3s55 NADPutative short-chain dehydrogenase/reductase / 0.653
4e5y NDPGDP-L-fucose synthase 1.1.1.271 0.653
4idg NADPutative UDP-glucose 4-epimerase / 0.653
4is3 NAD3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 1.17.98.1 0.653
4plp NADHomospermidine synthase 2.5.1.44 0.653
1rwb NADGlucose 1-dehydrogenase 1.1.1.47 0.652
3qvt NAIMyo-inositol-1-phosphate synthase (Ino1) / 0.652
4tqg NDPPutative dTDP-d-glucose 4 6-dehydratase / 0.652
2dkn NAI3-alpha-hydroxysteroid dehydrogenase / 0.651
3ruf NADUDP-N-acetylglucosamine 4-epimerase / 0.651
2gdz NAD15-hydroxyprostaglandin dehydrogenase [NAD(+)] 1.1.1.141 0.650
3n7u NADFormate dehydrogenase, chloroplastic/mitochondrial / 0.650
3o26 NDPSalutaridine reductase / 0.650
4iqg NAPShort-chain dehydrogenase/reductase SDR / 0.650
4k28 NADShikimate dehydrogenase family protein / 0.650