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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
2pk3 A2R GDP-6-deoxy-D-mannose reductase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2pk3 A2RGDP-6-deoxy-D-mannose reductase / 1.167
2c59 NADGDP-mannose 3,5-epimerase 5.1.3.18 0.798
2c54 NADGDP-mannose 3,5-epimerase 5.1.3.18 0.779
1n7h NDPGDP-mannose 4,6 dehydratase 2 4.2.1.47 0.770
2ggs NDPdTDP-4-dehydrorhamnose reductase / 0.765
2x6t NAPADP-L-glycero-D-manno-heptose-6-epimerase / 0.758
1rpn NDPGDP-mannose 4,6-dehydratase / 0.755
4u7w NDPMxaA / 0.752
3uce NDPDehydrogenase / 0.751
1n7g NDPGDP-mannose 4,6 dehydratase 2 4.2.1.47 0.750
2x86 NAPADP-L-glycero-D-manno-heptose-6-epimerase / 0.750
1kc1 NDPdTDP-4-dehydrorhamnose reductase 1.1.1.133 0.747
1n2s NAIdTDP-4-dehydrorhamnose reductase 1.1.1.133 0.745
1wvg APRCDP-glucose 4,6-dehydratase 4.2.1.45 0.744
2q1w NADPutative nucleotide sugar epimerase/ dehydratase / 0.738
2z1m NDPGDP-mannose 4,6-dehydratase / 0.737
2gn8 NAPUDP-N-acetylglucosamine 4,6-dehydratase (inverting) 4.2.1.115 0.735
1t2a NDPGDP-mannose 4,6 dehydratase 4.2.1.47 0.734
1w8d NAP2,4-dienoyl-CoA reductase, mitochondrial 1.3.1.34 0.729
4fc7 NAPPeroxisomal 2,4-dienoyl-CoA reductase 1.3.1.34 0.727
1nah NADUDP-glucose 4-epimerase 5.1.3.2 0.726
2q1u NADPutative nucleotide sugar epimerase/ dehydratase / 0.726
1w73 NAP2,4-dienoyl-CoA reductase, mitochondrial 1.3.1.34 0.721
3sxp NADADP-L-glycero-D-mannoheptose-6-epimerase / 0.721
4lis NADUDP-glucose 4-epimerase (Eurofung) / 0.721
2bfo NDPPteridine reductase 1 1.5.1.33 0.719
1bxk NADdTDP-glucose 4,6-dehydratase 2 / 0.717
1eq2 NAPADP-L-glycero-D-manno-heptose-6-epimerase / 0.712
1kvr NADUDP-glucose 4-epimerase 5.1.3.2 0.711
2wdz NADGalactitol dehydrogenase / 0.709
3bmo NAPPteridine reductase / 0.709
2c29 NAPDihydroflavonol 4-reductase / 0.708
1bws NDPGDP-L-fucose synthase / 0.706
1rkx NADCDP-D-glucose-4,6-dehydratase / 0.703
3ehe NADUDP-glucose 4-epimerase (GalE-1) / 0.703
4clo NAPPteridine reductase / 0.703
2nnl NAPDihydroflavonol 4-reductase 1.1.1.219 0.702
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.701
4e5y NDPGDP-L-fucose synthase 1.1.1.271 0.699
2q1t NADPutative nucleotide sugar epimerase/ dehydratase / 0.698
1pr9 NAPL-xylulose reductase 1.1.1.10 0.691
3ak4 NADNADH-dependent quinuclidinone reductase / 0.691
3wmx NADNAD dependent epimerase/dehydratase / 0.690
3nug NADPyridoxal 4-dehydrogenase 1.1.1.107 0.687
1fxs NAPGDP-L-fucose synthase / 0.686
1g1a NADdTDP-glucose 4,6-dehydratase / 0.685
1xse NDPCorticosteroid 11-beta-dehydrogenase isozyme 1 1.1.1.146 0.684
3d3w NAPL-xylulose reductase 1.1.1.10 0.683
5jyd NADShort chain dehydrogenase / 0.683
2z95 NDPGDP-mannose 4,6-dehydratase / 0.682
3ruc NADUDP-N-acetylglucosamine 4-epimerase / 0.682
1evj NADGlucose--fructose oxidoreductase 1.1.99.28 0.680
4nbu NAI3-oxoacyl-(Acyl-carrier-protein) reductase / 0.680
3rj9 NADAlcohol dehydrogenase 1.1.1.1 0.679
4idg NADPutative UDP-glucose 4-epimerase / 0.679
4yr9 NADL-threonine 3-dehydrogenase, mitochondrial 1.1.1.103 0.679
5bsg NAPPyrroline-5-carboxylate reductase / 0.679
2dte NAIGlucose 1-dehydrogenase related protein / 0.677
3iah NAPPutative oxoacyl-(Acyl carrier protein) reductase / 0.676
2dkn NAI3-alpha-hydroxysteroid dehydrogenase / 0.675
2ekp NAD2-deoxy-D-gluconate 3-dehydrogenase / 0.675
3rue NADUDP-N-acetylglucosamine 4-epimerase / 0.675
3ruf NADUDP-N-acetylglucosamine 4-epimerase / 0.674
1bsv NDPGDP-L-fucose synthase / 0.673
2o23 NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.673
4imp NDPPolyketide synthase extender modules 3-4 / 0.673
1b15 NAEAlcohol dehydrogenase 1.1.1.1 0.671
1mg5 NAIAlcohol dehydrogenase 1.1.1.1 0.671
3o03 NAPDehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) / 0.671
3a4v NADNDP-sugar epimerase / 0.670
3uxy NADShort-chain dehydrogenase/reductase SDR / 0.669
4o0l NDPNADPH-dependent 3-quinuclidinone reductase / 0.669
3ijr NADOxidoreductase, short chain dehydrogenase/reductase family / 0.668
5d2e NAPMlnE / 0.668
1i3l NADUDP-glucose 4-epimerase / 0.667
4hxy NDPPlm1 / 0.667
1gco NADGlucose 1-dehydrogenase 1.1.1.47 0.666
2yy7 NADL-threonine dehydrogenase / 0.666
3mje NDPAmphB / 0.666
3ndr NADPyridoxal 4-dehydrogenase 1.1.1.107 0.666
4z3d NDPCarbonyl reductase [NADPH] 1 1.1.1.184 0.665
1e3s NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.664
2jah NDPClavaldehyde dehydrogenase / 0.664
3ru9 NADUDP-N-acetylglucosamine 4-epimerase / 0.664
3p19 NDPPutative blue fluorescent protein / 0.663
3lu1 NADUDP-N-acetylglucosamine 4-epimerase / 0.662
3rku NAPNADP-dependent 3-hydroxy acid dehydrogenase / 0.662
4plp NADHomospermidine synthase 2.5.1.44 0.662
1gee NADGlucose 1-dehydrogenase 1.1.1.47 0.661
1n5d NDPCarbonyl reductase [NADPH] 1 / 0.661
2yut NAPPutative short-chain oxidoreductase / 0.661
4pvd NDPNADPH-dependent methylglyoxal reductase GRE2 / 0.661
1g6k NADGlucose 1-dehydrogenase 1.1.1.47 0.660
1nai NADUDP-glucose 4-epimerase 5.1.3.2 0.660
1oaa NAPSepiapterin reductase 1.1.1.153 0.660
2q1s NAIPutative nucleotide sugar epimerase/ dehydratase / 0.657
5idw NAPShort-chain dehydrogenase/reductase SDR / 0.657
4dc1 NDPPutative ketoacyl reductase 1.3.1 0.656
4yag NAIC alpha-dehydrogenase / 0.656
5bt9 NAP3-oxoacyl-(Acyl-carrier-protein) reductase / 0.655
1rwb NADGlucose 1-dehydrogenase 1.1.1.47 0.654
3bhi NAPCarbonyl reductase [NADPH] 1 1.1.1.184 0.654
3sx2 NADUncharacterized protein / 0.654
4dc0 NDPPutative ketoacyl reductase 1.3.1 0.654
3i6q NDPPutative leucoanthocyanidin reductase 1 / 0.653
3ko8 NADNAD-dependent epimerase/dehydratase / 0.653
4j7x NAPSepiapterin reductase 1.1.1.153 0.653
1xg5 NAPDehydrogenase/reductase SDR family member 11 / 0.652
3gy0 NAPNAD(P)-dependent oxidoreductase / 0.651
4id9 NADPutative UDP-glucose 4-epimerase / 0.651
1sby NADAlcohol dehydrogenase 1.1.1.1 0.650
4egb NADdTDP-glucose 4,6-dehydratase / 0.650