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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
2x6t NAP ADP-L-glycero-D-manno-heptose-6-epimerase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2x6t NAPADP-L-glycero-D-manno-heptose-6-epimerase / 1.389
1eq2 NAPADP-L-glycero-D-manno-heptose-6-epimerase / 1.179
4ej0 NAPADP-L-glycero-D-manno-heptose-6-epimerase / 1.167
2x86 NAPADP-L-glycero-D-manno-heptose-6-epimerase / 1.152
3sxp NADADP-L-glycero-D-mannoheptose-6-epimerase / 0.854
2q1t NADPutative nucleotide sugar epimerase/ dehydratase / 0.831
3ruf NADUDP-N-acetylglucosamine 4-epimerase / 0.829
1kvr NADUDP-glucose 4-epimerase 5.1.3.2 0.815
1i3l NADUDP-glucose 4-epimerase / 0.809
3rua NADUDP-N-acetylglucosamine 4-epimerase / 0.809
2q1u NADPutative nucleotide sugar epimerase/ dehydratase / 0.804
3mje NDPAmphB / 0.797
3ehe NADUDP-glucose 4-epimerase (GalE-1) / 0.795
5d2e NAPMlnE / 0.787
3nug NADPyridoxal 4-dehydrogenase 1.1.1.107 0.784
1nah NADUDP-glucose 4-epimerase 5.1.3.2 0.781
3aw9 NADNAD-dependent epimerase/dehydratase / 0.780
3lu1 NADUDP-N-acetylglucosamine 4-epimerase / 0.779
3rud NADUDP-N-acetylglucosamine 4-epimerase / 0.777
3ru9 NADUDP-N-acetylglucosamine 4-epimerase / 0.776
4lis NADUDP-glucose 4-epimerase (Eurofung) / 0.772
3ruc NADUDP-N-acetylglucosamine 4-epimerase / 0.771
3icp NADNAD-dependent epimerase/dehydratase / 0.766
2yy7 NADL-threonine dehydrogenase / 0.764
2q1w NADPutative nucleotide sugar epimerase/ dehydratase / 0.763
2q1s NAIPutative nucleotide sugar epimerase/ dehydratase / 0.762
3ko8 NADNAD-dependent epimerase/dehydratase / 0.762
2c54 NADGDP-mannose 3,5-epimerase 5.1.3.18 0.758
2pk3 A2RGDP-6-deoxy-D-mannose reductase / 0.758
4z3d NDPCarbonyl reductase [NADPH] 1 1.1.1.184 0.752
4hxy NDPPlm1 / 0.751
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.749
4idg NADPutative UDP-glucose 4-epimerase / 0.748
3ruh NADUDP-N-acetylglucosamine 4-epimerase / 0.744
1bxk NADdTDP-glucose 4,6-dehydratase 2 / 0.742
1zem NADXylitol dehydrogenase / 0.742
3ru7 NADUDP-N-acetylglucosamine 4-epimerase / 0.742
5lc1 NADL-threonine 3-dehydrogenase / 0.742
2z1m NDPGDP-mannose 4,6-dehydratase / 0.738
2c59 NADGDP-mannose 3,5-epimerase 5.1.3.18 0.737
2p5y NADUDP-glucose 4-epimerase / 0.737
3ndr NADPyridoxal 4-dehydrogenase 1.1.1.107 0.735
2wdz NADGalactitol dehydrogenase / 0.734
2b69 NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.733
1gco NADGlucose 1-dehydrogenase 1.1.1.47 0.732
1gee NADGlucose 1-dehydrogenase 1.1.1.47 0.732
1rpn NDPGDP-mannose 4,6-dehydratase / 0.729
2c29 NAPDihydroflavonol 4-reductase / 0.729
4lk3 NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.729
4u7w NDPMxaA / 0.727
2ggs NDPdTDP-4-dehydrorhamnose reductase / 0.726
3iah NAPPutative oxoacyl-(Acyl carrier protein) reductase / 0.726
4o0l NDPNADPH-dependent 3-quinuclidinone reductase / 0.726
4fc7 NAPPeroxisomal 2,4-dienoyl-CoA reductase 1.3.1.34 0.722
4gh5 NADShort-chain dehydrogenase/reductase SDR / 0.718
4imp NDPPolyketide synthase extender modules 3-4 / 0.718
1orr NADCDP-paratose 2-epimerase / 0.716
3oa2 NADUDP-N-acetyl-2-amino-2-deoxy-D-glucuronate oxidase / 0.714
2d1y NADOxidoreductase, short-chain dehydrogenase/reductase family / 0.713
3ai3 NDPNADPH-sorbose reductase / 0.712
3ak4 NADNADH-dependent quinuclidinone reductase / 0.711
3wmx NADNAD dependent epimerase/dehydratase / 0.711
2wsb NADGalactitol dehydrogenase / 0.710
3rue NADUDP-N-acetylglucosamine 4-epimerase / 0.710
1n5d NDPCarbonyl reductase [NADPH] 1 / 0.708
4c7k NAPCorticosteroid 11-beta-dehydrogenase isozyme 1 1.1.1.146 0.707
2o23 NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.706
1nai NADUDP-glucose 4-epimerase 5.1.3.2 0.705
1rkx NADCDP-D-glucose-4,6-dehydratase / 0.705
2nnl NAPDihydroflavonol 4-reductase 1.1.1.219 0.705
2yut NAPPutative short-chain oxidoreductase / 0.705
4j7x NAPSepiapterin reductase 1.1.1.153 0.705
1rwb NADGlucose 1-dehydrogenase 1.1.1.47 0.704
1x7g NAPPutative ketoacyl reductase 1.3.1 0.704
4k6f NAPPutative Acetoacetyl-CoA reductase / 0.704
3ajr NADNDP-sugar epimerase / 0.703
4qec NAPElxO / 0.703
4nbt NAD3-oxoacyl-[acyl-carrier-protein] reductase / 0.702
4qed NAPElxO / 0.702
2gn8 NAPUDP-N-acetylglucosamine 4,6-dehydratase (inverting) 4.2.1.115 0.701
3uce NDPDehydrogenase / 0.700
1vl8 NAPOxidoreductase, short chain dehydrogenase/reductase family / 0.699
4pvd NDPNADPH-dependent methylglyoxal reductase GRE2 / 0.699
4gll NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.698
5a03 NDPGlucose-fructose oxidoreductase / 0.697
5js6 NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.697
2hrb NAPCarbonyl reductase [NADPH] 3 1.1.1.184 0.696
2wyv NADEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.696
2z95 NDPGDP-mannose 4,6-dehydratase / 0.696
1g1a NADdTDP-glucose 4,6-dehydratase / 0.694
4iqg NAPShort-chain dehydrogenase/reductase SDR / 0.694
1e6w NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.693
4j7u NAPSepiapterin reductase 1.1.1.153 0.693
1pr9 NAPL-xylulose reductase 1.1.1.10 0.692
3a9w NADNDP-sugar epimerase / 0.692
5b1y NDP3-oxoacyl-[acyl-carrier-protein] reductase / 0.692
1u7t NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.691
1geg NADDiacetyl reductase [(S)-acetoin forming] 1.1.1.304 0.690
1n7h NDPGDP-mannose 4,6 dehydratase 2 4.2.1.47 0.690
2rbe NDPCorticosteroid 11-beta-dehydrogenase isozyme 1 1.1.1.146 0.688
3a4v NADNDP-sugar epimerase / 0.688
1e3w NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.687
4id9 NADPutative UDP-glucose 4-epimerase / 0.685
4tvb NADHomospermidine synthase 2.5.1.44 0.685
4wec NADShort chain dehydrogenase / 0.684
1e3s NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.683
3o9z NADLipopolysaccaride biosynthesis protein wbpB / 0.683
3pgx NADUncharacterized NAD-dependent oxidoreductase MAP_4146 / 0.683
4dmm NAP3-oxoacyl-[acyl-carrier-protein] reductase / 0.683
1evj NADGlucose--fructose oxidoreductase 1.1.99.28 0.682
1h6d NDPGlucose--fructose oxidoreductase 1.1.99.28 0.681
5a05 NDPGlucose-fructose oxidoreductase / 0.681
1h6b NDPGlucose--fructose oxidoreductase 1.1.99.28 0.680
4dc0 NDPPutative ketoacyl reductase 1.3.1 0.680
4nbu NAI3-oxoacyl-(Acyl-carrier-protein) reductase / 0.680
4twr NADNAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase / 0.680
1h6a NDPGlucose--fructose oxidoreductase 1.1.99.28 0.679
1zh8 NAPUncharacterized protein / 0.679
3jv7 NADSecondary alcohol dehydrogenase / 0.679
4m87 NADEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.679
4hwk NAPSepiapterin reductase 1.1.1.153 0.677
5idw NAPShort-chain dehydrogenase/reductase SDR / 0.677
1h6c NDPGlucose--fructose oxidoreductase 1.1.99.28 0.676
4n5n NAPAcetoacetyl-CoA reductase 1.1.1.36 0.675
3of2 NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.672
4fn4 NADShort chain dehydrogenase / 0.672
4rf2 NAPNADPH dependent R-specific alcohol dehydrogenase / 0.672
3qwf NAP17beta-hydroxysteroid dehydrogenase / 0.671
3ai2 NDPNADPH-sorbose reductase / 0.669
3qrw NDPPutative ketoacyl reductase 1.3.1 0.669
5a04 NDPGlucose-fructose oxidoreductase / 0.669
5jsf NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.669
2ag5 NAD3-hydroxybutyrate dehydrogenase type 2 / 0.668
2ztu NADD(-)-3-hydroxybutyrate dehydrogenase / 0.667
5kcp NAJAlcohol dehydrogenase E chain 1.1.1.1 0.667
1nvm NADAcetaldehyde dehydrogenase 1.2.1.10 0.665
2ohx NADAlcohol dehydrogenase E chain 1.1.1.1 0.665
2p9g NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.665
4xqc NADHomospermidine synthase 2.5.1.44 0.665
4xrg NADHomospermidine synthase 2.5.1.44 0.665
3a28 NADL-2,3-butanediol dehydrogenase 1.1.1.76 0.664
5a06 NDPGlucose-fructose oxidoreductase / 0.664
3sx2 NADUncharacterized protein / 0.663
4cql NADEstradiol 17-beta-dehydrogenase 8 1.1.1.62 0.663
4plp NADHomospermidine synthase 2.5.1.44 0.663
5a02 NAPGlucose-fructose oxidoreductase / 0.663
3pdu NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.662
3qvs NADMyo-inositol-1-phosphate synthase (Ino1) / 0.660
4dbz NDPPutative ketoacyl reductase 1.3.1 0.660
1kc1 NDPdTDP-4-dehydrorhamnose reductase 1.1.1.133 0.659
3w8d NAD3-hydroxybutyrate dehydrogenase / 0.659
4e5k NADPhosphonate dehydrogenase 1.20.1.1 0.659
2p5u NADUDP-glucose 4-epimerase / 0.658
3d64 NADAdenosylhomocysteinase / 0.658
5jy1 NADPutative short-chain dehydrogenase/reductase / 0.658
5koi NADEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.658
1het NADAlcohol dehydrogenase E chain 1.1.1.1 0.657
2nv6 ZIDEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.657
4xd2 NAIAlcohol dehydrogenase E chain 1.1.1.1 0.657
3tn7 NJPShort-chain alcohol dehydrogenase / 0.656
4nbw NADShort-chain dehydrogenase/reductase SDR / 0.656
5bsg NAPPyrroline-5-carboxylate reductase / 0.656
2q2v NADBeta-D-hydroxybutyrate dehydrogenase / 0.655
3o26 NDPSalutaridine reductase / 0.655
4b79 NADProbable short-chain dehydrogenase / 0.655
2dkn NAI3-alpha-hydroxysteroid dehydrogenase / 0.654
2g76 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.654
3rj9 NADAlcohol dehydrogenase 1.1.1.1 0.654
2eer NADNAD-dependent alcohol dehydrogenase 1.1.1.1 0.653
3l77 NJPShort-chain alcohol dehydrogenase / 0.653
3sj7 NDP3-oxoacyl-(Acyl-carrier-protein) reductase, putative / 0.653
4xq9 NADHomospermidine synthase 2.5.1.44 0.652
1dxy NADD-2-hydroxyisocaproate dehydrogenase 1.1.1 0.651
4e5y NDPGDP-L-fucose synthase 1.1.1.271 0.651
5kjc NAJAlcohol dehydrogenase E chain 1.1.1.1 0.651