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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
4imp NDP Polyketide synthase extender modules 3-4

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4imp NDPPolyketide synthase extender modules 3-4 / 1.193
4hxy NDPPlm1 / 0.860
3p19 NDPPutative blue fluorescent protein / 0.792
2c29 NAPDihydroflavonol 4-reductase / 0.789
5j23 A2RPutative 2-hydroxyacid dehydrogenase / 0.789
4i5e NAPAlclohol dehydrogenase/short-chain dehydrogenase / 0.788
4dc1 NDPPutative ketoacyl reductase 1.3.1 0.787
2gn8 NAPUDP-N-acetylglucosamine 4,6-dehydratase (inverting) 4.2.1.115 0.786
3l77 NJPShort-chain alcohol dehydrogenase / 0.786
4dbz NDPPutative ketoacyl reductase 1.3.1 0.781
3tn7 NJPShort-chain alcohol dehydrogenase / 0.776
5d2e NAPMlnE / 0.776
2jah NDPClavaldehyde dehydrogenase / 0.773
3rku NAPNADP-dependent 3-hydroxy acid dehydrogenase / 0.771
1w8d NAP2,4-dienoyl-CoA reductase, mitochondrial 1.3.1.34 0.766
3icp NADNAD-dependent epimerase/dehydratase / 0.766
3a4v NADNDP-sugar epimerase / 0.760
2q1t NADPutative nucleotide sugar epimerase/ dehydratase / 0.754
3ai2 NDPNADPH-sorbose reductase / 0.752
4fc7 NAPPeroxisomal 2,4-dienoyl-CoA reductase 1.3.1.34 0.752
2nnl NAPDihydroflavonol 4-reductase 1.1.1.219 0.750
4dc0 NDPPutative ketoacyl reductase 1.3.1 0.748
3uce NDPDehydrogenase / 0.744
1x7h NDPPutative ketoacyl reductase 1.3.1 0.742
1xg5 NAPDehydrogenase/reductase SDR family member 11 / 0.742
3aw9 NADNAD-dependent epimerase/dehydratase / 0.734
5lc1 NADL-threonine 3-dehydrogenase / 0.734
1ipe NDPTropinone reductase 2 1.1.1.236 0.731
1n5d NDPCarbonyl reductase [NADPH] 1 / 0.731
1rpn NDPGDP-mannose 4,6-dehydratase / 0.730
3ai3 NDPNADPH-sorbose reductase / 0.727
2o23 NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.726
3mje NDPAmphB / 0.726
1n7g NDPGDP-mannose 4,6 dehydratase 2 4.2.1.47 0.724
2wdz NADGalactitol dehydrogenase / 0.724
2x86 NAPADP-L-glycero-D-manno-heptose-6-epimerase / 0.724
4hwk NAPSepiapterin reductase 1.1.1.153 0.723
1w4z NAPPutative ketoacyl reductase 1.3.1 0.719
2x6t NAPADP-L-glycero-D-manno-heptose-6-epimerase / 0.718
3o26 NDPSalutaridine reductase / 0.717
1rkx NADCDP-D-glucose-4,6-dehydratase / 0.715
4qec NAPElxO / 0.715
2wsb NADGalactitol dehydrogenase / 0.714
3ko8 NADNAD-dependent epimerase/dehydratase / 0.713
1g1a NADdTDP-glucose 4,6-dehydratase / 0.712
4bms NAPAlclohol dehydrogenase/short-chain dehydrogenase / 0.710
4fj2 NAP17beta-hydroxysteroid dehydrogenase / 0.709
3gy0 NAPNAD(P)-dependent oxidoreductase / 0.708
2pzj NADPutative nucleotide sugar epimerase/ dehydratase / 0.707
2q1u NADPutative nucleotide sugar epimerase/ dehydratase / 0.707
1w73 NAP2,4-dienoyl-CoA reductase, mitochondrial 1.3.1.34 0.706
3iah NAPPutative oxoacyl-(Acyl carrier protein) reductase / 0.706
3tox NAPPutative oxidoreductase / 0.706
4dmm NAP3-oxoacyl-[acyl-carrier-protein] reductase / 0.704
4z3d NDPCarbonyl reductase [NADPH] 1 1.1.1.184 0.704
2c54 NADGDP-mannose 3,5-epimerase 5.1.3.18 0.702
3qrw NDPPutative ketoacyl reductase 1.3.1 0.702
4rf2 NAPNADPH dependent R-specific alcohol dehydrogenase / 0.700
2c59 NADGDP-mannose 3,5-epimerase 5.1.3.18 0.698
3w8d NAD3-hydroxybutyrate dehydrogenase / 0.698
4tqg NDPPutative dTDP-d-glucose 4 6-dehydratase / 0.697
3rud NADUDP-N-acetylglucosamine 4-epimerase / 0.696
4hfm NAP2-alkenal reductase (NADP(+)-dependent) / 0.696
4qed NAPElxO / 0.694
2p5y NADUDP-glucose 4-epimerase / 0.693
3a9w NADNDP-sugar epimerase / 0.692
4ej0 NAPADP-L-glycero-D-manno-heptose-6-epimerase / 0.692
1kvr NADUDP-glucose 4-epimerase 5.1.3.2 0.691
3baz NAPHydroxyphenylpyruvate reductase 1.1.1.237 0.690
4j7x NAPSepiapterin reductase 1.1.1.153 0.690
1t2a NDPGDP-mannose 4,6 dehydratase 4.2.1.47 0.689
3qwf NAP17beta-hydroxysteroid dehydrogenase / 0.688
3ruh NADUDP-N-acetylglucosamine 4-epimerase / 0.688
4nbt NAD3-oxoacyl-[acyl-carrier-protein] reductase / 0.688
2q1s NAIPutative nucleotide sugar epimerase/ dehydratase / 0.687
3rj5 NADAlcohol dehydrogenase 1.1.1.1 0.687
4o0l NDPNADPH-dependent 3-quinuclidinone reductase / 0.687
1zem NADXylitol dehydrogenase / 0.686
4fj1 NAP17beta-hydroxysteroid dehydrogenase / 0.686
1h5q NAPNADP-dependent mannitol dehydrogenase 1.1.1.138 0.685
1n7h NDPGDP-mannose 4,6 dehydratase 2 4.2.1.47 0.685
2bd0 NAPSepiapterin reductase / 0.685
2gdz NAD15-hydroxyprostaglandin dehydrogenase [NAD(+)] 1.1.1.141 0.685
3rua NADUDP-N-acetylglucosamine 4-epimerase / 0.685
1bxk NADdTDP-glucose 4,6-dehydratase 2 / 0.684
2yy7 NADL-threonine dehydrogenase / 0.684
4b4o NDPEpimerase family protein SDR39U1 / 0.684
1vl8 NAPOxidoreductase, short chain dehydrogenase/reductase family / 0.682
3bhi NAPCarbonyl reductase [NADPH] 1 1.1.1.184 0.682
1i2b NADUDP-sulfoquinovose synthase, chloroplastic 3.13.1.1 0.680
4u7w NDPMxaA / 0.680
1eq2 NAPADP-L-glycero-D-manno-heptose-6-epimerase / 0.679
1fdu NAPEstradiol 17-beta-dehydrogenase 1 1.1.1.62 0.679
1cyd NDPCarbonyl reductase [NADPH] 2 1.1.1.184 0.678
2yut NAPPutative short-chain oxidoreductase / 0.678
3w8f NAD3-hydroxybutyrate dehydrogenase / 0.678
1pr9 NAPL-xylulose reductase 1.1.1.10 0.677
3o03 NAPDehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) / 0.677
3sxp NADADP-L-glycero-D-mannoheptose-6-epimerase / 0.676
2b5v NAPGlucose 1-dehydrogenase / 0.675
3sj7 NDP3-oxoacyl-(Acyl-carrier-protein) reductase, putative / 0.675
3ru7 NADUDP-N-acetylglucosamine 4-epimerase / 0.674
2pk3 A2RGDP-6-deoxy-D-mannose reductase / 0.673
3nug NADPyridoxal 4-dehydrogenase 1.1.1.107 0.673
4j7u NAPSepiapterin reductase 1.1.1.153 0.672
1nff NAD3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase 1.1.1.53 0.671
2q1w NADPutative nucleotide sugar epimerase/ dehydratase / 0.671
1i3l NADUDP-glucose 4-epimerase / 0.670
1wvg APRCDP-glucose 4,6-dehydratase 4.2.1.45 0.670
3o4r NAPDehydrogenase/reductase SDR family member 4 1.1.1.184 0.669
3rue NADUDP-N-acetylglucosamine 4-epimerase / 0.668
1edo NAP3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic 1.1.1.100 0.667
1ae1 NAPTropinone reductase 1 / 0.666
1e3s NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.666
2v6g NAP3-oxo-Delta(4,5)-steroid 5-beta-reductase / 0.666
3u4c NDPNADPH-dependent reductase BacG / 0.665
2p5u NADUDP-glucose 4-epimerase / 0.664
3wmx NADNAD dependent epimerase/dehydratase / 0.664
4bmv NAPShort-chain dehydrogenase / 0.664
4fj0 NAP17beta-hydroxysteroid dehydrogenase / 0.664
4lis NADUDP-glucose 4-epimerase (Eurofung) / 0.664
1e6w NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.663
1xse NDPCorticosteroid 11-beta-dehydrogenase isozyme 1 1.1.1.146 0.663
2ggs NDPdTDP-4-dehydrorhamnose reductase / 0.663
2rbe NDPCorticosteroid 11-beta-dehydrogenase isozyme 1 1.1.1.146 0.663
4kwh NAPReductase homolog / 0.663
4twr NADNAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase / 0.663
4k6f NAPPutative Acetoacetyl-CoA reductase / 0.662
1sny NAPLD36273p / 0.661
4id9 NADPutative UDP-glucose 4-epimerase / 0.661
4xq9 NADHomospermidine synthase 2.5.1.44 0.661
3lu1 NADUDP-N-acetylglucosamine 4-epimerase / 0.660
5aq1 NDPGlucose-6-phosphate 1-dehydrogenase / 0.660
2hun NAD336aa long hypothetical dTDP-glucose 4,6-dehydratase / 0.659
3d3w NAPL-xylulose reductase 1.1.1.10 0.659
5js6 NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.659
4plp NADHomospermidine synthase 2.5.1.44 0.658
4xyb NDPFormate dehydrogenase / 0.658
1xkq NDPUncharacterized protein / 0.657
1mg5 NAIAlcohol dehydrogenase 1.1.1.1 0.656
3ak4 NADNADH-dependent quinuclidinone reductase / 0.656
4e5y NDPGDP-L-fucose synthase 1.1.1.271 0.656
1ek5 NADUDP-glucose 4-epimerase / 0.655
3ehe NADUDP-glucose 4-epimerase (GalE-1) / 0.655
5a03 NDPGlucose-fructose oxidoreductase / 0.653
4ge9 0L0Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial 2.6.1.39 0.652
5b1y NDP3-oxoacyl-[acyl-carrier-protein] reductase / 0.652
1u5a BIKL-lactate dehydrogenase 1.1.1.27 0.651
2bgm NAJSecoisolariciresinol dehydrogenase 1.1.1.331 0.651
2ztl NADD(-)-3-hydroxybutyrate dehydrogenase / 0.651
5a04 NDPGlucose-fructose oxidoreductase / 0.651
5a05 NDPGlucose-fructose oxidoreductase / 0.651
1gee NADGlucose 1-dehydrogenase 1.1.1.47 0.650
2dte NAIGlucose 1-dehydrogenase related protein / 0.650
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.650
3mvq NDPGlutamate dehydrogenase 1, mitochondrial 1.4.1.3 0.650