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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
4lk3 NAD UDP-glucuronic acid decarboxylase 1 4.1.1.35

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4lk3 NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 1.140
2b69 NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.987
4gll NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.962
3ko8 NADNAD-dependent epimerase/dehydratase / 0.945
3icp NADNAD-dependent epimerase/dehydratase / 0.922
4m55 NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.921
2q1t NADPutative nucleotide sugar epimerase/ dehydratase / 0.911
2pzj NADPutative nucleotide sugar epimerase/ dehydratase / 0.910
2q1s NAIPutative nucleotide sugar epimerase/ dehydratase / 0.909
2q1u NADPutative nucleotide sugar epimerase/ dehydratase / 0.901
2p5y NADUDP-glucose 4-epimerase / 0.880
2q1w NADPutative nucleotide sugar epimerase/ dehydratase / 0.861
3rua NADUDP-N-acetylglucosamine 4-epimerase / 0.861
3ruf NADUDP-N-acetylglucosamine 4-epimerase / 0.861
3ru9 NADUDP-N-acetylglucosamine 4-epimerase / 0.845
3lu1 NADUDP-N-acetylglucosamine 4-epimerase / 0.822
3ru7 NADUDP-N-acetylglucosamine 4-epimerase / 0.815
3rud NADUDP-N-acetylglucosamine 4-epimerase / 0.812
2c59 NADGDP-mannose 3,5-epimerase 5.1.3.18 0.809
3sxp NADADP-L-glycero-D-mannoheptose-6-epimerase / 0.800
3ruh NADUDP-N-acetylglucosamine 4-epimerase / 0.796
3aw9 NADNAD-dependent epimerase/dehydratase / 0.793
1i3l NADUDP-glucose 4-epimerase / 0.789
4lis NADUDP-glucose 4-epimerase (Eurofung) / 0.789
1kvr NADUDP-glucose 4-epimerase 5.1.3.2 0.786
4idg NADPutative UDP-glucose 4-epimerase / 0.782
1rkx NADCDP-D-glucose-4,6-dehydratase / 0.777
3ruc NADUDP-N-acetylglucosamine 4-epimerase / 0.776
4id9 NADPutative UDP-glucose 4-epimerase / 0.776
1orr NADCDP-paratose 2-epimerase / 0.765
4hxy NDPPlm1 / 0.748
4ej0 NAPADP-L-glycero-D-manno-heptose-6-epimerase / 0.747
3rue NADUDP-N-acetylglucosamine 4-epimerase / 0.746
1eq2 NAPADP-L-glycero-D-manno-heptose-6-epimerase / 0.744
1g1a NADdTDP-glucose 4,6-dehydratase / 0.740
2x86 NAPADP-L-glycero-D-manno-heptose-6-epimerase / 0.734
3nug NADPyridoxal 4-dehydrogenase 1.1.1.107 0.734
3ehe NADUDP-glucose 4-epimerase (GalE-1) / 0.731
2x6t NAPADP-L-glycero-D-manno-heptose-6-epimerase / 0.729
1i2b NADUDP-sulfoquinovose synthase, chloroplastic 3.13.1.1 0.726
1nah NADUDP-glucose 4-epimerase 5.1.3.2 0.720
3ndr NADPyridoxal 4-dehydrogenase 1.1.1.107 0.719
4u7w NDPMxaA / 0.716
2gn8 NAPUDP-N-acetylglucosamine 4,6-dehydratase (inverting) 4.2.1.115 0.715
2p5u NADUDP-glucose 4-epimerase / 0.714
3sj7 NDP3-oxoacyl-(Acyl-carrier-protein) reductase, putative / 0.714
1g6k NADGlucose 1-dehydrogenase 1.1.1.47 0.713
2c54 NADGDP-mannose 3,5-epimerase 5.1.3.18 0.712
3o03 NAPDehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) / 0.712
1e3w NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.709
1n7g NDPGDP-mannose 4,6 dehydratase 2 4.2.1.47 0.708
2y99 NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase 1.3.1.56 0.708
4twr NADNAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase / 0.703
1bxk NADdTDP-glucose 4,6-dehydratase 2 / 0.701
2c29 NAPDihydroflavonol 4-reductase / 0.701
3rfx NADUronate dehydrogenase / 0.700
3pgx NADUncharacterized NAD-dependent oxidoreductase MAP_4146 / 0.699
1w73 NAP2,4-dienoyl-CoA reductase, mitochondrial 1.3.1.34 0.698
4iqg NAPShort-chain dehydrogenase/reductase SDR / 0.698
1n5d NDPCarbonyl reductase [NADPH] 1 / 0.697
3wmx NADNAD dependent epimerase/dehydratase / 0.696
4k6f NAPPutative Acetoacetyl-CoA reductase / 0.696
4hwk NAPSepiapterin reductase 1.1.1.153 0.695
5js6 NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.694
4nbt NAD3-oxoacyl-[acyl-carrier-protein] reductase / 0.693
4fc7 NAPPeroxisomal 2,4-dienoyl-CoA reductase 1.3.1.34 0.692
2d1y NADOxidoreductase, short-chain dehydrogenase/reductase family / 0.691
2c20 NADUDP-glucose 4-epimerase / 0.690
1geg NADDiacetyl reductase [(S)-acetoin forming] 1.1.1.304 0.686
1nai NADUDP-glucose 4-epimerase 5.1.3.2 0.686
2dkn NAI3-alpha-hydroxysteroid dehydrogenase / 0.686
3rj5 NADAlcohol dehydrogenase 1.1.1.1 0.686
4egb NADdTDP-glucose 4,6-dehydratase / 0.686
2hrb NAPCarbonyl reductase [NADPH] 3 1.1.1.184 0.684
4hp8 NAP2-deoxy-D-gluconate 3-dehydrogenase / 0.684
2dte NAIGlucose 1-dehydrogenase related protein / 0.683
1iy8 NADLevodione reductase / 0.682
3a28 NADL-2,3-butanediol dehydrogenase 1.1.1.76 0.682
1rpn NDPGDP-mannose 4,6-dehydratase / 0.681
3aut NAIGlucose 1-dehydrogenase 4 1.1.1.47 0.680
4is3 NAD3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 1.17.98.1 0.680
1u7t NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.679
2ztm NADD(-)-3-hydroxybutyrate dehydrogenase / 0.679
5jsf NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.679
1rwb NADGlucose 1-dehydrogenase 1.1.1.47 0.678
5jyd NADShort chain dehydrogenase / 0.678
4dbz NDPPutative ketoacyl reductase 1.3.1 0.677
4dc0 NDPPutative ketoacyl reductase 1.3.1 0.677
4o0l NDPNADPH-dependent 3-quinuclidinone reductase / 0.677
3sx2 NADUncharacterized protein / 0.676
1e6w NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.675
2bgm NAJSecoisolariciresinol dehydrogenase 1.1.1.331 0.674
2zat NAPDehydrogenase/reductase SDR family member 4 1.1.1.184 0.673
1nff NAD3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase 1.1.1.53 0.672
2z95 NDPGDP-mannose 4,6-dehydratase / 0.672
1bdb NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase / 0.671
3r3s NADPutative oxidoreductase / 0.670
4tqg NDPPutative dTDP-d-glucose 4 6-dehydratase / 0.670
1gco NADGlucose 1-dehydrogenase 1.1.1.47 0.669
2yy7 NADL-threonine dehydrogenase / 0.669
3oa2 NADUDP-N-acetyl-2-amino-2-deoxy-D-glucuronate oxidase / 0.669
1h5q NAPNADP-dependent mannitol dehydrogenase 1.1.1.138 0.668
2ekp NAD2-deoxy-D-gluconate 3-dehydrogenase / 0.668
3tsc NADUncharacterized protein / 0.668
3wds NADNADH-dependent quinuclidinone reductase / 0.668
4b79 NADProbable short-chain dehydrogenase / 0.667
2z1m NDPGDP-mannose 4,6-dehydratase / 0.666
2wyv NADEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.663
3h4v NAPPteridine reductase 1 1.5.1.33 0.663
4e5y NDPGDP-L-fucose synthase 1.1.1.271 0.663
1t2a NDPGDP-mannose 4,6 dehydratase 4.2.1.47 0.662
4nbu NAI3-oxoacyl-(Acyl-carrier-protein) reductase / 0.662
3s55 NADPutative short-chain dehydrogenase/reductase / 0.661
4j7u NAPSepiapterin reductase 1.1.1.153 0.661
4yr9 NADL-threonine 3-dehydrogenase, mitochondrial 1.1.1.103 0.661
1g0n NDPTetrahydroxynaphthalene reductase 1.1.1.252 0.660
1x7g NAPPutative ketoacyl reductase 1.3.1 0.660
3a4v NADNDP-sugar epimerase / 0.660
4nbw NADShort-chain dehydrogenase/reductase SDR / 0.660
4rf2 NAPNADPH dependent R-specific alcohol dehydrogenase / 0.660
2yut NAPPutative short-chain oxidoreductase / 0.659
3of2 NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.659
4pvd NDPNADPH-dependent methylglyoxal reductase GRE2 / 0.659
1e3s NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.658
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.658
3rku NAPNADP-dependent 3-hydroxy acid dehydrogenase / 0.657
3uic NADEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.657
4b8z NAPGDP-L-fucose synthase 1.1.1.271 0.657
4bmv NAPShort-chain dehydrogenase / 0.657
4i1i NADMalate dehydrogenase / 0.657
4clo NAPPteridine reductase / 0.656
1gee NADGlucose 1-dehydrogenase 1.1.1.47 0.655
4c7k NAPCorticosteroid 11-beta-dehydrogenase isozyme 1 1.1.1.146 0.655
4cr8 NADN-acylmannosamine 1-dehydrogenase 1.1.1.233 0.655
2gdz NAD15-hydroxyprostaglandin dehydrogenase [NAD(+)] 1.1.1.141 0.654
1oaa NAPSepiapterin reductase 1.1.1.153 0.653
1u7t TDT3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.653
2o23 NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.653
3oey NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.653
2rbe NDPCorticosteroid 11-beta-dehydrogenase isozyme 1 1.1.1.146 0.652
3rj9 NADAlcohol dehydrogenase 1.1.1.1 0.652
4kwh NAPReductase homolog / 0.652
1ipe NDPTropinone reductase 2 1.1.1.236 0.651
1kc1 NDPdTDP-4-dehydrorhamnose reductase 1.1.1.133 0.651
1vl8 NAPOxidoreductase, short chain dehydrogenase/reductase family / 0.651
1ae1 NAPTropinone reductase 1 / 0.650
4b4o NDPEpimerase family protein SDR39U1 / 0.650