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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
4m55 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
4m55 NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 1.207
4lk3 NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.921
4gll NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.916
2q1w NADPutative nucleotide sugar epimerase/ dehydratase / 0.877
2b69 NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.876
3ko8 NADNAD-dependent epimerase/dehydratase / 0.860
3icp NADNAD-dependent epimerase/dehydratase / 0.834
2p5y NADUDP-glucose 4-epimerase / 0.833
2q1t NADPutative nucleotide sugar epimerase/ dehydratase / 0.828
3lu1 NADUDP-N-acetylglucosamine 4-epimerase / 0.825
3rud NADUDP-N-acetylglucosamine 4-epimerase / 0.815
2q1s NAIPutative nucleotide sugar epimerase/ dehydratase / 0.814
3ruf NADUDP-N-acetylglucosamine 4-epimerase / 0.814
2q1u NADPutative nucleotide sugar epimerase/ dehydratase / 0.809
3aw9 NADNAD-dependent epimerase/dehydratase / 0.795
2pzj NADPutative nucleotide sugar epimerase/ dehydratase / 0.792
4idg NADPutative UDP-glucose 4-epimerase / 0.792
1i2b NADUDP-sulfoquinovose synthase, chloroplastic 3.13.1.1 0.790
3ru9 NADUDP-N-acetylglucosamine 4-epimerase / 0.789
4id9 NADPutative UDP-glucose 4-epimerase / 0.789
2gn8 NAPUDP-N-acetylglucosamine 4,6-dehydratase (inverting) 4.2.1.115 0.788
3rua NADUDP-N-acetylglucosamine 4-epimerase / 0.785
3ruc NADUDP-N-acetylglucosamine 4-epimerase / 0.785
3ru7 NADUDP-N-acetylglucosamine 4-epimerase / 0.782
1i3l NADUDP-glucose 4-epimerase / 0.764
3ruh NADUDP-N-acetylglucosamine 4-epimerase / 0.753
4twr NADNAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase / 0.751
3sxp NADADP-L-glycero-D-mannoheptose-6-epimerase / 0.746
2hun NAD336aa long hypothetical dTDP-glucose 4,6-dehydratase / 0.743
1zem NADXylitol dehydrogenase / 0.735
3wmx NADNAD dependent epimerase/dehydratase / 0.735
1g1a NADdTDP-glucose 4,6-dehydratase / 0.733
4lis NADUDP-glucose 4-epimerase (Eurofung) / 0.727
1orr NADCDP-paratose 2-epimerase / 0.726
2c59 NADGDP-mannose 3,5-epimerase 5.1.3.18 0.725
1nai NADUDP-glucose 4-epimerase 5.1.3.2 0.724
3ehe NADUDP-glucose 4-epimerase (GalE-1) / 0.721
2bgm NAJSecoisolariciresinol dehydrogenase 1.1.1.331 0.720
2p5u NADUDP-glucose 4-epimerase / 0.714
2z95 NDPGDP-mannose 4,6-dehydratase / 0.713
1n7h NDPGDP-mannose 4,6 dehydratase 2 4.2.1.47 0.712
1bxk NADdTDP-glucose 4,6-dehydratase 2 / 0.707
3sx2 NADUncharacterized protein / 0.707
2z1m NDPGDP-mannose 4,6-dehydratase / 0.705
3s55 NADPutative short-chain dehydrogenase/reductase / 0.703
1ek5 NADUDP-glucose 4-epimerase / 0.700
2hmv ADPKtr system potassium uptake protein A / 0.700
4ej0 NAPADP-L-glycero-D-manno-heptose-6-epimerase / 0.700
1n7g NDPGDP-mannose 4,6 dehydratase 2 4.2.1.47 0.699
1t2a NDPGDP-mannose 4,6 dehydratase 4.2.1.47 0.698
2d1y NADOxidoreductase, short-chain dehydrogenase/reductase family / 0.696
1nah NADUDP-glucose 4-epimerase 5.1.3.2 0.695
3rfx NADUronate dehydrogenase / 0.695
5jy1 NADPutative short-chain dehydrogenase/reductase / 0.695
2gdz NAD15-hydroxyprostaglandin dehydrogenase [NAD(+)] 1.1.1.141 0.693
3a28 NADL-2,3-butanediol dehydrogenase 1.1.1.76 0.693
1rpn NDPGDP-mannose 4,6-dehydratase / 0.691
2o07 MTASpermidine synthase 2.5.1.16 0.688
2yut NAPPutative short-chain oxidoreductase / 0.688
2yy7 NADL-threonine dehydrogenase / 0.688
1eq2 NAPADP-L-glycero-D-manno-heptose-6-epimerase / 0.687
4u7w NDPMxaA / 0.687
2c20 NADUDP-glucose 4-epimerase / 0.686
5ig2 NADShort-chain dehydrogenase/reductase SDR / 0.683
1kvr NADUDP-glucose 4-epimerase 5.1.3.2 0.679
2ji7 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.679
2c31 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.678
3ndr NADPyridoxal 4-dehydrogenase 1.1.1.107 0.678
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.677
3nug NADPyridoxal 4-dehydrogenase 1.1.1.107 0.677
4tqg NDPPutative dTDP-d-glucose 4 6-dehydratase / 0.675
3qvs NADMyo-inositol-1-phosphate synthase (Ino1) / 0.674
4e5y NDPGDP-L-fucose synthase 1.1.1.271 0.674
1rkx NADCDP-D-glucose-4,6-dehydratase / 0.673
1e3w NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.672
3qvt NAIMyo-inositol-1-phosphate synthase (Ino1) / 0.672
3rue NADUDP-N-acetylglucosamine 4-epimerase / 0.672
3tsc NADUncharacterized protein / 0.672
4egb NADdTDP-glucose 4,6-dehydratase / 0.672
3a9w NADNDP-sugar epimerase / 0.669
1geg NADDiacetyl reductase [(S)-acetoin forming] 1.1.1.304 0.668
3aut NAIGlucose 1-dehydrogenase 4 1.1.1.47 0.668
3qvx NADMyo-inositol-1-phosphate synthase (Ino1) / 0.668
3tox NAPPutative oxidoreductase / 0.667
1dhr NADDihydropteridine reductase 1.5.1.34 0.666
1g0n NDPTetrahydroxynaphthalene reductase 1.1.1.252 0.666
1dir NADDihydropteridine reductase 1.5.1.34 0.663
1wy7 SAHUncharacterized protein / 0.663
4hxy NDPPlm1 / 0.663
1w73 NAP2,4-dienoyl-CoA reductase, mitochondrial 1.3.1.34 0.662
2ixb NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.662
1h5q NAPNADP-dependent mannitol dehydrogenase 1.1.1.138 0.661
2wdz NADGalactitol dehydrogenase / 0.661
4plp NADHomospermidine synthase 2.5.1.44 0.661
2ggs NDPdTDP-4-dehydrorhamnose reductase / 0.660
3a4v NADNDP-sugar epimerase / 0.660
3h4v NAPPteridine reductase 1 1.5.1.33 0.660
4xrg NADHomospermidine synthase 2.5.1.44 0.660
3ak4 NADNADH-dependent quinuclidinone reductase / 0.659
3sj7 NDP3-oxoacyl-(Acyl-carrier-protein) reductase, putative / 0.659
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.658
1g6k NADGlucose 1-dehydrogenase 1.1.1.47 0.657
2np6 NEAModification methylase TaqI 2.1.1.72 0.657
4b8z NAPGDP-L-fucose synthase 1.1.1.271 0.657
3oet NADErythronate-4-phosphate dehydrogenase / 0.656
5jla NADPutative short-chain dehydrogenase/reductase / 0.656
2o23 NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.655
2c4c FAD[F-actin]-methionine sulfoxide oxidase MICAL1 1.14.13 0.654
2hrb NAPCarbonyl reductase [NADPH] 3 1.1.1.184 0.653
3ajr NADNDP-sugar epimerase / 0.653
1pr9 NAPL-xylulose reductase 1.1.1.10 0.651
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.651
4nbu NAI3-oxoacyl-(Acyl-carrier-protein) reductase / 0.651
1la2 NADInositol-3-phosphate synthase 5.5.1.4 0.650
2ztm NADD(-)-3-hydroxybutyrate dehydrogenase / 0.650
4j7x NAPSepiapterin reductase 1.1.1.153 0.650