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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
3jyq NAD Quinate/shikimate dehydrogenase (NAD(+))

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3jyq NADQuinate/shikimate dehydrogenase (NAD(+)) / 1.000
3jyp NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.904
3jyo NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.866
3adp NAILambda-crystallin 1.1.1.45 0.729
3ec7 NADInositol 2-dehydrogenase / 0.724
4j49 NADUncharacterized protein / 0.700
4l4s NAIL-lactate dehydrogenase A chain 1.1.1.27 0.698
3m2t NADProbable dehydrogenase / 0.697
1bdb NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase / 0.694
1lld NADL-lactate dehydrogenase 2 1.1.1.27 0.694
1uxj NADMalate dehydrogenase / 0.693
4tvb NADHomospermidine synthase 2.5.1.44 0.691
2dfv NADL-threonine 3-dehydrogenase / 0.690
2g76 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.690
3pgx NADUncharacterized NAD-dependent oxidoreductase MAP_4146 / 0.687
4k28 NADShikimate dehydrogenase family protein / 0.687
4xrg NADHomospermidine synthase 2.5.1.44 0.687
2fkn NADUrocanate hydratase 4.2.1.49 0.686
2yy7 NADL-threonine dehydrogenase / 0.686
5g3t FDAFlavin-dependent L-tryptophan oxidase VioA / 0.686
2v7g NADUrocanate hydratase 4.2.1.49 0.685
3ruf NADUDP-N-acetylglucosamine 4-epimerase / 0.684
5g3s FDAFlavin-dependent L-tryptophan oxidase VioA / 0.684
4yai NAIC alpha-dehydrogenase / 0.683
2dt5 NADRedox-sensing transcriptional repressor Rex / 0.682
2hun NAD336aa long hypothetical dTDP-glucose 4,6-dehydratase / 0.682
4xqc NADHomospermidine synthase 2.5.1.44 0.682
3n7u NADFormate dehydrogenase, chloroplastic/mitochondrial / 0.681
4xq9 NADHomospermidine synthase 2.5.1.44 0.681
1p1h NADInositol-3-phosphate synthase 5.5.1.4 0.680
2qg4 NADUDP-glucose 6-dehydrogenase 1.1.1.22 0.680
4j4b NAIUncharacterized protein / 0.679
4ng5 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.679
2ldb NADL-lactate dehydrogenase 1.1.1.27 0.677
4e5n NADPhosphonate dehydrogenase 1.20.1.1 0.677
3ldf SAHUncharacterized protein / 0.676
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.676
1guy NADMalate dehydrogenase / 0.675
4plp NADHomospermidine synthase 2.5.1.44 0.675
3int FDAUDP-galactopyranose mutase 5.4.99.9 0.673
3lcc SAHThiocyanate methyltransferase 1 / 0.673
2p35 SAHTrans-aconitate 2-methyltransferase / 0.672
2q3e NAIUDP-glucose 6-dehydrogenase 1.1.1.22 0.672
1kol NADGlutathione-independent formaldehyde dehydrogenase / 0.671
4nfs NAJAlcohol dehydrogenase E chain 1.1.1.1 0.670
2i9k SAHModification methylase HhaI 2.1.1.37 0.669
1skm SAHModification methylase HhaI 2.1.1.37 0.668
3fpf MTAUncharacterized protein / 0.668
5ig2 NADShort-chain dehydrogenase/reductase SDR / 0.667
3ru9 NADUDP-N-acetylglucosamine 4-epimerase / 0.666
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.666
5lc1 NADL-threonine 3-dehydrogenase / 0.666
1u3v NADAlcohol dehydrogenase 1B 1.1.1.1 0.665
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.665
2vhz NAIAlanine dehydrogenase 1.4.1.1 0.665
3nt2 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.665
1c1d NAIPhenylalanine dehydrogenase / 0.664
1zem NADXylitol dehydrogenase / 0.664
3nt2 NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.664
3ruc NADUDP-N-acetylglucosamine 4-epimerase / 0.664
1h2h NADL-aspartate dehydrogenase 1.4.1.21 0.663
1ie3 NADMalate dehydrogenase / 0.663
1xcb NADRedox-sensing transcriptional repressor Rex / 0.663
2pa3 NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.663
3nt4 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.663
1pl6 NADSorbitol dehydrogenase 1.1.1.14 0.662
4j49 NAIUncharacterized protein / 0.662
1ht0 NADAlcohol dehydrogenase 1C 1.1.1.1 0.661
3aw9 NADNAD-dependent epimerase/dehydratase / 0.661
4xcx SAHSmall RNA 2'-O-methyltransferase / 0.661
2fzw NADAlcohol dehydrogenase class-3 1.1.1.1 0.660
1p1i NADInositol-3-phosphate synthase 5.5.1.4 0.659
1f0y NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.658
1o9b NAIQuinate/shikimate dehydrogenase / 0.658
2fze APRAlcohol dehydrogenase class-3 1.1.1.1 0.658
4jnk NAIL-lactate dehydrogenase A chain 1.1.1.27 0.658
2g5c NADPrephenate dehydrogenase / 0.657
3x2e NAIAdenosylhomocysteinase / 0.657
3keo NADRedox-sensing transcriptional repressor Rex / 0.656
4okn NAIL-lactate dehydrogenase A chain 1.1.1.27 0.656
5je4 SAHMethyl transferase / 0.656
1ib6 NADMalate dehydrogenase / 0.655
1rp0 AHZThiamine thiazole synthase, chloroplastic / 0.655
1y56 ATPUncharacterized protein / 0.655
2q1s NAIPutative nucleotide sugar epimerase/ dehydratase / 0.655
4e5p NADPhosphonate dehydrogenase 1.20.1.1 0.655
4lcj NADC-terminal-binding protein 2 / 0.654
1e3s NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.653
2xyr SFGReplicase polyprotein 1ab 2.1.1 0.653
2z6u SAHModification methylase HhaI 2.1.1.37 0.653
3sxp NADADP-L-glycero-D-mannoheptose-6-epimerase / 0.653
4u8l FDAUDP-galactopyranose mutase / 0.653
1npd NADQuinate/shikimate dehydrogenase / 0.652
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.652
9mht SAHModification methylase HhaI 2.1.1.37 0.652
2c7q SAHModification methylase HhaI 2.1.1.37 0.651
2eq7 NADDihydrolipoyl dehydrogenase / 0.651
2jhf NADAlcohol dehydrogenase E chain 1.1.1.1 0.651
4c04 SFGProtein arginine N-methyltransferase 6 / 0.651
4u8j FDAUDP-galactopyranose mutase / 0.651
7mht SAHModification methylase HhaI 2.1.1.37 0.651
1r37 NADNAD-dependent alcohol dehydrogenase 1.1.1.1 0.650
2q1t NADPutative nucleotide sugar epimerase/ dehydratase / 0.650
3mj4 FADUDP-galactopyranose mutase / 0.650
3oet NADErythronate-4-phosphate dehydrogenase / 0.650
3tsc NADUncharacterized protein / 0.650