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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
1nq5 NAD Glyceraldehyde-3-phosphate dehydrogenase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1nq5 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.985
1nqo NADGlyceraldehyde-3-phosphate dehydrogenase / 0.948
3hja NADGlyceraldehyde-3-phosphate dehydrogenase / 0.926
1npt NADGlyceraldehyde-3-phosphate dehydrogenase / 0.916
1nqa NADGlyceraldehyde-3-phosphate dehydrogenase / 0.915
1gd1 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.914
3cmc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.909
1hdg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.908
4p8r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.905
1u8f NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.900
5c7o NADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific 1.2.1.12 0.884
2vyv NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.883
4lsm NADGlyceraldehyde-3-phosphate dehydrogenase / 0.880
4o59 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.880
1vsv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.877
3cif NADGlyceraldehyde-3-phosphate dehydrogenase / 0.877
2g82 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.875
3lvf NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.873
4k9d NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.873
1gad NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.871
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.859
4dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.855
3cps NADGlyceraldehyde-3-phosphate dehydrogenase / 0.854
2ep7 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.851
3b1j NADGlyceraldehyde-3-phosphate dehydrogenase / 0.847
3zdf NADGlyceraldehyde-3-phosphate dehydrogenase / 0.840
3doc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.830
3l4s NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.828
3v1y NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.827
4boy NADGlyceraldehyde-3-phosphate dehydrogenase / 0.827
3pym NADGlyceraldehyde-3-phosphate dehydrogenase 3 1.2.1.12 0.821
3zcx NADGlyceraldehyde-3-phosphate dehydrogenase / 0.819
1rm3 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.818
1dc6 NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.815
1cer NADGlyceraldehyde-3-phosphate dehydrogenase / 0.814
2vyn NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.814
1gyp NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.810
1nbo NADGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.808
3qv1 NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.808
3ksd NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.801
3dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.800
3dmt NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.799
4z0h NADGlyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic 1.2.1.12 0.793
2b4r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.792
2d2i NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.791
3k2b NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.791
4o63 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.791
1szj NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.788
1ywg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.779
1dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.767
1dss NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.766
1jn0 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.759
1a7k NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.758
2dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.752
1rm4 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.747
1qxs NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.746
1znq NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.746
1j0x NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.740
1vc2 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.733
3e5r NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.731
1ml3 NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.725
3ggp NADPrephenate dehydrogenase / 0.723
1rm5 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.718
1nvm NADAcetaldehyde dehydrogenase 1.2.1.10 0.715
1gae NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.713
1m75 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.713
2o4c NADErythronate-4-phosphate dehydrogenase / 0.713
1m76 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.711
3b20 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.710
1f0y NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.708
2g5c NADPrephenate dehydrogenase / 0.699
2i9p NAD3-hydroxyisobutyrate dehydrogenase, mitochondrial 1.1.1.31 0.696
1guy NADMalate dehydrogenase / 0.695
4ywj NAD4-hydroxy-tetrahydrodipicolinate reductase / 0.695
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.694
4om8 NAD3-hydroxybutyryl-coA dehydrogenase / 0.693
1o6z NADMalate dehydrogenase / 0.689
2q3e NAIUDP-glucose 6-dehydrogenase 1.1.1.22 0.688
3keq NADRedox-sensing transcriptional repressor Rex / 0.688
3ec7 NADInositol 2-dehydrogenase / 0.686
1sc6 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.683
3cin NADMyo-inositol-1-phosphate synthase-related protein / 0.682
3qvs NADMyo-inositol-1-phosphate synthase (Ino1) / 0.682
4xr9 NADCalS8 / 0.681
1il0 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.680
1c1d NAIPhenylalanine dehydrogenase / 0.679
2pv7 NADT-protein 1.3.1.12 0.679
1gl3 NDPAspartate-semialdehyde dehydrogenase / 0.678
1h2b NAJNAD-dependent alcohol dehydrogenase / 0.676
3ggo NAIPrephenate dehydrogenase / 0.673
4k28 NADShikimate dehydrogenase family protein / 0.673
4xb1 NDP319aa long hypothetical homoserine dehydrogenase / 0.673
3uko NADAlcohol dehydrogenase class-3 / 0.672
3pef NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.671
3l0d NADGlyceraldehyde-3-phosphate dehydrogenase / 0.670
4wji NAPPutative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase / 0.670
2ekl NADD-3-phosphoglycerate dehydrogenase / 0.669
2pkr NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.669
2rcy NAPPyrroline-5-carboxylate reductase / 0.669
3w6u NAP6-phosphogluconate dehydrogenase, NAD-binding protein / 0.669
3keo NADRedox-sensing transcriptional repressor Rex / 0.668
3tri NAPPyrroline-5-carboxylate reductase / 0.668
4j43 NADUncharacterized protein / 0.668
1f8f NADBenzyl alcohol dehydrogenase / 0.667
5eio NAP[LysW]-L-2-aminoadipate 6-phosphate reductase / 0.667
2fze APRAlcohol dehydrogenase class-3 1.1.1.1 0.666
2vhw NAIAlanine dehydrogenase 1.4.1.1 0.665
3qvt NAIMyo-inositol-1-phosphate synthase (Ino1) / 0.665
3ikt NADRedox-sensing transcriptional repressor Rex / 0.663
3ntq NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.663
3ket NADRedox-sensing transcriptional repressor Rex / 0.662
5ein NAP[LysW]-L-2-aminoadipate 6-phosphate reductase / 0.659
2ixb NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.658
3adp NAILambda-crystallin 1.1.1.45 0.658
4xgi NADGlutamate dehydrogenase / 0.658
1f17 NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.656
4j4b NAIUncharacterized protein / 0.656
1rsg FADPolyamine oxidase FMS1 / 0.655
3q3c NADNAD-dependent L-serine dehydrogenase / 0.655
1ihx SNDGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.654
1psd NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.654
3d4p NADL-lactate dehydrogenase 1 1.1.1.27 0.654
1orr NADCDP-paratose 2-epimerase / 0.653
3gnq NADGlyceraldehyde-3-phosphate dehydrogenase / 0.653
4j49 NAIUncharacterized protein / 0.653
4lcj NADC-terminal-binding protein 2 / 0.653
1gv0 NADMalate dehydrogenase / 0.652
3had NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.651
1hsz NADAlcohol dehydrogenase 1B 1.1.1.1 0.650
3jyp NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.650
4gkv NADAlcohol dehydrogenase, propanol-preferring 1.1.1.1 0.650
4kug NAD3-hydroxybutyryl-CoA dehydrogenase / 0.650