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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
2g82 NAD Glyceraldehyde-3-phosphate dehydrogenase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2g82 NADGlyceraldehyde-3-phosphate dehydrogenase / 1.099
1gd1 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.977
3hja NADGlyceraldehyde-3-phosphate dehydrogenase / 0.977
3lvf NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.964
3cmc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.962
1nqa NADGlyceraldehyde-3-phosphate dehydrogenase / 0.947
1hdg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.943
1npt NADGlyceraldehyde-3-phosphate dehydrogenase / 0.930
1nqo NADGlyceraldehyde-3-phosphate dehydrogenase / 0.928
1gad NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.920
4dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.917
4lsm NADGlyceraldehyde-3-phosphate dehydrogenase / 0.917
4k9d NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.916
4p8r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.914
4o59 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.905
2vyn NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.894
3v1y NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.894
3zdf NADGlyceraldehyde-3-phosphate dehydrogenase / 0.888
3cif NADGlyceraldehyde-3-phosphate dehydrogenase / 0.885
1u8f NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.884
3qv1 NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.881
1dss NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.878
4boy NADGlyceraldehyde-3-phosphate dehydrogenase / 0.876
1nq5 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.875
2vyv NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.875
2ep7 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.873
3b1j NADGlyceraldehyde-3-phosphate dehydrogenase / 0.872
3ksd NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.872
1rm3 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.869
1vsv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.862
3zcx NADGlyceraldehyde-3-phosphate dehydrogenase / 0.851
2dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.842
3doc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.837
1a7k NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.835
5c7o NADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific 1.2.1.12 0.821
3dmt NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.820
3l4s NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.818
1dc6 NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.814
1dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.813
1cer NADGlyceraldehyde-3-phosphate dehydrogenase / 0.812
1ywg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.807
1jn0 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.796
1nbo NADGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.794
3dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.790
4o63 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.790
1szj NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.780
3cps NADGlyceraldehyde-3-phosphate dehydrogenase / 0.769
3had NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.764
4z0h NADGlyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic 1.2.1.12 0.764
1rm4 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.759
3pym NADGlyceraldehyde-3-phosphate dehydrogenase 3 1.2.1.12 0.758
2d2i NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.754
1m75 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.751
2b4r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.751
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.748
1o6z NADMalate dehydrogenase / 0.747
3e5r NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.747
1m76 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.745
1qxs NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.745
1znq NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.745
1j0x NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.744
3k2b NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.743
1nvm NADAcetaldehyde dehydrogenase 1.2.1.10 0.742
1gyp NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.741
3f3s NADLambda-crystallin homolog / 0.741
1vc2 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.735
1f0y NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.732
1rm5 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.732
3adp NAILambda-crystallin 1.1.1.45 0.727
4yac NAIC alpha-dehydrogenase / 0.725
2pkr NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.714
2hdh NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.711
3ikt NADRedox-sensing transcriptional repressor Rex / 0.711
2g5c NADPrephenate dehydrogenase / 0.710
2q3e NAIUDP-glucose 6-dehydrogenase 1.1.1.22 0.709
3nt2 NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.709
4wji NAPPutative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase / 0.704
4k5r FADOxygenase / 0.703
4yag NAIC alpha-dehydrogenase / 0.703
1hyh NADL-2-hydroxyisocaproate dehydrogenase / 0.700
1il0 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.698
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.697
3cin NADMyo-inositol-1-phosphate synthase-related protein / 0.695
1cf2 NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.694
2vhw NAIAlanine dehydrogenase 1.4.1.1 0.691
1p1h NADInositol-3-phosphate synthase 5.5.1.4 0.690
3q2k NAIProbable oxidoreductase / 0.688
2f1k NAPPrephenate dehydrogenase / 0.687
1gae NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.686
3k7m FAD6-hydroxy-L-nicotine oxidase / 0.685
3ou2 SAHSAM-dependent methyltransferase / 0.685
2vhz NAIAlanine dehydrogenase 1.4.1.1 0.684
4a99 FADTetX family tetracycline inactivation enzyme / 0.684
2wsb NADGalactitol dehydrogenase / 0.682
3pef NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.681
3keq NADRedox-sensing transcriptional repressor Rex / 0.680
2x0i NAIMalate dehydrogenase / 0.678
1ihx SNDGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.677
2npx NADNADH peroxidase 1.11.1.1 0.676
1ml3 NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.675
3wv7 ADPHmd co-occurring protein HcgE / 0.675
1h83 FADPolyamine oxidase 1.5.3.14 0.674
2ixb NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.674
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.673
1psd NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.673
1geg NADDiacetyl reductase [(S)-acetoin forming] 1.1.1.304 0.672
3q3c NADNAD-dependent L-serine dehydrogenase / 0.672
4gus FADLysine-specific histone demethylase 1B 1 0.672
4yai NAIC alpha-dehydrogenase / 0.672
1hsz NADAlcohol dehydrogenase 1B 1.1.1.1 0.671
5bsg NAPPyrroline-5-carboxylate reductase / 0.671
1agn NADAlcohol dehydrogenase class 4 mu/sigma chain 1.1.1.1 0.670
2i9p NAD3-hydroxyisobutyrate dehydrogenase, mitochondrial 1.1.1.31 0.670
3oa2 NADUDP-N-acetyl-2-amino-2-deoxy-D-glucuronate oxidase / 0.669
3s55 NADPutative short-chain dehydrogenase/reductase / 0.669
1e3w NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.668
2eq7 NADDihydrolipoyl dehydrogenase / 0.668
2o4c NADErythronate-4-phosphate dehydrogenase / 0.668
2o23 NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.667
3hdh NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.667
4plp NADHomospermidine synthase 2.5.1.44 0.667
1hku NADC-terminal-binding protein 1 1.1.1 0.666
3a4v NADNDP-sugar epimerase / 0.666
3d4p NADL-lactate dehydrogenase 1 1.1.1.27 0.666
5js6 NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.666
1bw9 NADPhenylalanine dehydrogenase / 0.665
4pzd NAD3-Hydroxyacyl-CoA dehydrogenase / 0.665
1gl3 NDPAspartate-semialdehyde dehydrogenase / 0.664
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.664
5ein NAP[LysW]-L-2-aminoadipate 6-phosphate reductase / 0.664
2cvz NDP3-hydroxyisobutyrate dehydrogenase / 0.663
1c1d NAIPhenylalanine dehydrogenase / 0.662
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.662
2vhx NADAlanine dehydrogenase 1.4.1.1 0.660
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.660
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.660
1mo9 FAD2-oxopropyl-CoM reductase, carboxylating 1.8.1.5 0.659
4dpl NAPMalonyl-CoA reductase 1.2.1.75 0.659
1f17 NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.658
1fec FADTrypanothione reductase 1.8.1.12 0.658
2x0r NADMalate dehydrogenase / 0.658
3b20 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.657
3grv ADNProbable ribosomal RNA small subunit methyltransferase A / 0.657
3kve FADL-amino-acid oxidase / 0.657
3ntq NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.657
2qg4 NADUDP-glucose 6-dehydrogenase 1.1.1.22 0.656
3l0d NADGlyceraldehyde-3-phosphate dehydrogenase / 0.656
4e5p NADPhosphonate dehydrogenase 1.20.1.1 0.656
3rua NADUDP-N-acetylglucosamine 4-epimerase / 0.655
4tlx FDAKtzI / 0.655
3cbg SAHO-methyltransferase / 0.654
3cos NADAlcohol dehydrogenase 4 1.1.1.1 0.654
3nlc FADUncharacterized protein / 0.654
4j33 FADKynurenine 3-monooxygenase / 0.654
1h7w FADDihydropyrimidine dehydrogenase [NADP(+)] 1.3.1.2 0.653
3duw SAHO-methyltransferase, putative / 0.653
3ec7 NADInositol 2-dehydrogenase / 0.653
3ntr NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.653
3w6u NAP6-phosphogluconate dehydrogenase, NAD-binding protein / 0.653
4rdi ATPtRNA threonylcarbamoyladenosine dehydratase 6.1 0.653
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.652
4fk1 FADPutative thioredoxin reductase / 0.652
4gdp FADPolyamine oxidase FMS1 / 0.652
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.652
4tlz FADKtzI / 0.652
4tm0 FADKtzI / 0.652
5kjf NAJAlcohol dehydrogenase E chain 1.1.1.1 0.652
5lc1 NADL-threonine 3-dehydrogenase / 0.652
1g1a NADdTDP-glucose 4,6-dehydratase / 0.651
1la2 NADInositol-3-phosphate synthase 5.5.1.4 0.651
2g76 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.651
2gdz NAD15-hydroxyprostaglandin dehydrogenase [NAD(+)] 1.1.1.141 0.651
3nt4 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.651
3ruc NADUDP-N-acetylglucosamine 4-epimerase / 0.651
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.650
3gnq NADGlyceraldehyde-3-phosphate dehydrogenase / 0.650
3gvi ADPMalate dehydrogenase / 0.650
4k28 NADShikimate dehydrogenase family protein / 0.650