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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
3qv1 NAD Glyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3qv1 NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 1.143
3b1j NADGlyceraldehyde-3-phosphate dehydrogenase / 0.950
3zdf NADGlyceraldehyde-3-phosphate dehydrogenase / 0.946
1gd1 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.910
1hdg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.895
3lvf NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.885
1gad NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.881
2g82 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.881
1dss NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.879
5c7o NADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific 1.2.1.12 0.878
4boy NADGlyceraldehyde-3-phosphate dehydrogenase / 0.875
3zcx NADGlyceraldehyde-3-phosphate dehydrogenase / 0.870
3cmc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.868
4dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.863
4lsm NADGlyceraldehyde-3-phosphate dehydrogenase / 0.861
1u8f NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.851
2ep7 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.851
3ksd NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.846
4p8r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.841
2vyn NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.840
2vyv NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.838
1rm3 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.837
3l4s NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.833
4o59 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.830
3cps NADGlyceraldehyde-3-phosphate dehydrogenase / 0.821
3v1y NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.821
1cer NADGlyceraldehyde-3-phosphate dehydrogenase / 0.820
3hja NADGlyceraldehyde-3-phosphate dehydrogenase / 0.819
1nbo NADGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.818
1a7k NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.817
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.809
1nq5 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.808
3cif NADGlyceraldehyde-3-phosphate dehydrogenase / 0.808
1npt NADGlyceraldehyde-3-phosphate dehydrogenase / 0.807
1nqo NADGlyceraldehyde-3-phosphate dehydrogenase / 0.804
1ywg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.799
3dmt NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.792
4k9d NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.792
1szj NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.790
1nqa NADGlyceraldehyde-3-phosphate dehydrogenase / 0.788
2d2i NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.787
3dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.787
3pym NADGlyceraldehyde-3-phosphate dehydrogenase 3 1.2.1.12 0.786
3k2b NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.784
1jn0 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.782
1vsv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.780
1dc6 NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.779
3doc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.779
1gyp NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.774
4o63 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.774
2dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.771
4z0h NADGlyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic 1.2.1.12 0.769
1dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.764
2b4r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.759
1nvm NADAcetaldehyde dehydrogenase 1.2.1.10 0.758
1rm4 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.756
3b20 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.746
1qxs NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.744
1vc2 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.744
1rm5 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.713
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.712
1ml3 NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.706
2ixb NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.706
1j0x NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.703
1il0 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.702
1m76 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.701
3e5r NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.701
2pv7 NADT-protein 1.3.1.12 0.700
3ikt NADRedox-sensing transcriptional repressor Rex / 0.698
3keo NADRedox-sensing transcriptional repressor Rex / 0.696
3adp NAILambda-crystallin 1.1.1.45 0.695
3ggp NADPrephenate dehydrogenase / 0.695
2pkr NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.694
1p1h NADInositol-3-phosphate synthase 5.5.1.4 0.692
3d4p NADL-lactate dehydrogenase 1 1.1.1.27 0.692
3ru9 NADUDP-N-acetylglucosamine 4-epimerase / 0.692
1h2b NAJNAD-dependent alcohol dehydrogenase / 0.689
1znq NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.688
3rua NADUDP-N-acetylglucosamine 4-epimerase / 0.687
4plp NADHomospermidine synthase 2.5.1.44 0.687
1sc6 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.683
4yai NAIC alpha-dehydrogenase / 0.682
1q0q NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase 1.1.1.267 0.680
1c1d NAIPhenylalanine dehydrogenase / 0.679
1f17 NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.679
3cin NADMyo-inositol-1-phosphate synthase-related protein / 0.678
3f3s NADLambda-crystallin homolog / 0.678
3n7u NADFormate dehydrogenase, chloroplastic/mitochondrial / 0.676
1hsz NADAlcohol dehydrogenase 1B 1.1.1.1 0.675
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.675
3hdh NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.675
3nt2 NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.674
3qvt NAIMyo-inositol-1-phosphate synthase (Ino1) / 0.674
4twr NADNAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase / 0.674
3ish FADThioredoxin reductase 1.8.1.9 0.673
4hb9 FADUncharacterized protein / 0.673
2fzw NADAlcohol dehydrogenase class-3 1.1.1.1 0.672
4dpl NAPMalonyl-CoA reductase 1.2.1.75 0.672
4xrg NADHomospermidine synthase 2.5.1.44 0.672
1h6d NDPGlucose--fructose oxidoreductase 1.1.99.28 0.670
1la2 NADInositol-3-phosphate synthase 5.5.1.4 0.670
2rgj FADFlavin-containing monooxygenase / 0.670
1cf2 NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.669
2g76 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.669
2vhx NADAlanine dehydrogenase 1.4.1.1 0.669
1o6z NADMalate dehydrogenase / 0.668
3hwr NDP2-dehydropantoate 2-reductase / 0.668
5bsg NAPPyrroline-5-carboxylate reductase / 0.667
1pl6 NADSorbitol dehydrogenase 1.1.1.14 0.666
2dkn NAI3-alpha-hydroxysteroid dehydrogenase / 0.666
4xqc NADHomospermidine synthase 2.5.1.44 0.666
3wv7 ADPHmd co-occurring protein HcgE / 0.665
2cvz NDP3-hydroxyisobutyrate dehydrogenase / 0.664
4j49 NADUncharacterized protein / 0.663
4wji NAPPutative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase / 0.661
2hun NAD336aa long hypothetical dTDP-glucose 4,6-dehydratase / 0.660
2vhz NAIAlanine dehydrogenase 1.4.1.1 0.660
1jnz FADAdenylylsulfate reductase, subunit A (AprA) / 0.659
4j49 NAIUncharacterized protein / 0.659
5lc1 NADL-threonine 3-dehydrogenase / 0.659
1axe NADAlcohol dehydrogenase E chain 1.1.1.1 0.658
2ekl NADD-3-phosphoglycerate dehydrogenase / 0.657
3x2f NAIAdenosylhomocysteinase / 0.657
2o06 MTASpermidine synthase 2.5.1.16 0.656
4y0k NAPAntE / 0.655
3a14 NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase / 0.654
5g3s FDAFlavin-dependent L-tryptophan oxidase VioA / 0.654
3had NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.652
3tri NAPPyrroline-5-carboxylate reductase / 0.652
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.651
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.651
3ing NDPHomoserine dehydrogenase related protein / 0.651
4cr8 NADN-acylmannosamine 1-dehydrogenase 1.1.1.233 0.651