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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
5c7o NAD Glyceraldehyde-3-phosphate dehydrogenase, testis-specific 1.2.1.12

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
5c7o NADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific 1.2.1.12 1.018
1vsv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.981
1u8f NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.973
4o59 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.953
4o63 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.940
4k9d NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.934
1dss NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.927
1hdg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.921
3zcx NADGlyceraldehyde-3-phosphate dehydrogenase / 0.918
3cif NADGlyceraldehyde-3-phosphate dehydrogenase / 0.917
3cmc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.905
3v1y NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.904
4boy NADGlyceraldehyde-3-phosphate dehydrogenase / 0.901
3pym NADGlyceraldehyde-3-phosphate dehydrogenase 3 1.2.1.12 0.900
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.893
1nq5 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.884
3hja NADGlyceraldehyde-3-phosphate dehydrogenase / 0.882
4dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.882
1ywg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.878
3qv1 NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.878
1gd1 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.874
1gad NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.872
3lvf NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.871
3zdf NADGlyceraldehyde-3-phosphate dehydrogenase / 0.868
1dc6 NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.863
3cps NADGlyceraldehyde-3-phosphate dehydrogenase / 0.863
4lsm NADGlyceraldehyde-3-phosphate dehydrogenase / 0.861
1rm3 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.858
3ksd NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.858
2b4r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.856
4p8r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.853
1szj NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.852
1a7k NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.835
1cer NADGlyceraldehyde-3-phosphate dehydrogenase / 0.835
1nqo NADGlyceraldehyde-3-phosphate dehydrogenase / 0.834
4z0h NADGlyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic 1.2.1.12 0.832
3b1j NADGlyceraldehyde-3-phosphate dehydrogenase / 0.830
3dmt NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.830
1npt NADGlyceraldehyde-3-phosphate dehydrogenase / 0.825
1nqa NADGlyceraldehyde-3-phosphate dehydrogenase / 0.825
2vyv NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.825
2ep7 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.824
2vyn NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.824
2g82 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.821
3l4s NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.810
1znq NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.808
1j0x NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.807
3dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.804
3doc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.799
2d2i NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.795
1jn0 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.794
1nbo NADGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.784
3f3s NADLambda-crystallin homolog / 0.779
2dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.770
3e5r NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.767
1rm4 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.765
3k2b NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.765
1dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.750
1gyp NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.749
2o4c NADErythronate-4-phosphate dehydrogenase / 0.749
1vc2 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.748
2g5c NADPrephenate dehydrogenase / 0.739
3had NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.732
1m76 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.731
3b20 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.731
3ggp NADPrephenate dehydrogenase / 0.729
1qxs NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.724
3cin NADMyo-inositol-1-phosphate synthase-related protein / 0.720
1m75 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.719
1f0y NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.714
2pkr NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.714
3oet NADErythronate-4-phosphate dehydrogenase / 0.713
3l0d NADGlyceraldehyde-3-phosphate dehydrogenase / 0.702
4wji NAPPutative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase / 0.701
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.699
1cf2 NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.698
1ml3 NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.698
3keo NADRedox-sensing transcriptional repressor Rex / 0.697
4om8 NAD3-hydroxybutyryl-coA dehydrogenase / 0.697
1q0q NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase 1.1.1.267 0.696
4xq9 NADHomospermidine synthase 2.5.1.44 0.696
3qvs NADMyo-inositol-1-phosphate synthase (Ino1) / 0.692
4xrg NADHomospermidine synthase 2.5.1.44 0.692
3adp NAILambda-crystallin 1.1.1.45 0.690
1nvm NADAcetaldehyde dehydrogenase 1.2.1.10 0.688
3pqf NADL-lactate dehydrogenase 1.1.1.27 0.686
3qvt NAIMyo-inositol-1-phosphate synthase (Ino1) / 0.684
3wv8 ATPHmd co-occurring protein HcgE / 0.684
4gae NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic 1.1.1.267 0.683
1uxk NADMalate dehydrogenase / 0.682
2i9p NAD3-hydroxyisobutyrate dehydrogenase, mitochondrial 1.1.1.31 0.682
3nt4 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.680
4j43 NADUncharacterized protein / 0.680
2ixb NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.679
4xgi NADGlutamate dehydrogenase / 0.679
2f1k NAPPrephenate dehydrogenase / 0.678
3anm NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase 1.1.1.267 0.677
1ihx SNDGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.676
3oa2 NADUDP-N-acetyl-2-amino-2-deoxy-D-glucuronate oxidase / 0.676
1f17 NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.675
1guy NADMalate dehydrogenase / 0.675
5eio NAP[LysW]-L-2-aminoadipate 6-phosphate reductase / 0.675
1agn NADAlcohol dehydrogenase class 4 mu/sigma chain 1.1.1.1 0.674
3ikt NADRedox-sensing transcriptional repressor Rex / 0.674
1yjq NAP2-dehydropantoate 2-reductase 1.1.1.169 0.673
3nt2 NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.673
1gae NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.672
2hu2 NADC-terminal binding protein 1 / 0.672
2vhx NADAlanine dehydrogenase 1.4.1.1 0.671
3t4e NADQuinate/shikimate dehydrogenase / 0.671
3tri NAPPyrroline-5-carboxylate reductase / 0.671
3wsw NADL-lactate dehydrogenase / 0.671
2rcy NAPPyrroline-5-carboxylate reductase / 0.669
3hwr NDP2-dehydropantoate 2-reductase / 0.669
4j4b NAIUncharacterized protein / 0.669
3ket NADRedox-sensing transcriptional repressor Rex / 0.667
2pa3 NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.665
3wv7 ADPHmd co-occurring protein HcgE / 0.665
4dlb NADS-(hydroxymethyl)glutathione dehydrogenase / 0.664
1gl3 NDPAspartate-semialdehyde dehydrogenase / 0.662
2yyy NAPGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.59 0.662
4j49 NAIUncharacterized protein / 0.662
1dxy NADD-2-hydroxyisocaproate dehydrogenase 1.1.1 0.661
1h2b NAJNAD-dependent alcohol dehydrogenase / 0.661
1i36 NAPConserved protein / 0.661
4j49 NADUncharacterized protein / 0.661
1e3l NADAlcohol dehydrogenase 4 1.1.1.1 0.659
3qvw NADMyo-inositol-1-phosphate synthase (Ino1) / 0.659
3uko NADAlcohol dehydrogenase class-3 / 0.659
4jk3 NADUncharacterized protein / 0.659
2vhz NAIAlanine dehydrogenase 1.4.1.1 0.658
4k28 NADShikimate dehydrogenase family protein / 0.658
4nfh NAJAlcohol dehydrogenase E chain 1.1.1.1 0.658
1hku NADC-terminal-binding protein 1 1.1.1 0.657
2vhw NAIAlanine dehydrogenase 1.4.1.1 0.657
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.657
1pjc NADAlanine dehydrogenase / 0.656
1uxj NADMalate dehydrogenase / 0.656
1sow NADL-lactate dehydrogenase 1.1.1.27 0.655
2q3e NAIUDP-glucose 6-dehydrogenase 1.1.1.22 0.655
3o9z NADLipopolysaccaride biosynthesis protein wbpB / 0.655
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.654
2hdh NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.654
3gnq NADGlyceraldehyde-3-phosphate dehydrogenase / 0.654
3qw2 NADMyo-inositol-1-phosphate synthase (Ino1) / 0.654
4xb1 NDP319aa long hypothetical homoserine dehydrogenase / 0.654
1f8f NADBenzyl alcohol dehydrogenase / 0.653
1vi2 NADQuinate/shikimate dehydrogenase / 0.653
2nad NADFormate dehydrogenase / 0.653
1mp0 NADAlcohol dehydrogenase class-3 1.1.1.1 0.652
2gsd NADFormate dehydrogenase / 0.652
3pef NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.652
4gl4 NAIAlcohol dehydrogenase class-3 / 0.652
5kje NAJAlcohol dehydrogenase E chain 1.1.1.1 0.652
1e3e NAIAlcohol dehydrogenase 4 1.1.1.1 0.651
1rm5 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.651
4nd4 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.650