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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
3pym NAD Glyceraldehyde-3-phosphate dehydrogenase 3 1.2.1.12

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3pym NADGlyceraldehyde-3-phosphate dehydrogenase 3 1.2.1.12 0.972
4k9d NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.916
4o63 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.909
5c7o NADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific 1.2.1.12 0.900
1vsv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.897
3cif NADGlyceraldehyde-3-phosphate dehydrogenase / 0.885
3cps NADGlyceraldehyde-3-phosphate dehydrogenase / 0.882
1u8f NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.881
4o59 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.881
1hdg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.879
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.872
2vyv NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.867
1dc6 NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.859
4p8r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.858
1szj NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.855
2b4r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.855
3v1y NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.851
3hja NADGlyceraldehyde-3-phosphate dehydrogenase / 0.850
3zcx NADGlyceraldehyde-3-phosphate dehydrogenase / 0.848
4boy NADGlyceraldehyde-3-phosphate dehydrogenase / 0.847
1gad NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.841
4z0h NADGlyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic 1.2.1.12 0.833
1znq NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.829
4lsm NADGlyceraldehyde-3-phosphate dehydrogenase / 0.827
1cer NADGlyceraldehyde-3-phosphate dehydrogenase / 0.825
1nq5 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.821
3cmc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.820
1nqo NADGlyceraldehyde-3-phosphate dehydrogenase / 0.817
3lvf NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.817
1a7k NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.810
4dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.808
1gd1 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.798
1rm3 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.798
3zdf NADGlyceraldehyde-3-phosphate dehydrogenase / 0.794
3ksd NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.789
2vyn NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.788
3e5r NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.786
3qv1 NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.786
1nbo NADGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.781
1npt NADGlyceraldehyde-3-phosphate dehydrogenase / 0.781
1j0x NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.780
3b1j NADGlyceraldehyde-3-phosphate dehydrogenase / 0.775
1ywg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.771
3l4s NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.770
3k2b NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.767
1dss NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.765
3dmt NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.763
2g82 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.758
2d2i NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.756
3dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.754
1nqa NADGlyceraldehyde-3-phosphate dehydrogenase / 0.743
1vc2 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.742
2g5c NADPrephenate dehydrogenase / 0.740
3doc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.739
2dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.736
2ep7 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.735
1gyp NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.732
3had NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.731
1ihx SNDGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.726
1jn0 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.726
3b20 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.721
3cin NADMyo-inositol-1-phosphate synthase-related protein / 0.719
3ggp NADPrephenate dehydrogenase / 0.718
1qxs NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.717
3oet NADErythronate-4-phosphate dehydrogenase / 0.717
1rm4 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.715
1m75 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.705
4wji NAPPutative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase / 0.698
2i9p NAD3-hydroxyisobutyrate dehydrogenase, mitochondrial 1.1.1.31 0.697
3keo NADRedox-sensing transcriptional repressor Rex / 0.691
3ket NADRedox-sensing transcriptional repressor Rex / 0.689
1m76 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.688
5eio NAP[LysW]-L-2-aminoadipate 6-phosphate reductase / 0.687
3pqf NADL-lactate dehydrogenase 1.1.1.27 0.686
2vhx NADAlanine dehydrogenase 1.4.1.1 0.685
4dl9 NADS-(hydroxymethyl)glutathione dehydrogenase / 0.685
1uxk NADMalate dehydrogenase / 0.684
3f3s NADLambda-crystallin homolog / 0.684
1dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.682
3keq NADRedox-sensing transcriptional repressor Rex / 0.682
3l0d NADGlyceraldehyde-3-phosphate dehydrogenase / 0.682
1hku NADC-terminal-binding protein 1 1.1.1 0.681
2ome NADC-terminal-binding protein 2 / 0.681
4lcj NADC-terminal-binding protein 2 / 0.681
4okn NAIL-lactate dehydrogenase A chain 1.1.1.27 0.681
5lc1 NADL-threonine 3-dehydrogenase / 0.678
1f17 NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.677
1guy NADMalate dehydrogenase / 0.677
1q0q NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase 1.1.1.267 0.677
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.675
4j4b NAIUncharacterized protein / 0.675
1hyh NADL-2-hydroxyisocaproate dehydrogenase / 0.674
3nt4 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.674
3wsw NADL-lactate dehydrogenase / 0.674
1cf2 NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.673
1gae NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.673
3ec7 NADInositol 2-dehydrogenase / 0.673
4k28 NADShikimate dehydrogenase family protein / 0.673
3qvs NADMyo-inositol-1-phosphate synthase (Ino1) / 0.672
2yyy NAPGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.59 0.671
3d64 NADAdenosylhomocysteinase / 0.671
4plp NADHomospermidine synthase 2.5.1.44 0.671
2voj NADAlanine dehydrogenase 1.4.1.1 0.669
3gnq NADGlyceraldehyde-3-phosphate dehydrogenase / 0.669
4dlb NADS-(hydroxymethyl)glutathione dehydrogenase / 0.669
4xqc NADHomospermidine synthase 2.5.1.44 0.668
3adp NAILambda-crystallin 1.1.1.45 0.667
1sc6 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.665
2pkr NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.665
3pdu NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.665
4om8 NAD3-hydroxybutyryl-coA dehydrogenase / 0.665
3anm NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase 1.1.1.267 0.664
4j43 NADUncharacterized protein / 0.664
4jji NADAlcohol dehydrogenase class-3 / 0.664
4jk3 NADUncharacterized protein / 0.663
1il0 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.662
3nt2 NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.662
3uko NADAlcohol dehydrogenase class-3 / 0.662
4tvb NADHomospermidine synthase 2.5.1.44 0.662
4j49 NADUncharacterized protein / 0.661
1la2 NADInositol-3-phosphate synthase 5.5.1.4 0.660
4wct FADFructosyl amine:oxygen oxidoreductase / 0.660
1h2b NAJNAD-dependent alcohol dehydrogenase / 0.659
1o6z NADMalate dehydrogenase / 0.659
3hdh NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.659
3qvt NAIMyo-inositol-1-phosphate synthase (Ino1) / 0.658
3tri NAPPyrroline-5-carboxylate reductase / 0.657
2pv7 NADT-protein 1.3.1.12 0.656
2x0i NAIMalate dehydrogenase / 0.656
3cos NADAlcohol dehydrogenase 4 1.1.1.1 0.656
3qvx NADMyo-inositol-1-phosphate synthase (Ino1) / 0.656
1f0y NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.655
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.655
3ikt NADRedox-sensing transcriptional repressor Rex / 0.655
2ixb NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.654
5cdg NAJAlcohol dehydrogenase E chain 1.1.1.1 0.653
1nvm NADAcetaldehyde dehydrogenase 1.2.1.10 0.652
1dxy NADD-2-hydroxyisocaproate dehydrogenase 1.1.1 0.651
1i2b NADUDP-sulfoquinovose synthase, chloroplastic 3.13.1.1 0.651
3oc4 FADOxidoreductase, pyridine nucleotide-disulfide family / 0.651
3qw2 NADMyo-inositol-1-phosphate synthase (Ino1) / 0.650