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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
2d2i NAP Glyceraldehyde-3-phosphate dehydrogenase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2d2i NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.998
1rm3 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.834
1hdg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.830
1u8f NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.808
1vc2 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.798
3zcx NADGlyceraldehyde-3-phosphate dehydrogenase / 0.795
5c7o NADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific 1.2.1.12 0.795
1jn0 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.793
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.793
1nq5 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.791
3qv1 NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.787
2ep7 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.781
1cer NADGlyceraldehyde-3-phosphate dehydrogenase / 0.780
4o59 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.778
1gd1 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.775
3zdf NADGlyceraldehyde-3-phosphate dehydrogenase / 0.775
3cps NADGlyceraldehyde-3-phosphate dehydrogenase / 0.771
4k9d NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.771
1rm4 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.770
1vsv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.770
3hja NADGlyceraldehyde-3-phosphate dehydrogenase / 0.770
3k2b NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.766
3lvf NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.765
2dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.764
3cmc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.764
1dss NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.761
4o63 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.758
1a7k NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.756
3dmt NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.756
3pym NADGlyceraldehyde-3-phosphate dehydrogenase 3 1.2.1.12 0.756
2vyv NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.755
2g82 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.754
3b1j NADGlyceraldehyde-3-phosphate dehydrogenase / 0.754
1nbo NADGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.753
1nqo NADGlyceraldehyde-3-phosphate dehydrogenase / 0.753
4z0h NADGlyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic 1.2.1.12 0.752
4p8r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.749
1dc6 NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.748
4lsm NADGlyceraldehyde-3-phosphate dehydrogenase / 0.745
2b4r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.742
4boy NADGlyceraldehyde-3-phosphate dehydrogenase / 0.742
4dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.742
3cif NADGlyceraldehyde-3-phosphate dehydrogenase / 0.737
3dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.734
1ywg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.733
3b20 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.733
1gyp NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.732
2pkr NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.727
1gad NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.725
1znq NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.725
3l4s NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.718
3v1y NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.718
1nqa NADGlyceraldehyde-3-phosphate dehydrogenase / 0.717
1j0x NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.716
1npt NADGlyceraldehyde-3-phosphate dehydrogenase / 0.715
1szj NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.715
3doc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.696
3ksd NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.695
3e5r NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.692
1m75 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.691
3adp NAILambda-crystallin 1.1.1.45 0.690
2vyn NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.687
1m76 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.685
3hwr NDP2-dehydropantoate 2-reductase / 0.685
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.683
1q0q NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase 1.1.1.267 0.678
3f3s NADLambda-crystallin homolog / 0.677
1f0y NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.675
5ein NAP[LysW]-L-2-aminoadipate 6-phosphate reductase / 0.675
3tri NAPPyrroline-5-carboxylate reductase / 0.674
1qxs NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.673
1ml3 NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.669
5bsg NAPPyrroline-5-carboxylate reductase / 0.669
1dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.665
1nvm NADAcetaldehyde dehydrogenase 1.2.1.10 0.665
2dbz NAPGlyoxylate reductase 1.1.1.26 0.665
1e3l NADAlcohol dehydrogenase 4 1.1.1.1 0.662
1guy NADMalate dehydrogenase / 0.661
1il0 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.661
3had NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.659
3ikt NADRedox-sensing transcriptional repressor Rex / 0.659
1gl3 NDPAspartate-semialdehyde dehydrogenase / 0.658
3pef NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.656
4k28 NADShikimate dehydrogenase family protein / 0.655
3t4e NADQuinate/shikimate dehydrogenase / 0.654
2rcy NAPPyrroline-5-carboxylate reductase / 0.652
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.651
4xgi NADGlutamate dehydrogenase / 0.651