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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
3k2b 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
3k2b NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.913
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.836
1u8f NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.821
4o59 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.821
4lsm NADGlyceraldehyde-3-phosphate dehydrogenase / 0.808
4p8r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.806
1npt NADGlyceraldehyde-3-phosphate dehydrogenase / 0.805
1vsv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.804
1gd1 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.800
4k9d NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.800
1dss NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.799
1nbo NADGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.799
4dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.797
1nq5 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.791
1gad NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.790
1dc6 NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.784
1hdg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.784
3qv1 NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.784
1nqo NADGlyceraldehyde-3-phosphate dehydrogenase / 0.783
4boy NADGlyceraldehyde-3-phosphate dehydrogenase / 0.783
3zcx NADGlyceraldehyde-3-phosphate dehydrogenase / 0.780
3cif NADGlyceraldehyde-3-phosphate dehydrogenase / 0.773
2ep7 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.772
3cmc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.772
3cps NADGlyceraldehyde-3-phosphate dehydrogenase / 0.772
3b1j NADGlyceraldehyde-3-phosphate dehydrogenase / 0.769
4z0h NADGlyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic 1.2.1.12 0.769
2vyv NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.768
3pym NADGlyceraldehyde-3-phosphate dehydrogenase 3 1.2.1.12 0.767
2d2i NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.766
1rm3 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.765
3doc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.765
5c7o NADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific 1.2.1.12 0.765
3hja NADGlyceraldehyde-3-phosphate dehydrogenase / 0.762
3dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.756
1nqa NADGlyceraldehyde-3-phosphate dehydrogenase / 0.753
3dmt NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.753
1a7k NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.752
1cer NADGlyceraldehyde-3-phosphate dehydrogenase / 0.752
1vc2 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.750
1szj NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.748
3lvf NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.748
1gyp NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.746
2g82 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.743
4o63 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.743
1rm4 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.742
3zdf NADGlyceraldehyde-3-phosphate dehydrogenase / 0.729
3ksd NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.727
2dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.726
1znq NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.724
3l4s NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.724
2vyn NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.716
3e5r NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.716
3v1y NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.715
1ywg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.712
1qxs NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.711
1jn0 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.706
1m75 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.700
1j0x NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.698
3qvs NADMyo-inositol-1-phosphate synthase (Ino1) / 0.696
1ml3 NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.688
3ikt NADRedox-sensing transcriptional repressor Rex / 0.685
1f0y NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.684
1gl3 NDPAspartate-semialdehyde dehydrogenase / 0.684
3qvw NADMyo-inositol-1-phosphate synthase (Ino1) / 0.683
3qvx NADMyo-inositol-1-phosphate synthase (Ino1) / 0.680
1hyh NADL-2-hydroxyisocaproate dehydrogenase / 0.679
1sc6 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.676
3f3s NADLambda-crystallin homolog / 0.676
3keo NADRedox-sensing transcriptional repressor Rex / 0.674
2pkr NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.670
3ec7 NADInositol 2-dehydrogenase / 0.668
2g5c NADPrephenate dehydrogenase / 0.666
4om8 NAD3-hydroxybutyryl-coA dehydrogenase / 0.665
1il0 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.664
1rm5 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.664
3qvt NAIMyo-inositol-1-phosphate synthase (Ino1) / 0.664
4ywj NAD4-hydroxy-tetrahydrodipicolinate reductase / 0.663
1nvm NADAcetaldehyde dehydrogenase 1.2.1.10 0.662
3adp NAILambda-crystallin 1.1.1.45 0.661
3nt2 NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.660
1f17 NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.658
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.658
1h2b NAJNAD-dependent alcohol dehydrogenase / 0.656
1ihx SNDGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.655
4e5p NADPhosphonate dehydrogenase 1.20.1.1 0.655
2pv7 NADT-protein 1.3.1.12 0.654
3ggp NADPrephenate dehydrogenase / 0.654
1gae NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.652
2a92 NAIL-lactate dehydrogenase / 0.650
3ntq NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.650
3uko NADAlcohol dehydrogenase class-3 / 0.650