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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
3doc NAD Glyceraldehyde-3-phosphate dehydrogenase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3doc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.903
1u8f NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.846
4lsm NADGlyceraldehyde-3-phosphate dehydrogenase / 0.843
4p8r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.843
1gad NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.838
2g82 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.837
3cmc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.837
3hja NADGlyceraldehyde-3-phosphate dehydrogenase / 0.836
3lvf NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.836
2vyv NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.831
1nq5 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.830
3cif NADGlyceraldehyde-3-phosphate dehydrogenase / 0.828
3v1y NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.826
1hdg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.820
1nqo NADGlyceraldehyde-3-phosphate dehydrogenase / 0.820
4o59 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.816
4boy NADGlyceraldehyde-3-phosphate dehydrogenase / 0.815
1vsv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.809
1dc6 NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.808
4k9d NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.805
1gd1 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.803
3cps NADGlyceraldehyde-3-phosphate dehydrogenase / 0.800
5c7o NADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific 1.2.1.12 0.799
3zcx NADGlyceraldehyde-3-phosphate dehydrogenase / 0.795
1nqa NADGlyceraldehyde-3-phosphate dehydrogenase / 0.794
1npt NADGlyceraldehyde-3-phosphate dehydrogenase / 0.793
1nbo NADGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.788
2ep7 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.786
4dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.785
2vyn NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.779
3qv1 NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.779
1ywg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.772
3dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.771
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.770
3k2b NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.765
1dss NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.764
3l4s NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.763
3b1j NADGlyceraldehyde-3-phosphate dehydrogenase / 0.760
3zdf NADGlyceraldehyde-3-phosphate dehydrogenase / 0.757
1rm3 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.750
3pym NADGlyceraldehyde-3-phosphate dehydrogenase 3 1.2.1.12 0.739
4z0h NADGlyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic 1.2.1.12 0.738
1szj NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.737
4o63 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.736
3ksd NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.730
1a7k NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.726
1znq NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.725
3dmt NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.725
1j0x NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.722
3e5r NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.716
1cer NADGlyceraldehyde-3-phosphate dehydrogenase / 0.712
2b4r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.705
2d2i NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.696
1qxs NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.695
2dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.695
1gae NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.690
1sc6 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.690
1rm4 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.688
1jn0 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.685
4plp NADHomospermidine synthase 2.5.1.44 0.683
1b3r NADAdenosylhomocysteinase 3.3.1.1 0.682
4xq9 NADHomospermidine synthase 2.5.1.44 0.681
1gyp NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.680
3ket NADRedox-sensing transcriptional repressor Rex / 0.679
3keo NADRedox-sensing transcriptional repressor Rex / 0.678
2o4c NADErythronate-4-phosphate dehydrogenase / 0.673
4tvb NADHomospermidine synthase 2.5.1.44 0.673
1o6z NADMalate dehydrogenase / 0.672
1vc2 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.672
3l0d NADGlyceraldehyde-3-phosphate dehydrogenase / 0.672
3f3s NADLambda-crystallin homolog / 0.671
1t2c NAIL-lactate dehydrogenase 1.1.1.27 0.670
2g5c NADPrephenate dehydrogenase / 0.670
1nvm NADAcetaldehyde dehydrogenase 1.2.1.10 0.669
2dt5 NADRedox-sensing transcriptional repressor Rex / 0.667
1dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.665
1lso NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.664
1c1d NAIPhenylalanine dehydrogenase / 0.663
3ggp NADPrephenate dehydrogenase / 0.663
1psd NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.662
2fn7 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.662
1f17 NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.660
3d64 NADAdenosylhomocysteinase / 0.660
4xqc NADHomospermidine synthase 2.5.1.44 0.659
1sow NADL-lactate dehydrogenase 1.1.1.27 0.658
1wwk NAD307aa long hypothetical phosphoglycerate dehydrogenase / 0.658
3tri NAPPyrroline-5-carboxylate reductase / 0.658
2vhv NAIAlanine dehydrogenase 1.4.1.1 0.657
1rm5 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.655
3cin NADMyo-inositol-1-phosphate synthase-related protein / 0.655
3nt4 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.655
4i1i NADMalate dehydrogenase / 0.655
3uko NADAlcohol dehydrogenase class-3 / 0.654
1ihx SNDGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.653
2vhx NADAlanine dehydrogenase 1.4.1.1 0.652
1hyh NADL-2-hydroxyisocaproate dehydrogenase / 0.651
3m2t NADProbable dehydrogenase / 0.651
4jji NADAlcohol dehydrogenase class-3 / 0.651
4yac NAIC alpha-dehydrogenase / 0.651
4j49 NAIUncharacterized protein / 0.650
4ywj NAD4-hydroxy-tetrahydrodipicolinate reductase / 0.650