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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
3dmt NAD Glyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3dmt NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 1.113
3cmc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.880
1gd1 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.873
4p8r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.861
1npt NADGlyceraldehyde-3-phosphate dehydrogenase / 0.853
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.842
3zcx NADGlyceraldehyde-3-phosphate dehydrogenase / 0.839
2vyn NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.838
4boy NADGlyceraldehyde-3-phosphate dehydrogenase / 0.838
1u8f NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.837
3cps NADGlyceraldehyde-3-phosphate dehydrogenase / 0.836
1vsv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.833
1hdg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.832
5c7o NADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific 1.2.1.12 0.830
1a7k NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.826
3cif NADGlyceraldehyde-3-phosphate dehydrogenase / 0.822
4k9d NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.822
2g82 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.820
4lsm NADGlyceraldehyde-3-phosphate dehydrogenase / 0.819
1rm3 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.818
1nqa NADGlyceraldehyde-3-phosphate dehydrogenase / 0.816
1nqo NADGlyceraldehyde-3-phosphate dehydrogenase / 0.816
2ep7 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.811
1dss NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.806
3zdf NADGlyceraldehyde-3-phosphate dehydrogenase / 0.801
1gad NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.800
1nq5 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.799
3b1j NADGlyceraldehyde-3-phosphate dehydrogenase / 0.798
3lvf NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.797
4dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.794
3ksd NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.793
3qv1 NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.792
3hja NADGlyceraldehyde-3-phosphate dehydrogenase / 0.785
3dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.780
2vyv NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.778
3v1y NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.778
1dc6 NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.777
4o63 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.776
2dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.766
3pym NADGlyceraldehyde-3-phosphate dehydrogenase 3 1.2.1.12 0.763
1cer NADGlyceraldehyde-3-phosphate dehydrogenase / 0.758
2d2i NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.756
4o59 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.754
3k2b NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.753
1jn0 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.751
3e5r NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.739
2b4r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.735
1nbo NADGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.734
3l4s NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.732
1vc2 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.730
1ywg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.730
1f0y NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.729
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.729
1gyp NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.728
3doc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.725
1m75 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.718
2ixb NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.715
1il0 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.714
1znq NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.712
1szj NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.710
4z0h NADGlyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic 1.2.1.12 0.710
3b20 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.709
1j0x NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.707
1nvm NADAcetaldehyde dehydrogenase 1.2.1.10 0.701
1m76 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.700
3l0d NADGlyceraldehyde-3-phosphate dehydrogenase / 0.698
3qw2 NADMyo-inositol-1-phosphate synthase (Ino1) / 0.697
1rm4 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.696
4om8 NAD3-hydroxybutyryl-coA dehydrogenase / 0.695
3qvt NAIMyo-inositol-1-phosphate synthase (Ino1) / 0.691
1dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.685
1i2b NADUDP-sulfoquinovose synthase, chloroplastic 3.13.1.1 0.682
1ml3 NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.680
1qxs NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.680
4k28 NADShikimate dehydrogenase family protein / 0.679
3tsc NADUncharacterized protein / 0.678
4wji NAPPutative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase / 0.677
3sx2 NADUncharacterized protein / 0.675
1gl3 NDPAspartate-semialdehyde dehydrogenase / 0.674
2yyy NAPGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.59 0.674
3n7u NADFormate dehydrogenase, chloroplastic/mitochondrial / 0.671
3oet NADErythronate-4-phosphate dehydrogenase / 0.671
4j43 NADUncharacterized protein / 0.671
2dvm NAD439aa long hypothetical malate oxidoreductase (NAD) [malic enzyme] / 0.670
2vhw NAIAlanine dehydrogenase 1.4.1.1 0.670
2vhx NADAlanine dehydrogenase 1.4.1.1 0.670
3f3s NADLambda-crystallin homolog / 0.669
4jk3 NADUncharacterized protein / 0.669
1cf2 NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.668
2pv7 NADT-protein 1.3.1.12 0.666
2nad NADFormate dehydrogenase / 0.665
3qvw NADMyo-inositol-1-phosphate synthase (Ino1) / 0.663
1f17 NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.662
1kvr NADUDP-glucose 4-epimerase 5.1.3.2 0.662
2f1k NAPPrephenate dehydrogenase / 0.662
3ggp NADPrephenate dehydrogenase / 0.662
4gae NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic 1.1.1.267 0.662
4j4b NAIUncharacterized protein / 0.662
3oa2 NADUDP-N-acetyl-2-amino-2-deoxy-D-glucuronate oxidase / 0.661
3pgx NADUncharacterized NAD-dependent oxidoreductase MAP_4146 / 0.661
1nah NADUDP-glucose 4-epimerase 5.1.3.2 0.658
3hwr NDP2-dehydropantoate 2-reductase / 0.656
5eio NAP[LysW]-L-2-aminoadipate 6-phosphate reductase / 0.655
1wy7 SAHUncharacterized protein / 0.654
4plp NADHomospermidine synthase 2.5.1.44 0.654
2q1s NAIPutative nucleotide sugar epimerase/ dehydratase / 0.653
2vhz NAIAlanine dehydrogenase 1.4.1.1 0.653
2g5c NADPrephenate dehydrogenase / 0.652
2g76 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.651
3d64 NADAdenosylhomocysteinase / 0.651