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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
4k9d NAD Glyceraldehyde-3-phosphate dehydrogenase 1.2.1.12

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4k9d NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 1.062
4o59 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.986
1u8f NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.984
3cif NADGlyceraldehyde-3-phosphate dehydrogenase / 0.967
1vsv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.959
4p8r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.954
3v1y NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.951
5c7o NADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific 1.2.1.12 0.934
3hja NADGlyceraldehyde-3-phosphate dehydrogenase / 0.933
2vyv NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.917
2g82 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.916
3pym NADGlyceraldehyde-3-phosphate dehydrogenase 3 1.2.1.12 0.916
4lsm NADGlyceraldehyde-3-phosphate dehydrogenase / 0.915
1hdg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.914
3cps NADGlyceraldehyde-3-phosphate dehydrogenase / 0.898
1dss NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.887
4o63 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.887
3cmc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.886
4boy NADGlyceraldehyde-3-phosphate dehydrogenase / 0.885
3lvf NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.884
3zcx NADGlyceraldehyde-3-phosphate dehydrogenase / 0.882
1gad NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.880
2vyn NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.874
1nq5 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.873
1gd1 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.869
1nqa NADGlyceraldehyde-3-phosphate dehydrogenase / 0.869
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.867
2ep7 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.866
1nqo NADGlyceraldehyde-3-phosphate dehydrogenase / 0.865
1ywg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.858
3ksd NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.854
1npt NADGlyceraldehyde-3-phosphate dehydrogenase / 0.852
1rm3 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.848
1szj NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.846
2b4r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.843
1znq NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.842
4z0h NADGlyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic 1.2.1.12 0.830
4dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.829
3zdf NADGlyceraldehyde-3-phosphate dehydrogenase / 0.827
3dmt NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.822
3doc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.805
1nbo NADGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.804
3e5r NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.804
1dc6 NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.803
3l4s NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.801
3k2b NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.800
3b1j NADGlyceraldehyde-3-phosphate dehydrogenase / 0.793
3qv1 NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.792
1j0x NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.791
1cer NADGlyceraldehyde-3-phosphate dehydrogenase / 0.774
2d2i NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.771
3dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.771
2dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.765
1rm4 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.763
1gyp NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.761
3f3s NADLambda-crystallin homolog / 0.756
1a7k NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.753
1jn0 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.747
1m76 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.730
3ggp NADPrephenate dehydrogenase / 0.726
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.725
3tri NAPPyrroline-5-carboxylate reductase / 0.722
3keo NADRedox-sensing transcriptional repressor Rex / 0.721
2ixb NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.718
3cin NADMyo-inositol-1-phosphate synthase-related protein / 0.717
2g5c NADPrephenate dehydrogenase / 0.715
1rm5 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.713
3oet NADErythronate-4-phosphate dehydrogenase / 0.712
4wct FADFructosyl amine:oxygen oxidoreductase / 0.711
1cf2 NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.709
1vc2 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.709
1ihx SNDGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.706
1f0y NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.704
3b20 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.704
2i9p NAD3-hydroxyisobutyrate dehydrogenase, mitochondrial 1.1.1.31 0.703
1gae NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.701
4plp NADHomospermidine synthase 2.5.1.44 0.701
4wji NAPPutative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase / 0.700
1dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.698
2rcy NAPPyrroline-5-carboxylate reductase / 0.698
3l0d NADGlyceraldehyde-3-phosphate dehydrogenase / 0.697
1q0q NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase 1.1.1.267 0.695
1qxs NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.695
3ket NADRedox-sensing transcriptional repressor Rex / 0.694
4xq9 NADHomospermidine synthase 2.5.1.44 0.694
4om8 NAD3-hydroxybutyryl-coA dehydrogenase / 0.693
1guy NADMalate dehydrogenase / 0.688
2ome NADC-terminal-binding protein 2 / 0.686
3had NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.685
3keq NADRedox-sensing transcriptional repressor Rex / 0.685
1hku NADC-terminal-binding protein 1 1.1.1 0.682
5lc1 NADL-threonine 3-dehydrogenase / 0.681
1il0 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.680
1nvm NADAcetaldehyde dehydrogenase 1.2.1.10 0.680
2pkr NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.680
2yyy NAPGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.59 0.678
4kug NAD3-hydroxybutyryl-CoA dehydrogenase / 0.678
3hwr NDP2-dehydropantoate 2-reductase / 0.677
3ntr NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.677
3ntq NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.676
4xwz FADFructosyl amine:oxygen oxidoreductase / 0.676
1m75 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.673
2f1k NAPPrephenate dehydrogenase / 0.673
3gnq NADGlyceraldehyde-3-phosphate dehydrogenase / 0.673
1f17 NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.672
1i36 NAPConserved protein / 0.672
3ikt NADRedox-sensing transcriptional repressor Rex / 0.671
2ahr NAPPyrroline-5-carboxylate reductase / 0.669
4gae NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic 1.1.1.267 0.668
1o6z NADMalate dehydrogenase / 0.667
2hu2 NADC-terminal binding protein 1 / 0.666
4lcj NADC-terminal-binding protein 2 / 0.666
4pzd NAD3-Hydroxyacyl-CoA dehydrogenase / 0.666
1lso NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.665
3qvx NADMyo-inositol-1-phosphate synthase (Ino1) / 0.664
1ml3 NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.663
2hdh NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.663
2vhw NAIAlanine dehydrogenase 1.4.1.1 0.663
3wsw NADL-lactate dehydrogenase / 0.663
4xqc NADHomospermidine synthase 2.5.1.44 0.663
1gl3 NDPAspartate-semialdehyde dehydrogenase / 0.662
2pa3 NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.662
4fn4 NADShort chain dehydrogenase / 0.661
1h2b NAJNAD-dependent alcohol dehydrogenase / 0.660
2voj NADAlanine dehydrogenase 1.4.1.1 0.660
2vhx NADAlanine dehydrogenase 1.4.1.1 0.659
4j4b NAIUncharacterized protein / 0.659
4xrg NADHomospermidine synthase 2.5.1.44 0.659
2yy7 NADL-threonine dehydrogenase / 0.658
1la2 NADInositol-3-phosphate synthase 5.5.1.4 0.657
2cvz NDP3-hydroxyisobutyrate dehydrogenase / 0.657
3d64 NADAdenosylhomocysteinase / 0.656
3zw9 NADPeroxisomal bifunctional enzyme 1.1.1.35 0.656
4wec NADShort chain dehydrogenase / 0.656
4dpl NAPMalonyl-CoA reductase 1.2.1.75 0.655
3a4v NADNDP-sugar epimerase / 0.654
4xb1 NDP319aa long hypothetical homoserine dehydrogenase / 0.654
5ein NAP[LysW]-L-2-aminoadipate 6-phosphate reductase / 0.654
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.653
3qvt NAIMyo-inositol-1-phosphate synthase (Ino1) / 0.653
3wbb NAPMeso-diaminopimelate D-dehydrogenase / 0.653
1psd NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.652
1yjq NAP2-dehydropantoate 2-reductase 1.1.1.169 0.651
2fkn NADUrocanate hydratase 4.2.1.49 0.651
3nt4 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.651
2x0i NAIMalate dehydrogenase / 0.650
3cea NADMyo-inositol 2-dehydrogenase-like (Promiscuous) / 0.650