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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
4p8r NAD Glyceraldehyde-3-phosphate dehydrogenase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4p8r NADGlyceraldehyde-3-phosphate dehydrogenase / 1.041
4lsm NADGlyceraldehyde-3-phosphate dehydrogenase / 0.982
3hja NADGlyceraldehyde-3-phosphate dehydrogenase / 0.964
1gd1 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.955
3cmc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.954
4k9d NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.954
1gad NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.948
2vyn NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.948
3cps NADGlyceraldehyde-3-phosphate dehydrogenase / 0.944
1hdg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.932
2vyv NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.929
1u8f NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.927
1vsv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.925
1nqo NADGlyceraldehyde-3-phosphate dehydrogenase / 0.917
2g82 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.914
3cif NADGlyceraldehyde-3-phosphate dehydrogenase / 0.911
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.911
1nqa NADGlyceraldehyde-3-phosphate dehydrogenase / 0.907
1nq5 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.905
4boy NADGlyceraldehyde-3-phosphate dehydrogenase / 0.900
3lvf NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.899
3ksd NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.895
3zcx NADGlyceraldehyde-3-phosphate dehydrogenase / 0.892
4o59 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.892
1nbo NADGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.884
3b1j NADGlyceraldehyde-3-phosphate dehydrogenase / 0.878
3v1y NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.875
1rm3 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.867
4dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.866
3dmt NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.861
1npt NADGlyceraldehyde-3-phosphate dehydrogenase / 0.858
3pym NADGlyceraldehyde-3-phosphate dehydrogenase 3 1.2.1.12 0.858
1dc6 NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.857
3zdf NADGlyceraldehyde-3-phosphate dehydrogenase / 0.856
5c7o NADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific 1.2.1.12 0.853
2ep7 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.846
3doc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.843
3qv1 NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.841
1dss NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.825
3l4s NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.824
1cer NADGlyceraldehyde-3-phosphate dehydrogenase / 0.821
2dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.820
2b4r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.817
3dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.808
3k2b NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.806
1a7k NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.803
1ywg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.798
4o63 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.777
1qxs NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.775
1znq NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.775
1szj NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.772
1gyp NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.765
3e5r NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.764
1dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.760
1rm4 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.760
4z0h NADGlyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic 1.2.1.12 0.756
3f3s NADLambda-crystallin homolog / 0.750
2d2i NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.749
1jn0 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.748
1m75 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.741
4om8 NAD3-hydroxybutyryl-coA dehydrogenase / 0.729
1ihx SNDGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.727
1j0x NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.724
3had NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.724
3tri NAPPyrroline-5-carboxylate reductase / 0.723
3ggp NADPrephenate dehydrogenase / 0.717
1nvm NADAcetaldehyde dehydrogenase 1.2.1.10 0.716
3l0d NADGlyceraldehyde-3-phosphate dehydrogenase / 0.715
3adp NAILambda-crystallin 1.1.1.45 0.714
2g5c NADPrephenate dehydrogenase / 0.712
1vc2 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.707
4xq9 NADHomospermidine synthase 2.5.1.44 0.707
1m76 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.703
1q0q NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase 1.1.1.267 0.703
2o4c NADErythronate-4-phosphate dehydrogenase / 0.700
1gl3 NDPAspartate-semialdehyde dehydrogenase / 0.698
4plp NADHomospermidine synthase 2.5.1.44 0.698
3q3c NADNAD-dependent L-serine dehydrogenase / 0.696
3qvs NADMyo-inositol-1-phosphate synthase (Ino1) / 0.695
1il0 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.694
4yac NAIC alpha-dehydrogenase / 0.694
1f0y NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.693
1gae NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.691
1h2b NAJNAD-dependent alcohol dehydrogenase / 0.691
2i9p NAD3-hydroxyisobutyrate dehydrogenase, mitochondrial 1.1.1.31 0.691
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.690
2q3e NAIUDP-glucose 6-dehydrogenase 1.1.1.22 0.686
1sc6 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.684
3pef NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.683
3cin NADMyo-inositol-1-phosphate synthase-related protein / 0.681
3qvt NAIMyo-inositol-1-phosphate synthase (Ino1) / 0.681
3keq NADRedox-sensing transcriptional repressor Rex / 0.679
1ml3 NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.678
1rm5 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.678
4wji NAPPutative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase / 0.678
3ikt NADRedox-sensing transcriptional repressor Rex / 0.676
2fkn NADUrocanate hydratase 4.2.1.49 0.674
1psd NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.672
2vhw NAIAlanine dehydrogenase 1.4.1.1 0.667
3w6u NAP6-phosphogluconate dehydrogenase, NAD-binding protein / 0.667
3wsw NADL-lactate dehydrogenase / 0.667
1hyh NADL-2-hydroxyisocaproate dehydrogenase / 0.666
1ryi FADGlycine oxidase 1.4.3.19 0.666
2ixb NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.666
2vhz NAIAlanine dehydrogenase 1.4.1.1 0.666
1f17 NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.665
1hsz NADAlcohol dehydrogenase 1B 1.1.1.1 0.665
5ein NAP[LysW]-L-2-aminoadipate 6-phosphate reductase / 0.665
2ome NADC-terminal-binding protein 2 / 0.664
1c1d NAIPhenylalanine dehydrogenase / 0.663
2e37 NADL-lactate dehydrogenase / 0.663
3d4p NADL-lactate dehydrogenase 1 1.1.1.27 0.663
3uko NADAlcohol dehydrogenase class-3 / 0.663
3ru9 NADUDP-N-acetylglucosamine 4-epimerase / 0.662
3cgd FADCoenzyme A disulfide reductase / 0.661
4pzd NAD3-Hydroxyacyl-CoA dehydrogenase / 0.661
1bw9 NADPhenylalanine dehydrogenase / 0.660
5eio NAP[LysW]-L-2-aminoadipate 6-phosphate reductase / 0.660
1o6z NADMalate dehydrogenase / 0.659
2cvz NDP3-hydroxyisobutyrate dehydrogenase / 0.659
2hdh NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.659
2yyy NAPGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.59 0.659
3g5q FADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO / 0.659
4tvb NADHomospermidine synthase 2.5.1.44 0.659
2f1k NAPPrephenate dehydrogenase / 0.658
2yy7 NADL-threonine dehydrogenase / 0.658
1lso NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.657
2hun NAD336aa long hypothetical dTDP-glucose 4,6-dehydratase / 0.657
2wsb NADGalactitol dehydrogenase / 0.657
1wp4 NDP3-hydroxyisobutyrate dehydrogenase / 0.656
1yjq NAP2-dehydropantoate 2-reductase 1.1.1.169 0.656
3we0 FADLysine 2-monooxygenase / 0.656
4nfh NAJAlcohol dehydrogenase E chain 1.1.1.1 0.656
2a92 NAIL-lactate dehydrogenase / 0.655
3b20 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.655
3wmx NADNAD dependent epimerase/dehydratase / 0.655
1g1a NADdTDP-glucose 4,6-dehydratase / 0.654
3a4v NADNDP-sugar epimerase / 0.654
1e3e NAIAlcohol dehydrogenase 4 1.1.1.1 0.653
3jsk AHZThiamine thiazole synthase / 0.652
4l7v SAHProtein-L-isoaspartate O-methyltransferase / 0.652
3lby SAHUncharacterized protein / 0.651
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.651
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.650