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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
1szj 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
1szj NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.913
4z0h NADGlyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic 1.2.1.12 0.864
3pym NADGlyceraldehyde-3-phosphate dehydrogenase 3 1.2.1.12 0.855
4o59 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.855
4o63 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.855
1vsv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.854
1u8f NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.853
5c7o NADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific 1.2.1.12 0.852
4k9d NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.846
3cif NADGlyceraldehyde-3-phosphate dehydrogenase / 0.836
3cps NADGlyceraldehyde-3-phosphate dehydrogenase / 0.834
1dss NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.833
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.827
3v1y NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.817
1ywg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.815
1znq NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.801
1hdg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.798
1gad NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.797
2vyv NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.794
3qv1 NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.790
1nq5 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.788
4boy NADGlyceraldehyde-3-phosphate dehydrogenase / 0.785
3hja NADGlyceraldehyde-3-phosphate dehydrogenase / 0.781
2g82 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.780
3b1j NADGlyceraldehyde-3-phosphate dehydrogenase / 0.779
1dc6 NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.778
4lsm NADGlyceraldehyde-3-phosphate dehydrogenase / 0.774
4p8r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.772
3zdf NADGlyceraldehyde-3-phosphate dehydrogenase / 0.769
1gd1 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.768
1nqa NADGlyceraldehyde-3-phosphate dehydrogenase / 0.767
1j0x NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.766
3zcx NADGlyceraldehyde-3-phosphate dehydrogenase / 0.766
1cer NADGlyceraldehyde-3-phosphate dehydrogenase / 0.765
3cmc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.765
1nqo NADGlyceraldehyde-3-phosphate dehydrogenase / 0.764
3e5r NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.763
4dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.759
3lvf NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.758
1rm3 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.753
2vyn NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.752
3ksd NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.750
2b4r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.748
3k2b NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.748
1nbo NADGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.746
1a7k NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.743
1ihx SNDGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.740
3doc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.737
3l4s NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.718
3b20 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.717
2d2i NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.715
3f3s NADLambda-crystallin homolog / 0.715
1jn0 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.710
2ep7 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.710
3dmt NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.710
1m76 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.706
1m75 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.704
3dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.704
1npt NADGlyceraldehyde-3-phosphate dehydrogenase / 0.700
1rm4 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.700
3oet NADErythronate-4-phosphate dehydrogenase / 0.700
1gyp NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.699
2g5c NADPrephenate dehydrogenase / 0.699
3ikt NADRedox-sensing transcriptional repressor Rex / 0.699
1rm5 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.697
1il0 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.695
2ome NADC-terminal-binding protein 2 / 0.695
2o4c NADErythronate-4-phosphate dehydrogenase / 0.693
1ml3 NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.690
3pqf NADL-lactate dehydrogenase 1.1.1.27 0.687
1qxs NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.686
3gvi ADPMalate dehydrogenase / 0.683
1sc6 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.681
1dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.678
2aa3 AP0L-lactate dehydrogenase / 0.678
2pv7 NADT-protein 1.3.1.12 0.678
3ec7 NADInositol 2-dehydrogenase / 0.678
2dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.676
3ggp NADPrephenate dehydrogenase / 0.676
3nt2 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.675
3ket NADRedox-sensing transcriptional repressor Rex / 0.674
3wv7 ADPHmd co-occurring protein HcgE / 0.673
3had NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.672
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.671
4xq9 NADHomospermidine synthase 2.5.1.44 0.670
1p1i NADInositol-3-phosphate synthase 5.5.1.4 0.669
1f17 NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.668
1vc2 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.667
1gae NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.666
3keq NADRedox-sensing transcriptional repressor Rex / 0.666
3qvw NADMyo-inositol-1-phosphate synthase (Ino1) / 0.666
1lso NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.665
4tvb NADHomospermidine synthase 2.5.1.44 0.665
3l0d NADGlyceraldehyde-3-phosphate dehydrogenase / 0.664
1agn NADAlcohol dehydrogenase class 4 mu/sigma chain 1.1.1.1 0.663
1p1h NADInositol-3-phosphate synthase 5.5.1.4 0.663
2ixb NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.663
1t2c NAIL-lactate dehydrogenase 1.1.1.27 0.662
2q1w NADPutative nucleotide sugar epimerase/ dehydratase / 0.662
5eio NAP[LysW]-L-2-aminoadipate 6-phosphate reductase / 0.662
1wwk NAD307aa long hypothetical phosphoglycerate dehydrogenase / 0.661
5lc1 NADL-threonine 3-dehydrogenase / 0.661
1nvm NADAcetaldehyde dehydrogenase 1.2.1.10 0.660
1pjc NADAlanine dehydrogenase / 0.660
4wji NAPPutative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase / 0.660
4yac NAIC alpha-dehydrogenase / 0.660
1hyh NADL-2-hydroxyisocaproate dehydrogenase / 0.659
2pkr NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.659
3gnq NADGlyceraldehyde-3-phosphate dehydrogenase / 0.658
5ein NAP[LysW]-L-2-aminoadipate 6-phosphate reductase / 0.658
3cin NADMyo-inositol-1-phosphate synthase-related protein / 0.657
4xqc NADHomospermidine synthase 2.5.1.44 0.657
4xrg NADHomospermidine synthase 2.5.1.44 0.657
1hku NADC-terminal-binding protein 1 1.1.1 0.656
2i9p NAD3-hydroxyisobutyrate dehydrogenase, mitochondrial 1.1.1.31 0.656
3ntq NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.655
3d4p NADL-lactate dehydrogenase 1 1.1.1.27 0.654
3nt4 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.654
3qw2 NADMyo-inositol-1-phosphate synthase (Ino1) / 0.654
3tri NAPPyrroline-5-carboxylate reductase / 0.654
4ywj NAD4-hydroxy-tetrahydrodipicolinate reductase / 0.654
2pa3 NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.653
3g5q FADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO / 0.653
3ru9 NADUDP-N-acetylglucosamine 4-epimerase / 0.653
3uko NADAlcohol dehydrogenase class-3 / 0.653
1uxk NADMalate dehydrogenase / 0.652
3pef NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.652
3qvt NAIMyo-inositol-1-phosphate synthase (Ino1) / 0.652
3ojl NADCap5O / 0.651
3qvs NADMyo-inositol-1-phosphate synthase (Ino1) / 0.651
1c1d NAIPhenylalanine dehydrogenase / 0.650
1rsg FADPolyamine oxidase FMS1 / 0.650