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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
3cmc NAD Glyceraldehyde-3-phosphate dehydrogenase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3cmc NADGlyceraldehyde-3-phosphate dehydrogenase / 1.049
1gd1 NADGlyceraldehyde-3-phosphate dehydrogenase / 1.010
3hja NADGlyceraldehyde-3-phosphate dehydrogenase / 0.994
1hdg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.979
2g82 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.962
1npt NADGlyceraldehyde-3-phosphate dehydrogenase / 0.960
1nqo NADGlyceraldehyde-3-phosphate dehydrogenase / 0.959
4p8r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.954
1nqa NADGlyceraldehyde-3-phosphate dehydrogenase / 0.944
3zcx NADGlyceraldehyde-3-phosphate dehydrogenase / 0.930
3ksd NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.928
4lsm NADGlyceraldehyde-3-phosphate dehydrogenase / 0.925
4boy NADGlyceraldehyde-3-phosphate dehydrogenase / 0.923
1u8f NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.921
3lvf NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.920
1vsv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.910
1nq5 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.909
2vyn NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.909
1gad NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.905
5c7o NADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific 1.2.1.12 0.905
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.900
2ep7 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.899
3b1j NADGlyceraldehyde-3-phosphate dehydrogenase / 0.893
4o59 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.888
4k9d NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.886
3cps NADGlyceraldehyde-3-phosphate dehydrogenase / 0.885
3dmt NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.880
3cif NADGlyceraldehyde-3-phosphate dehydrogenase / 0.877
2vyv NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.876
3v1y NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.870
3qv1 NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.868
1rm3 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.866
3zdf NADGlyceraldehyde-3-phosphate dehydrogenase / 0.858
1nbo NADGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.851
1dss NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.848
4dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.845
1cer NADGlyceraldehyde-3-phosphate dehydrogenase / 0.837
3doc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.837
1a7k NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.833
3l4s NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.832
2dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.830
3dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.830
1ywg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.828
3pym NADGlyceraldehyde-3-phosphate dehydrogenase 3 1.2.1.12 0.820
2b4r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.816
1dc6 NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.794
1jn0 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.787
4o63 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.785
1gyp NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.780
3k2b NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.772
1qxs NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.770
4z0h NADGlyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic 1.2.1.12 0.766
1szj NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.765
2d2i NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.764
1dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.752
3e5r NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.747
1rm4 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.745
4plp NADHomospermidine synthase 2.5.1.44 0.745
1znq NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.743
1j0x NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.736
4om8 NAD3-hydroxybutyryl-coA dehydrogenase / 0.735
1m76 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.734
1cf2 NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.732
1f0y NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.728
1vc2 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.718
1nvm NADAcetaldehyde dehydrogenase 1.2.1.10 0.717
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.714
3keo NADRedox-sensing transcriptional repressor Rex / 0.714
2pv7 NADT-protein 1.3.1.12 0.712
3ggp NADPrephenate dehydrogenase / 0.712
3had NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.712
3qvs NADMyo-inositol-1-phosphate synthase (Ino1) / 0.711
2o4c NADErythronate-4-phosphate dehydrogenase / 0.709
4tvb NADHomospermidine synthase 2.5.1.44 0.701
1il0 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.700
3oet NADErythronate-4-phosphate dehydrogenase / 0.700
1ml3 NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.693
1gae NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.691
4wji NAPPutative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase / 0.691
2g5c NADPrephenate dehydrogenase / 0.689
2ixb NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.689
3nt2 NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.689
4j4b NAIUncharacterized protein / 0.688
2vhx NADAlanine dehydrogenase 1.4.1.1 0.686
3lzw FADFerredoxin--NADP reductase 2 1.18.1.2 0.686
3b20 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.684
3gnq NADGlyceraldehyde-3-phosphate dehydrogenase / 0.684
1rm5 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.683
3hwr NDP2-dehydropantoate 2-reductase / 0.682
3cin NADMyo-inositol-1-phosphate synthase-related protein / 0.681
4yac NAIC alpha-dehydrogenase / 0.681
3qvt NAIMyo-inositol-1-phosphate synthase (Ino1) / 0.680
1gl3 NDPAspartate-semialdehyde dehydrogenase / 0.679
2pkr NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.678
1f8f NADBenzyl alcohol dehydrogenase / 0.677
3nt4 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.677
5ig2 NADShort-chain dehydrogenase/reductase SDR / 0.677
1m75 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.676
1lso NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.675
3qvw NADMyo-inositol-1-phosphate synthase (Ino1) / 0.675
3qvx NADMyo-inositol-1-phosphate synthase (Ino1) / 0.675
2q3e NAIUDP-glucose 6-dehydrogenase 1.1.1.22 0.674
3oz2 FADDigeranylgeranylglycerophospholipid reductase / 0.673
2vhw NAIAlanine dehydrogenase 1.4.1.1 0.672
4xrg NADHomospermidine synthase 2.5.1.44 0.671
1f17 NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.670
2f1k NAPPrephenate dehydrogenase / 0.670
2fkn NADUrocanate hydratase 4.2.1.49 0.669
1uxj NADMalate dehydrogenase / 0.668
2wsb NADGalactitol dehydrogenase / 0.668
3l0d NADGlyceraldehyde-3-phosphate dehydrogenase / 0.668
1o6z NADMalate dehydrogenase / 0.666
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.665
1sc6 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.665
2rcy NAPPyrroline-5-carboxylate reductase / 0.665
4j43 NADUncharacterized protein / 0.665
1h2b NAJNAD-dependent alcohol dehydrogenase / 0.664
3anm NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase 1.1.1.267 0.664
4dl9 NADS-(hydroxymethyl)glutathione dehydrogenase / 0.664
4kug NAD3-hydroxybutyryl-CoA dehydrogenase / 0.664
1i2b NADUDP-sulfoquinovose synthase, chloroplastic 3.13.1.1 0.662
1b3r NADAdenosylhomocysteinase 3.3.1.1 0.661
1bdb NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase / 0.661
1e1k FADNADPH:adrenodoxin oxidoreductase, mitochondrial 1.18.1.6 0.661
2nad NADFormate dehydrogenase / 0.661
3ikt NADRedox-sensing transcriptional repressor Rex / 0.660
2o06 MTASpermidine synthase 2.5.1.16 0.659
2vhz NAIAlanine dehydrogenase 1.4.1.1 0.659
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.658
1mo9 FAD2-oxopropyl-CoM reductase, carboxylating 1.8.1.5 0.657
1zh8 NAPUncharacterized protein / 0.657
3m2t NADProbable dehydrogenase / 0.657
3wsw NADL-lactate dehydrogenase / 0.657
4k28 NADShikimate dehydrogenase family protein / 0.657
3ket NADRedox-sensing transcriptional repressor Rex / 0.656
3qw2 NADMyo-inositol-1-phosphate synthase (Ino1) / 0.656
4cr8 NADN-acylmannosamine 1-dehydrogenase 1.1.1.233 0.656
5cku FADL-ornithine N(5)-monooxygenase / 0.655
1i36 NAPConserved protein / 0.654
3t4e NADQuinate/shikimate dehydrogenase / 0.654
1c1d NAIPhenylalanine dehydrogenase / 0.653
3jyo NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.653
3keq NADRedox-sensing transcriptional repressor Rex / 0.653
1vi2 NADQuinate/shikimate dehydrogenase / 0.652
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.652
1e3e NAIAlcohol dehydrogenase 4 1.1.1.1 0.651
1hsz NADAlcohol dehydrogenase 1B 1.1.1.1 0.651
3ggo NAIPrephenate dehydrogenase / 0.651
3ou2 SAHSAM-dependent methyltransferase / 0.651
1p1i NADInositol-3-phosphate synthase 5.5.1.4 0.650
2pt6 S4MSpermidine synthase / 0.650
3d4p NADL-lactate dehydrogenase 1 1.1.1.27 0.650
3hdh NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.650
4e5p NADPhosphonate dehydrogenase 1.20.1.1 0.650