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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
1npt NAD Glyceraldehyde-3-phosphate dehydrogenase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1npt NADGlyceraldehyde-3-phosphate dehydrogenase / 1.016
1nqa NADGlyceraldehyde-3-phosphate dehydrogenase / 0.977
3cmc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.960
1gd1 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.953
1nqo NADGlyceraldehyde-3-phosphate dehydrogenase / 0.953
3hja NADGlyceraldehyde-3-phosphate dehydrogenase / 0.945
2g82 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.930
3lvf NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.927
1nq5 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.916
1hdg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.911
1gad NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.876
1u8f NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.862
3b1j NADGlyceraldehyde-3-phosphate dehydrogenase / 0.860
4lsm NADGlyceraldehyde-3-phosphate dehydrogenase / 0.860
4p8r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.858
3ksd NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.857
3dmt NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.853
4dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.852
4k9d NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.852
1vsv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.850
2ep7 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.848
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.848
3v1y NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.841
2vyv NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.838
4o59 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.836
3zdf NADGlyceraldehyde-3-phosphate dehydrogenase / 0.830
3dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.827
5c7o NADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific 1.2.1.12 0.825
4boy NADGlyceraldehyde-3-phosphate dehydrogenase / 0.824
1nbo NADGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.823
2vyn NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.810
3qv1 NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.807
1rm3 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.805
3k2b NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.805
1ywg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.797
3doc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.793
1a7k NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.791
1dc6 NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.791
3zcx NADGlyceraldehyde-3-phosphate dehydrogenase / 0.786
2dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.785
3cps NADGlyceraldehyde-3-phosphate dehydrogenase / 0.781
3pym NADGlyceraldehyde-3-phosphate dehydrogenase 3 1.2.1.12 0.781
2b4r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.776
1cer NADGlyceraldehyde-3-phosphate dehydrogenase / 0.774
1dss NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.774
1gyp NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.771
3cif NADGlyceraldehyde-3-phosphate dehydrogenase / 0.767
1qxs NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.755
3l4s NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.752
1dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.751
4o63 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.736
3e5r NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.725
1jn0 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.720
1ml3 NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.715
2d2i NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.715
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.708
1vc2 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.705
1j0x NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.700
1szj NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.700
3tri NAPPyrroline-5-carboxylate reductase / 0.698
3keo NADRedox-sensing transcriptional repressor Rex / 0.695
1m76 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.694
1rm4 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.694
1znq NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.693
1f0y NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.691
1jnz FADAdenylylsulfate reductase, subunit A (AprA) / 0.687
3f3s NADLambda-crystallin homolog / 0.685
4om8 NAD3-hydroxybutyryl-coA dehydrogenase / 0.685
1m75 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.684
2pv7 NADT-protein 1.3.1.12 0.683
1rm5 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.682
2o4c NADErythronate-4-phosphate dehydrogenase / 0.681
1c1d NAIPhenylalanine dehydrogenase / 0.680
1il0 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.678
4xwz FADFructosyl amine:oxygen oxidoreductase / 0.676
2pkr NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.675
3lzw FADFerredoxin--NADP reductase 2 1.18.1.2 0.673
1h2b NAJNAD-dependent alcohol dehydrogenase / 0.672
3s55 NADPutative short-chain dehydrogenase/reductase / 0.672
4j4b NAIUncharacterized protein / 0.672
4plp NADHomospermidine synthase 2.5.1.44 0.672
1jnr FADAdenylylsulfate reductase, subunit A (AprA) / 0.671
1gpe FADGlucose oxidase 1.1.3.4 0.670
3adp NAILambda-crystallin 1.1.1.45 0.670
4wct FADFructosyl amine:oxygen oxidoreductase / 0.670
3ikt NADRedox-sensing transcriptional repressor Rex / 0.669
3qvw NADMyo-inositol-1-phosphate synthase (Ino1) / 0.669
2fjd SFDAdenylylsulfate reductase, subunit A (AprA) / 0.668
1nvm NADAcetaldehyde dehydrogenase 1.2.1.10 0.666
3cin NADMyo-inositol-1-phosphate synthase-related protein / 0.666
5ig2 NADShort-chain dehydrogenase/reductase SDR / 0.665
1gae NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.662
3nt4 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.662
1yl7 NAI4-hydroxy-tetrahydrodipicolinate reductase / 0.661
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.660
2a94 AP0L-lactate dehydrogenase 1.1.1.27 0.658
3ruc NADUDP-N-acetylglucosamine 4-epimerase / 0.658
4k2x FADPolyketide oxygenase/hydroxylase / 0.658
2vhw NAIAlanine dehydrogenase 1.4.1.1 0.657
3bi5 FADPolyamine oxidase FMS1 / 0.657
3gnq NADGlyceraldehyde-3-phosphate dehydrogenase / 0.656
3tsc NADUncharacterized protein / 0.656
4cr8 NADN-acylmannosamine 1-dehydrogenase 1.1.1.233 0.656
2fje FADAdenylylsulfate reductase, subunit A (AprA) / 0.655
4z0h NADGlyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic 1.2.1.12 0.655
2ixb NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.654
3nt2 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.654
4jk3 NADUncharacterized protein / 0.654
1sc6 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.653
4k28 NADShikimate dehydrogenase family protein / 0.653
1psd NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.652
2o23 NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.652
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.652
1nfr NAD3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase 1.1.1.53 0.651
1p1i NADInositol-3-phosphate synthase 5.5.1.4 0.651
2rgj FADFlavin-containing monooxygenase / 0.651
3gvi ADPMalate dehydrogenase / 0.651
3utf FDAUDP-galactopyranose mutase / 0.651
1p1h NADInositol-3-phosphate synthase 5.5.1.4 0.650
5i39 FADL-amino acid deaminase / 0.650