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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
1gd1 NAD Glyceraldehyde-3-phosphate dehydrogenase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1gd1 NADGlyceraldehyde-3-phosphate dehydrogenase / 1.078
3cmc NADGlyceraldehyde-3-phosphate dehydrogenase / 1.010
3hja NADGlyceraldehyde-3-phosphate dehydrogenase / 0.988
2g82 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.977
1hdg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.969
1nqa NADGlyceraldehyde-3-phosphate dehydrogenase / 0.968
4p8r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.955
1npt NADGlyceraldehyde-3-phosphate dehydrogenase / 0.953
1nqo NADGlyceraldehyde-3-phosphate dehydrogenase / 0.946
1vsv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.931
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.926
1u8f NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.923
1nq5 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.914
3b1j NADGlyceraldehyde-3-phosphate dehydrogenase / 0.914
3lvf NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.912
3qv1 NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.910
4lsm NADGlyceraldehyde-3-phosphate dehydrogenase / 0.907
2vyv NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.903
3cps NADGlyceraldehyde-3-phosphate dehydrogenase / 0.902
3cif NADGlyceraldehyde-3-phosphate dehydrogenase / 0.901
3zcx NADGlyceraldehyde-3-phosphate dehydrogenase / 0.901
3ksd NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.900
1gad NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.898
4boy NADGlyceraldehyde-3-phosphate dehydrogenase / 0.890
3v1y NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.887
1rm3 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.884
2ep7 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.880
2dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.874
5c7o NADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific 1.2.1.12 0.874
3dmt NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.873
1cer NADGlyceraldehyde-3-phosphate dehydrogenase / 0.869
4k9d NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.869
4dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.868
3zdf NADGlyceraldehyde-3-phosphate dehydrogenase / 0.862
1nbo NADGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.860
4o59 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.853
3l4s NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.849
1a7k NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.848
3dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.847
2vyn NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.844
2b4r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.810
1dss NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.803
3doc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.803
1dc6 NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.801
1dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.800
3k2b NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.800
3pym NADGlyceraldehyde-3-phosphate dehydrogenase 3 1.2.1.12 0.798
1ywg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.790
4z0h NADGlyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic 1.2.1.12 0.780
2d2i NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.775
4o63 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.772
1szj NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.768
1jn0 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.763
1gyp NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.757
1znq NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.751
1rm4 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.744
1m76 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.743
1j0x NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.739
1f0y NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.737
3e5r NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.735
3ggp NADPrephenate dehydrogenase / 0.730
1cf2 NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.728
4om8 NAD3-hydroxybutyryl-coA dehydrogenase / 0.726
4xq9 NADHomospermidine synthase 2.5.1.44 0.726
1vc2 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.721
1rm5 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.715
4tvb NADHomospermidine synthase 2.5.1.44 0.715
4xrg NADHomospermidine synthase 2.5.1.44 0.714
1o6z NADMalate dehydrogenase / 0.713
2pv7 NADT-protein 1.3.1.12 0.713
3keo NADRedox-sensing transcriptional repressor Rex / 0.713
1nvm NADAcetaldehyde dehydrogenase 1.2.1.10 0.710
4fn4 NADShort chain dehydrogenase / 0.709
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.700
1qxs NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.699
3qvs NADMyo-inositol-1-phosphate synthase (Ino1) / 0.698
2o4c NADErythronate-4-phosphate dehydrogenase / 0.695
1sc6 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.692
2ixb NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.691
5ig2 NADShort-chain dehydrogenase/reductase SDR / 0.690
3nt2 NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.689
3b20 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.688
4j4b NAIUncharacterized protein / 0.687
4wji NAPPutative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase / 0.687
3lzw FADFerredoxin--NADP reductase 2 1.18.1.2 0.686
3tri NAPPyrroline-5-carboxylate reductase / 0.686
2g5c NADPrephenate dehydrogenase / 0.685
3q2k NAIProbable oxidoreductase / 0.684
3d4p NADL-lactate dehydrogenase 1 1.1.1.27 0.683
3ikt NADRedox-sensing transcriptional repressor Rex / 0.682
5ein NAP[LysW]-L-2-aminoadipate 6-phosphate reductase / 0.682
1uxk NADMalate dehydrogenase / 0.681
2fjb SFDAdenylylsulfate reductase, subunit A (AprA) / 0.681
3hdh NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.681
2vhx NADAlanine dehydrogenase 1.4.1.1 0.680
3cin NADMyo-inositol-1-phosphate synthase-related protein / 0.680
3qvt NAIMyo-inositol-1-phosphate synthase (Ino1) / 0.680
2fze APRAlcohol dehydrogenase class-3 1.1.1.1 0.679
4j43 NADUncharacterized protein / 0.679
1il0 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.678
1ml3 NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.678
2vhz NAIAlanine dehydrogenase 1.4.1.1 0.677
1m75 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.676
2vhw NAIAlanine dehydrogenase 1.4.1.1 0.676
1gae NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.675
3oz2 FADDigeranylgeranylglycerophospholipid reductase / 0.675
2f1k NAPPrephenate dehydrogenase / 0.674
1b3r NADAdenosylhomocysteinase 3.3.1.1 0.673
2q3e NAIUDP-glucose 6-dehydrogenase 1.1.1.22 0.672
3m2t NADProbable dehydrogenase / 0.672
1f17 NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.669
2wsb NADGalactitol dehydrogenase / 0.669
3cgb FADCoenzyme A disulfide reductase / 0.668
3ish FADThioredoxin reductase 1.8.1.9 0.668
4yag NAIC alpha-dehydrogenase / 0.668
2fjd SFDAdenylylsulfate reductase, subunit A (AprA) / 0.667
3keq NADRedox-sensing transcriptional repressor Rex / 0.667
4k28 NADShikimate dehydrogenase family protein / 0.667
5jla NADPutative short-chain dehydrogenase/reductase / 0.666
4ywj NAD4-hydroxy-tetrahydrodipicolinate reductase / 0.665
1hsz NADAlcohol dehydrogenase 1B 1.1.1.1 0.664
4j49 NAIUncharacterized protein / 0.663
4plp NADHomospermidine synthase 2.5.1.44 0.663
1wwk NAD307aa long hypothetical phosphoglycerate dehydrogenase / 0.662
2e37 NADL-lactate dehydrogenase / 0.662
1mp0 NADAlcohol dehydrogenase class-3 1.1.1.1 0.661
1i2b NADUDP-sulfoquinovose synthase, chloroplastic 3.13.1.1 0.660
3ojl NADCap5O / 0.660
3nt4 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.659
1bdb NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase / 0.658
4hb9 FADUncharacterized protein / 0.658
3ket NADRedox-sensing transcriptional repressor Rex / 0.657
2pkr NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.656
4yac NAIC alpha-dehydrogenase / 0.656
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.655
5eio NAP[LysW]-L-2-aminoadipate 6-phosphate reductase / 0.655
1c1d NAIPhenylalanine dehydrogenase / 0.654
1iy8 NADLevodione reductase / 0.654
3anl NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase 1.1.1.267 0.654
3ggo NAIPrephenate dehydrogenase / 0.654
3oc4 FADOxidoreductase, pyridine nucleotide-disulfide family / 0.654
4kug NAD3-hydroxybutyryl-CoA dehydrogenase / 0.654
1e3e NAIAlcohol dehydrogenase 4 1.1.1.1 0.653
1ihx SNDGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.652
1lso NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.652
1psd NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.652
3gnq NADGlyceraldehyde-3-phosphate dehydrogenase / 0.652
1vi2 NADQuinate/shikimate dehydrogenase / 0.651
2zbw FADFerredoxin--NADP reductase / 0.651
3tsc NADUncharacterized protein / 0.651
4e5p NADPhosphonate dehydrogenase 1.20.1.1 0.651
1h2h NADL-aspartate dehydrogenase 1.4.1.21 0.650