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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
3zdf NAD Glyceraldehyde-3-phosphate dehydrogenase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3zdf NADGlyceraldehyde-3-phosphate dehydrogenase / 1.086
3b1j NADGlyceraldehyde-3-phosphate dehydrogenase / 0.989
3qv1 NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.946
3zcx NADGlyceraldehyde-3-phosphate dehydrogenase / 0.920
1hdg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.903
4boy NADGlyceraldehyde-3-phosphate dehydrogenase / 0.900
1rm3 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.898
3lvf NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.897
2g82 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.888
3hja NADGlyceraldehyde-3-phosphate dehydrogenase / 0.877
5c7o NADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific 1.2.1.12 0.868
1gd1 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.862
4dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.860
1nqo NADGlyceraldehyde-3-phosphate dehydrogenase / 0.858
3cmc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.858
4p8r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.856
3ksd NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.841
4o63 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.841
1nq5 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.840
3cif NADGlyceraldehyde-3-phosphate dehydrogenase / 0.840
2vyn NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.836
4o59 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.832
1nqa NADGlyceraldehyde-3-phosphate dehydrogenase / 0.831
1npt NADGlyceraldehyde-3-phosphate dehydrogenase / 0.830
2vyv NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.830
3v1y NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.829
2ep7 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.828
4k9d NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.827
4lsm NADGlyceraldehyde-3-phosphate dehydrogenase / 0.827
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.826
1vsv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.824
1gad NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.820
1dss NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.813
3cps NADGlyceraldehyde-3-phosphate dehydrogenase / 0.808
2dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.801
3dmt NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.801
1dc6 NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.794
3pym NADGlyceraldehyde-3-phosphate dehydrogenase 3 1.2.1.12 0.794
2b4r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.789
4z0h NADGlyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic 1.2.1.12 0.788
3dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.784
1a7k NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.775
1ywg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.773
1szj NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.769
1cer NADGlyceraldehyde-3-phosphate dehydrogenase / 0.764
1nbo NADGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.763
2d2i NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.759
1u8f NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.757
3doc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.757
1dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.754
3l4s NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.750
1jn0 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.746
1gyp NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.737
3k2b NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.729
3e5r NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.726
1znq NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.720
1rm4 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.719
3f3s NADLambda-crystallin homolog / 0.715
1nvm NADAcetaldehyde dehydrogenase 1.2.1.10 0.713
3had NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.711
1ml3 NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.700
1f0y NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.697
1qxs NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.697
1rm5 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.691
2g5c NADPrephenate dehydrogenase / 0.691
2pkr NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.690
2vhx NADAlanine dehydrogenase 1.4.1.1 0.688
3ggp NADPrephenate dehydrogenase / 0.686
1o6z NADMalate dehydrogenase / 0.683
1ju2 FAD(R)-mandelonitrile lyase 2 4.1.2.10 0.681
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.681
3hwr NDP2-dehydropantoate 2-reductase / 0.681
3pef NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.679
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.678
3ikt NADRedox-sensing transcriptional repressor Rex / 0.675
1m76 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.672
1f17 NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.669
1vc2 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.669
1ihx SNDGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.668
1nah NADUDP-glucose 4-epimerase 5.1.3.2 0.668
3ish FADThioredoxin reductase 1.8.1.9 0.668
5eio NAP[LysW]-L-2-aminoadipate 6-phosphate reductase / 0.665
1j0x NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.664
2hdh NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.664
4usr FADMonooxygenase / 0.663
3tri NAPPyrroline-5-carboxylate reductase / 0.662
1wwk NAD307aa long hypothetical phosphoglycerate dehydrogenase / 0.661
3a14 NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase / 0.660
3ing NDPHomoserine dehydrogenase related protein / 0.660
2cvz NDP3-hydroxyisobutyrate dehydrogenase / 0.659
2nad NADFormate dehydrogenase / 0.658
3wv7 ADPHmd co-occurring protein HcgE / 0.658
1gae NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.657
1il0 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.657
1wp4 NDP3-hydroxyisobutyrate dehydrogenase / 0.657
2vhz NAIAlanine dehydrogenase 1.4.1.1 0.657
3l0d NADGlyceraldehyde-3-phosphate dehydrogenase / 0.656
5bsg NAPPyrroline-5-carboxylate reductase / 0.656
1kvr NADUDP-glucose 4-epimerase 5.1.3.2 0.654
1vi2 NADQuinate/shikimate dehydrogenase / 0.654
3keo NADRedox-sensing transcriptional repressor Rex / 0.654
3ru9 NADUDP-N-acetylglucosamine 4-epimerase / 0.653
1sc6 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.652
3nt2 NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.652
2rcy NAPPyrroline-5-carboxylate reductase / 0.651
4gae NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic 1.1.1.267 0.650
5a06 NDPGlucose-fructose oxidoreductase / 0.650