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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
2ep7 NAD Glyceraldehyde-3-phosphate dehydrogenase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2ep7 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.967
3cmc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.899
4lsm NADGlyceraldehyde-3-phosphate dehydrogenase / 0.893
3hja NADGlyceraldehyde-3-phosphate dehydrogenase / 0.889
1gd1 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.880
1hdg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.879
3b1j NADGlyceraldehyde-3-phosphate dehydrogenase / 0.878
2g82 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.873
4boy NADGlyceraldehyde-3-phosphate dehydrogenase / 0.872
3zcx NADGlyceraldehyde-3-phosphate dehydrogenase / 0.868
4k9d NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.866
1nqo NADGlyceraldehyde-3-phosphate dehydrogenase / 0.862
3cif NADGlyceraldehyde-3-phosphate dehydrogenase / 0.857
3ksd NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.857
1nq5 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.851
3qv1 NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.851
1nqa NADGlyceraldehyde-3-phosphate dehydrogenase / 0.849
1gad NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.848
1npt NADGlyceraldehyde-3-phosphate dehydrogenase / 0.848
4p8r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.846
1u8f NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.840
1rm3 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.838
2vyv NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.834
4o59 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.834
3cps NADGlyceraldehyde-3-phosphate dehydrogenase / 0.833
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.833
1dss NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.828
3zdf NADGlyceraldehyde-3-phosphate dehydrogenase / 0.828
5c7o NADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific 1.2.1.12 0.824
1vsv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.821
3dmt NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.811
1nbo NADGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.806
3lvf NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.806
3v1y NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.801
1vc2 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.794
2vyn NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.792
3doc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.786
4dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.785
2d2i NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.781
2dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.779
3k2b NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.772
1cer NADGlyceraldehyde-3-phosphate dehydrogenase / 0.764
3dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.761
3l4s NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.757
1dc6 NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.756
1rm4 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.752
2b4r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.752
1gyp NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.745
1ywg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.743
1a7k NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.736
1jn0 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.735
3pym NADGlyceraldehyde-3-phosphate dehydrogenase 3 1.2.1.12 0.735
4o63 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.731
1qxs NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.714
3had NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.714
1j0x NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.713
1rm5 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.711
1m76 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.710
1szj NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.710
4z0h NADGlyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic 1.2.1.12 0.710
1dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.709
2pkr NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.707
2g5c NADPrephenate dehydrogenase / 0.704
3e5r NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.703
4a99 FADTetX family tetracycline inactivation enzyme / 0.699
1hyh NADL-2-hydroxyisocaproate dehydrogenase / 0.697
3tri NAPPyrroline-5-carboxylate reductase / 0.696
1guy NADMalate dehydrogenase / 0.695
1nvm NADAcetaldehyde dehydrogenase 1.2.1.10 0.695
3cin NADMyo-inositol-1-phosphate synthase-related protein / 0.695
1gae NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.694
1znq NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.688
3adp NAILambda-crystallin 1.1.1.45 0.684
1m75 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.681
1uxj NADMalate dehydrogenase / 0.681
1o6z NADMalate dehydrogenase / 0.678
3nt2 NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.678
4xrg NADHomospermidine synthase 2.5.1.44 0.678
1la2 NADInositol-3-phosphate synthase 5.5.1.4 0.677
3ec7 NADInositol 2-dehydrogenase / 0.676
3b20 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.675
3m2t NADProbable dehydrogenase / 0.675
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.673
1f0y NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.672
1q0q NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase 1.1.1.267 0.671
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.671
4a6n FADTetX family tetracycline inactivation enzyme / 0.670
1ihx SNDGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.669
2yg4 FADPutrescine oxidase / 0.668
1reo FADL-amino-acid oxidase 1.4.3.2 0.667
1uxk NADMalate dehydrogenase / 0.667
4gae NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic 1.1.1.267 0.667
4xb1 NDP319aa long hypothetical homoserine dehydrogenase / 0.667
3keq NADRedox-sensing transcriptional repressor Rex / 0.666
3qvw NADMyo-inositol-1-phosphate synthase (Ino1) / 0.666
4yac NAIC alpha-dehydrogenase / 0.666
1lld NADL-lactate dehydrogenase 2 1.1.1.27 0.665
1pjc NADAlanine dehydrogenase / 0.665
3l0d NADGlyceraldehyde-3-phosphate dehydrogenase / 0.665
4j33 FADKynurenine 3-monooxygenase / 0.664
4plp NADHomospermidine synthase 2.5.1.44 0.664
4tm3 FADKtzI / 0.664
1mp0 NADAlcohol dehydrogenase class-3 1.1.1.1 0.663
3nt4 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.663
4k5r FADOxygenase / 0.663
1cf2 NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.662
1h2b NAJNAD-dependent alcohol dehydrogenase / 0.662
3ntr NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.662
4pzd NAD3-Hydroxyacyl-CoA dehydrogenase / 0.662
1gl3 NDPAspartate-semialdehyde dehydrogenase / 0.661
2qa2 FADPolyketide oxygenase CabE / 0.661
4tlz FADKtzI / 0.661
1e3w NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.660
2g76 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.660
2o4c NADErythronate-4-phosphate dehydrogenase / 0.660
2x0i NAIMalate dehydrogenase / 0.660
3ou6 SAMSAM-dependent methyltransferase / 0.660
3wmx NADNAD dependent epimerase/dehydratase / 0.660
1e3l NADAlcohol dehydrogenase 4 1.1.1.1 0.659
3qvs NADMyo-inositol-1-phosphate synthase (Ino1) / 0.659
3jyp NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.658
4xqc NADHomospermidine synthase 2.5.1.44 0.657
1dxy NADD-2-hydroxyisocaproate dehydrogenase 1.1.1 0.656
2q3e NAIUDP-glucose 6-dehydrogenase 1.1.1.22 0.656
3d4p NADL-lactate dehydrogenase 1 1.1.1.27 0.656
3zw9 NADPeroxisomal bifunctional enzyme 1.1.1.35 0.656
3grv ADNProbable ribosomal RNA small subunit methyltransferase A / 0.655
5ein NAP[LysW]-L-2-aminoadipate 6-phosphate reductase / 0.655
3jv7 NADSecondary alcohol dehydrogenase / 0.653
3oa2 NADUDP-N-acetyl-2-amino-2-deoxy-D-glucuronate oxidase / 0.653
5eio NAP[LysW]-L-2-aminoadipate 6-phosphate reductase / 0.653
2gdz NAD15-hydroxyprostaglandin dehydrogenase [NAD(+)] 1.1.1.141 0.652
4gl4 NAIAlcohol dehydrogenase class-3 / 0.652
1sc6 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.651
2a92 NAIL-lactate dehydrogenase / 0.651
2pv7 NADT-protein 1.3.1.12 0.651
3anm NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase 1.1.1.267 0.651
5bsg NAPPyrroline-5-carboxylate reductase / 0.651
1lso NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.650
4jnk NAIL-lactate dehydrogenase A chain 1.1.1.27 0.650
4yag NAIC alpha-dehydrogenase / 0.650