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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
3cif NAD Glyceraldehyde-3-phosphate dehydrogenase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3cif NADGlyceraldehyde-3-phosphate dehydrogenase / 0.984
4k9d NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.967
1u8f NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.937
1vsv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.935
2vyv NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.935
4o59 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.923
3cps NADGlyceraldehyde-3-phosphate dehydrogenase / 0.920
3v1y NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.920
4lsm NADGlyceraldehyde-3-phosphate dehydrogenase / 0.918
5c7o NADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific 1.2.1.12 0.917
4p8r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.911
3hja NADGlyceraldehyde-3-phosphate dehydrogenase / 0.904
1gd1 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.901
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.888
4boy NADGlyceraldehyde-3-phosphate dehydrogenase / 0.886
2g82 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.885
3pym NADGlyceraldehyde-3-phosphate dehydrogenase 3 1.2.1.12 0.885
1gad NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.884
1nqo NADGlyceraldehyde-3-phosphate dehydrogenase / 0.884
1hdg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.883
1nq5 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.877
3cmc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.877
1dss NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.873
1nqa NADGlyceraldehyde-3-phosphate dehydrogenase / 0.871
3lvf NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.865
2vyn NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.860
4o63 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.859
2ep7 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.857
3zcx NADGlyceraldehyde-3-phosphate dehydrogenase / 0.848
3ksd NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.841
3zdf NADGlyceraldehyde-3-phosphate dehydrogenase / 0.840
1szj NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.836
1rm3 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.833
4dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.832
1ywg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.829
3doc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.828
3b1j NADGlyceraldehyde-3-phosphate dehydrogenase / 0.826
3dmt NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.822
4z0h NADGlyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic 1.2.1.12 0.821
1dc6 NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.820
3l4s NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.819
1nbo NADGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.812
1znq NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.812
3qv1 NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.808
2b4r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.798
1cer NADGlyceraldehyde-3-phosphate dehydrogenase / 0.781
1j0x NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.778
3k2b NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.773
3e5r NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.772
1npt NADGlyceraldehyde-3-phosphate dehydrogenase / 0.767
1a7k NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.765
2dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.763
3dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.754
1gyp NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.751
1ihx SNDGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.748
1rm4 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.746
2g5c NADPrephenate dehydrogenase / 0.742
2d2i NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.737
1jn0 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.735
3ggp NADPrephenate dehydrogenase / 0.732
3f3s NADLambda-crystallin homolog / 0.731
1dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.728
1o6z NADMalate dehydrogenase / 0.727
3cin NADMyo-inositol-1-phosphate synthase-related protein / 0.723
2o4c NADErythronate-4-phosphate dehydrogenase / 0.722
3oet NADErythronate-4-phosphate dehydrogenase / 0.718
1f0y NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.714
1qxs NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.708
1m76 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.705
3keo NADRedox-sensing transcriptional repressor Rex / 0.704
1nvm NADAcetaldehyde dehydrogenase 1.2.1.10 0.700
1rm5 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.699
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.699
4plp NADHomospermidine synthase 2.5.1.44 0.692
3qvs NADMyo-inositol-1-phosphate synthase (Ino1) / 0.690
1gae NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.689
1pjc NADAlanine dehydrogenase / 0.689
2yy7 NADL-threonine dehydrogenase / 0.688
3qvx NADMyo-inositol-1-phosphate synthase (Ino1) / 0.688
1hku NADC-terminal-binding protein 1 1.1.1 0.687
1hyh NADL-2-hydroxyisocaproate dehydrogenase / 0.687
1m75 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.685
3tri NAPPyrroline-5-carboxylate reductase / 0.685
4okn NAIL-lactate dehydrogenase A chain 1.1.1.27 0.685
4nd3 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.682
4xq9 NADHomospermidine synthase 2.5.1.44 0.682
4wct FADFructosyl amine:oxygen oxidoreductase / 0.681
2i9p NAD3-hydroxyisobutyrate dehydrogenase, mitochondrial 1.1.1.31 0.680
3b20 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.680
1lso NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.679
3qw2 NADMyo-inositol-1-phosphate synthase (Ino1) / 0.679
4gkv NADAlcohol dehydrogenase, propanol-preferring 1.1.1.1 0.679
3ket NADRedox-sensing transcriptional repressor Rex / 0.678
1vc2 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.677
2ome NADC-terminal-binding protein 2 / 0.676
1gl3 NDPAspartate-semialdehyde dehydrogenase / 0.675
3qvw NADMyo-inositol-1-phosphate synthase (Ino1) / 0.675
3ikt NADRedox-sensing transcriptional repressor Rex / 0.673
3qvt NAIMyo-inositol-1-phosphate synthase (Ino1) / 0.673
4om8 NAD3-hydroxybutyryl-coA dehydrogenase / 0.673
4wji NAPPutative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase / 0.673
1la2 NADInositol-3-phosphate synthase 5.5.1.4 0.672
1psd NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.672
2rcy NAPPyrroline-5-carboxylate reductase / 0.671
1t2c NAIL-lactate dehydrogenase 1.1.1.27 0.670
2a92 NAIL-lactate dehydrogenase / 0.669
4yac NAIC alpha-dehydrogenase / 0.669
2ixb NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.668
3pqf NADL-lactate dehydrogenase 1.1.1.27 0.668
1c1d NAIPhenylalanine dehydrogenase / 0.667
4hb9 FADUncharacterized protein / 0.667
1e3s NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.666
4xrg NADHomospermidine synthase 2.5.1.44 0.666
1b3r NADAdenosylhomocysteinase 3.3.1.1 0.665
1dxy NADD-2-hydroxyisocaproate dehydrogenase 1.1.1 0.665
3gvi ADPMalate dehydrogenase / 0.665
1cf2 NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.664
2nad NADFormate dehydrogenase / 0.664
1g1a NADdTDP-glucose 4,6-dehydratase / 0.663
1uxj NADMalate dehydrogenase / 0.662
3ajr NADNDP-sugar epimerase / 0.661
3d4p NADL-lactate dehydrogenase 1 1.1.1.27 0.660
4pzd NAD3-Hydroxyacyl-CoA dehydrogenase / 0.660
4ywj NAD4-hydroxy-tetrahydrodipicolinate reductase / 0.660
3i53 SAH2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase / 0.659
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.658
1ml3 NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.657
2ekl NADD-3-phosphoglycerate dehydrogenase / 0.657
3ru9 NADUDP-N-acetylglucosamine 4-epimerase / 0.657
3w6u NAP6-phosphogluconate dehydrogenase, NAD-binding protein / 0.657
3wmx NADNAD dependent epimerase/dehydratase / 0.657
2hu2 NADC-terminal binding protein 1 / 0.656
3ntr NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.656
3wsw NADL-lactate dehydrogenase / 0.656
1sow NADL-lactate dehydrogenase 1.1.1.27 0.655
2g76 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.655
1e3e NAIAlcohol dehydrogenase 4 1.1.1.1 0.654
1f17 NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.654
1lld NADL-lactate dehydrogenase 2 1.1.1.27 0.654
2aa3 AP0L-lactate dehydrogenase / 0.654
2v7g NADUrocanate hydratase 4.2.1.49 0.654
3ldg SAHUncharacterized protein / 0.654
4tm3 FADKtzI / 0.654
2fjd SFDAdenylylsulfate reductase, subunit A (AprA) / 0.653
3adp NAILambda-crystallin 1.1.1.45 0.653
3nt4 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.653
1rsg FADPolyamine oxidase FMS1 / 0.652
1yjq NAP2-dehydropantoate 2-reductase 1.1.1.169 0.652
3o9z NADLipopolysaccaride biosynthesis protein wbpB / 0.652
4k28 NADShikimate dehydrogenase family protein / 0.652
1e3w NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.651
4nd4 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.650