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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
3ids NAD Glyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 1.018
1vsv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.934
1gd1 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.926
1u8f NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.915
4p8r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.911
3cmc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.900
3cps NADGlyceraldehyde-3-phosphate dehydrogenase / 0.894
5c7o NADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific 1.2.1.12 0.893
1hdg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.888
3cif NADGlyceraldehyde-3-phosphate dehydrogenase / 0.888
2vyv NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.875
3pym NADGlyceraldehyde-3-phosphate dehydrogenase 3 1.2.1.12 0.872
4o63 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.869
4k9d NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.867
3v1y NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.866
4o59 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.866
3b1j NADGlyceraldehyde-3-phosphate dehydrogenase / 0.861
1a7k NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.860
1nqo NADGlyceraldehyde-3-phosphate dehydrogenase / 0.860
3lvf NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.860
1nq5 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.859
1nbo NADGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.852
1rm3 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.851
4boy NADGlyceraldehyde-3-phosphate dehydrogenase / 0.851
1gad NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.849
1nqa NADGlyceraldehyde-3-phosphate dehydrogenase / 0.849
3hja NADGlyceraldehyde-3-phosphate dehydrogenase / 0.849
1npt NADGlyceraldehyde-3-phosphate dehydrogenase / 0.848
3zcx NADGlyceraldehyde-3-phosphate dehydrogenase / 0.847
4lsm NADGlyceraldehyde-3-phosphate dehydrogenase / 0.845
3ksd NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.843
3dmt NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.842
3k2b NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.836
4dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.834
1cer NADGlyceraldehyde-3-phosphate dehydrogenase / 0.833
2ep7 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.833
1szj NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.827
3zdf NADGlyceraldehyde-3-phosphate dehydrogenase / 0.826
4z0h NADGlyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic 1.2.1.12 0.818
1dc6 NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.816
2b4r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.812
1ywg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.811
1gyp NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.810
3qv1 NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.809
3l4s NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.808
2vyn NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.799
3dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.795
2d2i NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.793
2dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.792
1vc2 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.786
1znq NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.781
3e5r NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.777
1dss NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.773
1j0x NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.772
3doc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.770
1jn0 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.764
1rm4 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.763
3b20 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.751
2g82 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.748
3tri NAPPyrroline-5-carboxylate reductase / 0.733
1dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.732
3oet NADErythronate-4-phosphate dehydrogenase / 0.732
3ec7 NADInositol 2-dehydrogenase / 0.720
2rcy NAPPyrroline-5-carboxylate reductase / 0.718
1qxs NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.715
1ihx SNDGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.713
3qvx NADMyo-inositol-1-phosphate synthase (Ino1) / 0.713
4plp NADHomospermidine synthase 2.5.1.44 0.713
3qvs NADMyo-inositol-1-phosphate synthase (Ino1) / 0.712
1nvm NADAcetaldehyde dehydrogenase 1.2.1.10 0.706
1q0q NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase 1.1.1.267 0.705
1rm5 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.704
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.702
4xrg NADHomospermidine synthase 2.5.1.44 0.701
3ggp NADPrephenate dehydrogenase / 0.700
4j2w FADKynurenine 3-monooxygenase / 0.700
4tm3 FADKtzI / 0.700
3d4p NADL-lactate dehydrogenase 1 1.1.1.27 0.699
3qw2 NADMyo-inositol-1-phosphate synthase (Ino1) / 0.699
4xqc NADHomospermidine synthase 2.5.1.44 0.699
2pv7 NADT-protein 1.3.1.12 0.697
3qvt NAIMyo-inositol-1-phosphate synthase (Ino1) / 0.697
1gae NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.696
3l0d NADGlyceraldehyde-3-phosphate dehydrogenase / 0.695
4xq9 NADHomospermidine synthase 2.5.1.44 0.695
1guy NADMalate dehydrogenase / 0.690
1h2b NAJNAD-dependent alcohol dehydrogenase / 0.689
2pkr NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.688
3oz2 FADDigeranylgeranylglycerophospholipid reductase / 0.688
3keo NADRedox-sensing transcriptional repressor Rex / 0.686
1f0y NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.685
3anm NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase 1.1.1.267 0.685
4j49 NAIUncharacterized protein / 0.685
3qvw NADMyo-inositol-1-phosphate synthase (Ino1) / 0.684
3oc4 FADOxidoreductase, pyridine nucleotide-disulfide family / 0.683
1sc6 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.682
2g5c NADPrephenate dehydrogenase / 0.682
4wji NAPPutative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase / 0.682
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.681
3adp NAILambda-crystallin 1.1.1.45 0.681
1gl3 NDPAspartate-semialdehyde dehydrogenase / 0.680
1la2 NADInositol-3-phosphate synthase 5.5.1.4 0.680
3ru9 NADUDP-N-acetylglucosamine 4-epimerase / 0.680
4xr9 NADCalS8 / 0.680
1m76 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.678
3d64 NADAdenosylhomocysteinase / 0.678
1nah NADUDP-glucose 4-epimerase 5.1.3.2 0.677
2ahr NAPPyrroline-5-carboxylate reductase / 0.676
1ml3 NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.675
4om8 NAD3-hydroxybutyryl-coA dehydrogenase / 0.675
3sx2 NADUncharacterized protein / 0.674
4j4b NAIUncharacterized protein / 0.674
1jnz FADAdenylylsulfate reductase, subunit A (AprA) / 0.673
2nad NADFormate dehydrogenase / 0.673
3had NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.673
2ixb NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.671
3cin NADMyo-inositol-1-phosphate synthase-related protein / 0.671
4gll NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.671
4ywj NAD4-hydroxy-tetrahydrodipicolinate reductase / 0.671
4hb9 FADUncharacterized protein / 0.670
1zem NADXylitol dehydrogenase / 0.669
3bg7 FADPyranose 2-oxidase / 0.669
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.669
4k28 NADShikimate dehydrogenase family protein / 0.669
4kug NAD3-hydroxybutyryl-CoA dehydrogenase / 0.669
4lcj NADC-terminal-binding protein 2 / 0.669
2rgj FADFlavin-containing monooxygenase / 0.667
3ntq NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.667
5ein NAP[LysW]-L-2-aminoadipate 6-phosphate reductase / 0.667
3ikt NADRedox-sensing transcriptional repressor Rex / 0.666
1kvr NADUDP-glucose 4-epimerase 5.1.3.2 0.665
4j43 NADUncharacterized protein / 0.665
5bsf NADPyrroline-5-carboxylate reductase / 0.665
1i36 NAPConserved protein / 0.664
3ruc NADUDP-N-acetylglucosamine 4-epimerase / 0.664
4xgi NADGlutamate dehydrogenase / 0.664
1f8f NADBenzyl alcohol dehydrogenase / 0.663
2vq3 NAPMetalloreductase STEAP3 / 0.662
3ruf NADUDP-N-acetylglucosamine 4-epimerase / 0.662
1uxj NADMalate dehydrogenase / 0.661
2o4c NADErythronate-4-phosphate dehydrogenase / 0.660
2vhx NADAlanine dehydrogenase 1.4.1.1 0.660
1c1d NAIPhenylalanine dehydrogenase / 0.659
1cf2 NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.659
3tnl NADShikimate dehydrogenase (NADP(+)) / 0.659
1yjq NAP2-dehydropantoate 2-reductase 1.1.1.169 0.658
3jyo NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.658
3nlc FADUncharacterized protein / 0.658
3nt4 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.658
3a4v NADNDP-sugar epimerase / 0.657
3lu1 NADUDP-N-acetylglucosamine 4-epimerase / 0.657
3lzw FADFerredoxin--NADP reductase 2 1.18.1.2 0.657
3oa2 NADUDP-N-acetyl-2-amino-2-deoxy-D-glucuronate oxidase / 0.657
3s5w FADL-ornithine N(5)-monooxygenase / 0.657
1il0 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.656
3hdh NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.656
3nt2 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.656
3t4e NADQuinate/shikimate dehydrogenase / 0.656
2voj NADAlanine dehydrogenase 1.4.1.1 0.655
3pqf NADL-lactate dehydrogenase 1.1.1.27 0.655
1e1m FADNADPH:adrenodoxin oxidoreductase, mitochondrial 1.18.1.6 0.653
4dl9 NADS-(hydroxymethyl)glutathione dehydrogenase / 0.653
1m75 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.652
1p1i NADInositol-3-phosphate synthase 5.5.1.4 0.652
2vhw NAIAlanine dehydrogenase 1.4.1.1 0.652
3gnq NADGlyceraldehyde-3-phosphate dehydrogenase / 0.652
3ics FADCoenzyme A disulfide reductase / 0.652
3ict FADCoenzyme A disulfide reductase / 0.652
3ish FADThioredoxin reductase 1.8.1.9 0.652
3jyp NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.652
3jyq NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.652
3keq NADRedox-sensing transcriptional repressor Rex / 0.652
3gvi ADPMalate dehydrogenase / 0.651
2ome NADC-terminal-binding protein 2 / 0.650
3nt6 FADFAD-dependent pyridine nucleotide-disulphide oxidoreductase / 0.650
3ojl NADCap5O / 0.650
4wct FADFructosyl amine:oxygen oxidoreductase / 0.650