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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
1cf2 NAP Glyceraldehyde-3-phosphate dehydrogenase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1cf2 NAPGlyceraldehyde-3-phosphate dehydrogenase / 1.209
2yyy NAPGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.59 0.985
2czc NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.59 0.766
1m76 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.740
3cmc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.732
3f3s NADLambda-crystallin homolog / 0.732
1f0y NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.729
1gd1 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.728
1hdg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.723
1zh8 NAPUncharacterized protein / 0.719
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.715
2rcy NAPPyrroline-5-carboxylate reductase / 0.713
3cps NADGlyceraldehyde-3-phosphate dehydrogenase / 0.711
4xb1 NDP319aa long hypothetical homoserine dehydrogenase / 0.711
1yjq NAP2-dehydropantoate 2-reductase 1.1.1.169 0.709
4k9d NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.709
2jcv NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase / 0.702
5c7o NADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific 1.2.1.12 0.698
4aic NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase / 0.697
3adp NAILambda-crystallin 1.1.1.45 0.695
2g82 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.694
2ydx NAPMethionine adenosyltransferase 2 subunit beta / 0.694
4boy NADGlyceraldehyde-3-phosphate dehydrogenase / 0.693
4o59 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.693
1gl3 NDPAspartate-semialdehyde dehydrogenase / 0.692
3ing NDPHomoserine dehydrogenase related protein / 0.692
1dss NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.691
1il0 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.691
2cvz NDP3-hydroxyisobutyrate dehydrogenase / 0.686
3tri NAPPyrroline-5-carboxylate reductase / 0.685
3zcx NADGlyceraldehyde-3-phosphate dehydrogenase / 0.685
1bsv NDPGDP-L-fucose synthase / 0.684
4om8 NAD3-hydroxybutyryl-coA dehydrogenase / 0.684
1u8f NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.682
1rm3 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.680
2b4r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.680
3anm NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase 1.1.1.267 0.680
3nt2 NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.678
3had NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.677
4xgi NADGlutamate dehydrogenase / 0.676
3b1j NADGlyceraldehyde-3-phosphate dehydrogenase / 0.674
4ebf NADPhosphonate dehydrogenase 1.20.1.1 0.674
3pym NADGlyceraldehyde-3-phosphate dehydrogenase 3 1.2.1.12 0.673
3wbb NAPMeso-diaminopimelate D-dehydrogenase / 0.673
1i36 NAPConserved protein / 0.672
3keo NADRedox-sensing transcriptional repressor Rex / 0.671
5ein NAP[LysW]-L-2-aminoadipate 6-phosphate reductase / 0.671
1q0q NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase 1.1.1.267 0.669
3qv1 NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.669
3dmt NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.668
3oet NADErythronate-4-phosphate dehydrogenase / 0.668
2q3e NAIUDP-glucose 6-dehydrogenase 1.1.1.22 0.667
3hwr NDP2-dehydropantoate 2-reductase / 0.667
3ulk NDPKetol-acid reductoisomerase (NADP(+)) / 0.667
4gae NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic 1.1.1.267 0.667
2f1k NAPPrephenate dehydrogenase / 0.666
3c3x NAPEugenol synthase 1 1.1.1.318 0.666
1jn0 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.665
3b20 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.665
4oqy NDP(S)-imine reductase / 0.665
3cif NADGlyceraldehyde-3-phosphate dehydrogenase / 0.664
2vyn NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.663
4e5p NADPhosphonate dehydrogenase 1.20.1.1 0.663
2ep7 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.662
3a9w NADNDP-sugar epimerase / 0.662
2b4q NAPRhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase 1.1.1.100 0.661
2ahr NAPPyrroline-5-carboxylate reductase / 0.660
2dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.660
1rm4 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.659
1wp4 NDP3-hydroxyisobutyrate dehydrogenase / 0.659
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.659
4xrg NADHomospermidine synthase 2.5.1.44 0.659
3ikt NADRedox-sensing transcriptional repressor Rex / 0.658
1vsv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.657
3cea NADMyo-inositol 2-dehydrogenase-like (Promiscuous) / 0.657
3v1y NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.657
4b65 NDPL-ornithine N(5)-monooxygenase / 0.657
2glx NDP1,5-anhydro-D-fructose reductase / 0.656
3baz NAPHydroxyphenylpyruvate reductase 1.1.1.237 0.656
5a02 NAPGlucose-fructose oxidoreductase / 0.656
1yon A2R2-dehydropantoate 2-reductase 1.1.1.169 0.655
1gq2 NAPNADP-dependent malic enzyme 1.1.1.40 0.654
3ggp NADPrephenate dehydrogenase / 0.654
3ras NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase / 0.654
4hp8 NAP2-deoxy-D-gluconate 3-dehydrogenase / 0.654
5eio NAP[LysW]-L-2-aminoadipate 6-phosphate reductase / 0.654
1o8c NDPProbable acrylyl-CoA reductase AcuI 1.3.1.84 0.653
1t2a NDPGDP-mannose 4,6 dehydratase 4.2.1.47 0.653
2fl2 ADPKinesin-like protein KIF11 / 0.653
3wbf NAPMeso-diaminopimelate D-dehydrogenase / 0.653
4a1z ADPKinesin-like protein KIF11 / 0.653
4l4x NDPAmphI / 0.653
1pjc NADAlanine dehydrogenase / 0.652
3anl NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase 1.1.1.267 0.652
3abi NADUncharacterized protein / 0.651
1mez GDPAdenylosuccinate synthetase isozyme 1 / 0.650
3a14 NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase / 0.650
3bts NADGalactose/lactose metabolism regulatory protein GAL80 / 0.650
3i6q NDPPutative leucoanthocyanidin reductase 1 / 0.650
4o63 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.650