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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
3mvq NDP Glutamate dehydrogenase 1, mitochondrial 1.4.1.3

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3mvq NDPGlutamate dehydrogenase 1, mitochondrial 1.4.1.3 1.320
4xgi NADGlutamate dehydrogenase / 0.933
3pef NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.745
2vq3 NAPMetalloreductase STEAP3 / 0.741
4xb2 NDP319aa long hypothetical homoserine dehydrogenase / 0.736
3etg NDPGlutamate dehydrogenase 1, mitochondrial 1.4.1.3 0.735
1i36 NAPConserved protein / 0.726
3ggp NADPrephenate dehydrogenase / 0.723
5ijz NAPNADP-specific glutamate dehydrogenase 1.4.1.4 0.711
1npd NADQuinate/shikimate dehydrogenase / 0.705
3t4e NADQuinate/shikimate dehydrogenase / 0.704
1o9b NAIQuinate/shikimate dehydrogenase / 0.702
1vi2 NADQuinate/shikimate dehydrogenase / 0.702
3h3j NADL-lactate dehydrogenase 1 1.1.1.27 0.702
4nu5 NADPhosphonate dehydrogenase 1.20.1.1 0.702
4xb1 NDP319aa long hypothetical homoserine dehydrogenase / 0.702
3phi NDPShikimate dehydrogenase (NADP(+)) / 0.700
3anm NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase 1.1.1.267 0.697
5eio NAP[LysW]-L-2-aminoadipate 6-phosphate reductase / 0.694
1hwz NDPGlutamate dehydrogenase 1, mitochondrial 1.4.1.3 0.692
1yjq NAP2-dehydropantoate 2-reductase 1.1.1.169 0.690
3two NDPMannitol dehydrogenase / 0.687
1c1d NAIPhenylalanine dehydrogenase / 0.685
2ixb NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.685
5a02 NAPGlucose-fructose oxidoreductase / 0.684
4dpl NAPMalonyl-CoA reductase 1.2.1.75 0.683
1wp4 NDP3-hydroxyisobutyrate dehydrogenase / 0.682
2cvz NDP3-hydroxyisobutyrate dehydrogenase / 0.682
2jd1 NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase / 0.681
1nyt NAPShikimate dehydrogenase (NADP(+)) / 0.680
3a14 NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase / 0.680
1q0q NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase 1.1.1.267 0.679
1yqx NAPSinapyl alcohol dehydrogenase / 0.677
4wji NAPPutative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase / 0.677
3zhb NAPPutative dehydrogenase / 0.676
3zcx NADGlyceraldehyde-3-phosphate dehydrogenase / 0.675
4qec NAPElxO / 0.675
3keq NADRedox-sensing transcriptional repressor Rex / 0.674
4nfs NAJAlcohol dehydrogenase E chain 1.1.1.1 0.673
1f0y NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.670
4o63 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.670
3hwr NDP2-dehydropantoate 2-reductase / 0.669
4ng5 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.669
1h6b NDPGlucose--fructose oxidoreductase 1.1.99.28 0.668
4nu6 NADPhosphonate dehydrogenase 1.20.1.1 0.668
1e5q NDPSaccharopine dehydrogenase [NADP(+), L-glutamate-forming] 1.5.1.10 0.666
3ing NDPHomoserine dehydrogenase related protein / 0.666
1hyh NADL-2-hydroxyisocaproate dehydrogenase / 0.664
2rcy NAPPyrroline-5-carboxylate reductase / 0.664
3geg NADShort-chain dehydrogenase/reductase SDR / 0.664
3ggo NAIPrephenate dehydrogenase / 0.664
1yqd NAPSinapyl alcohol dehydrogenase / 0.663
3nt2 NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.663
4kug NAD3-hydroxybutyryl-CoA dehydrogenase / 0.663
3dtt NAPNADP oxidoreductase, coenzyme F420-dependent / 0.662
5a05 NDPGlucose-fructose oxidoreductase / 0.662
4jbi NDPAlcohol dehydrogenase (Zinc) / 0.660
1qr6 NADNAD-dependent malic enzyme, mitochondrial 1.1.1.38 0.659
3iup NDPPossible NADH oxidoreductase / 0.659
4b8w NAPGDP-L-fucose synthase 1.1.1.271 0.658
5a03 NDPGlucose-fructose oxidoreductase / 0.658
2nad NADFormate dehydrogenase / 0.657
2yjz NAPMetalloreductase STEAP4 1.16.1 0.657
4tvb NADHomospermidine synthase 2.5.1.44 0.657
1pj2 NAINAD-dependent malic enzyme, mitochondrial 1.1.1.38 0.656
3cin NADMyo-inositol-1-phosphate synthase-related protein / 0.656
4xrg NADHomospermidine synthase 2.5.1.44 0.656
4oqy NDP(S)-imine reductase / 0.655
4y0k NAPAntE / 0.655
1j5p NADL-aspartate dehydrogenase 1.4.1.21 0.654
3o9z NADLipopolysaccaride biosynthesis protein wbpB / 0.654
4bkq NAIEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.654
5doz NDPJamJ / 0.654
1a71 NADAlcohol dehydrogenase E chain 1.1.1.1 0.653
1n7g NDPGDP-mannose 4,6 dehydratase 2 4.2.1.47 0.653
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.653
3p19 NDPPutative blue fluorescent protein / 0.653
3pdu NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.652
3wfj NAD2-dehydropantoate 2-reductase / 0.652
4e5m NAPPhosphonate dehydrogenase 1.20.1.1 0.652
1hdg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.651
1nfr NAD3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase 1.1.1.53 0.651
1vc2 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.651
4ebf NADPhosphonate dehydrogenase 1.20.1.1 0.651
4xyb NDPFormate dehydrogenase / 0.651
2ph5 NADHomospermidine synthase / 0.650
2q3e NAIUDP-glucose 6-dehydrogenase 1.1.1.22 0.650
4boy NADGlyceraldehyde-3-phosphate dehydrogenase / 0.650
4imp NDPPolyketide synthase extender modules 3-4 / 0.650