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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
1nyt NAP Shikimate dehydrogenase (NADP(+))

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1nyt NAPShikimate dehydrogenase (NADP(+)) / 1.328
2hk9 ATRShikimate dehydrogenase (NADP(+)) / 0.908
2ev9 NAPShikimate dehydrogenase (NADP(+)) / 0.878
3phi NDPShikimate dehydrogenase (NADP(+)) / 0.867
2hk9 NAPShikimate dehydrogenase (NADP(+)) / 0.866
2cy0 NAPShikimate dehydrogenase (NADP(+)) / 0.831
2jkv NAP6-phosphogluconate dehydrogenase, decarboxylating 1.1.1.44 0.821
3tnl NADShikimate dehydrogenase (NADP(+)) / 0.812
3t4e NADQuinate/shikimate dehydrogenase / 0.811
4bv9 NDPKetimine reductase mu-crystallin 1.5.1.25 0.778
4oqy NDP(S)-imine reductase / 0.754
5idw NAPShort-chain dehydrogenase/reductase SDR / 0.735
4y0k NAPAntE / 0.730
1o9b NAIQuinate/shikimate dehydrogenase / 0.721
1vi2 NADQuinate/shikimate dehydrogenase / 0.721
3bhi NAPCarbonyl reductase [NADPH] 1 1.1.1.184 0.720
3toz NADShikimate dehydrogenase (NADP(+)) / 0.719
1hdo NAPFlavin reductase (NADPH) / 0.718
1npd NADQuinate/shikimate dehydrogenase / 0.715
3o26 NDPSalutaridine reductase / 0.714
4y1b NAPAntE / 0.712
2iyp A2P6-phosphogluconate dehydrogenase, decarboxylating 1.1.1.44 0.705
2ph5 NADHomospermidine synthase / 0.705
4xqc NADHomospermidine synthase 2.5.1.44 0.698
4plp NADHomospermidine synthase 2.5.1.44 0.697
3f3s NADLambda-crystallin homolog / 0.690
4ovi N01Phenylacetone monooxygenase 1.14.13.92 0.690
1pjc NADAlanine dehydrogenase / 0.689
3iah NAPPutative oxoacyl-(Acyl carrier protein) reductase / 0.689
3dtt NAPNADP oxidoreductase, coenzyme F420-dependent / 0.688
4oaq NDPR-specific carbonyl reductase / 0.688
4tvb NADHomospermidine synthase 2.5.1.44 0.688
1nvt NAPShikimate dehydrogenase (NADP(+)) / 0.687
4xq9 NADHomospermidine synthase 2.5.1.44 0.686
4k28 NADShikimate dehydrogenase family protein / 0.685
4nfs NAJAlcohol dehydrogenase E chain 1.1.1.1 0.685
4xrg NADHomospermidine synthase 2.5.1.44 0.685
1guf NDPEnoyl-[acyl-carrier-protein] reductase 1, mitochondrial 1.3.1.10 0.684
3lzx NAPFerredoxin--NADP reductase 2 1.18.1.2 0.683
4ng5 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.682
3mvq NDPGlutamate dehydrogenase 1, mitochondrial 1.4.1.3 0.680
3pdu NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.679
4a5l NDPThioredoxin reductase / 0.679
4dwv NAJAlcohol dehydrogenase E chain 1.1.1.1 0.675
4nd4 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.675
4u7w NDPMxaA / 0.675
2vqb NAPPutative flavin-containing monooxygenase / 0.673
2q0l NAPThioredoxin reductase 1.8.1.9 0.672
5a9s NAPPutative dehydrogenase / 0.672
2c0c NAPProstaglandin reductase 3 1 0.669
2vhz NAIAlanine dehydrogenase 1.4.1.1 0.669
4hp8 NAP2-deoxy-D-gluconate 3-dehydrogenase / 0.669
3zhb NAPPutative dehydrogenase / 0.667
1p0f NAPNADP-dependent alcohol dehydrogenase 1.1.1.2 0.666
2vq3 NAPMetalloreductase STEAP3 / 0.666
5ijz NAPNADP-specific glutamate dehydrogenase 1.4.1.4 0.664
4gcm NAPThioredoxin reductase 1.8.1.9 0.663
3gwd NAPCyclohexanone monooxygenase / 0.662
3pef NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.662
4fda NAP3-oxoacyl-[acyl-carrier-protein] reductase 1.1.1.100 0.661
5kcz NAJAlcohol dehydrogenase E chain 1.1.1.1 0.660
4gkv NADAlcohol dehydrogenase, propanol-preferring 1.1.1.1 0.659
2c3c NAP2-oxopropyl-CoM reductase, carboxylating 1.8.1.5 0.658
1h6d NDPGlucose--fructose oxidoreductase 1.1.99.28 0.657
1qmg APXKetol-acid reductoisomerase, chloroplastic 1.1.1.86 0.657
2ylt NAPPhenylacetone monooxygenase 1.14.13.92 0.657
4d03 NAPPhenylacetone monooxygenase 1.14.13.92 0.657
4d04 NAPPhenylacetone monooxygenase 1.14.13.92 0.657
1f0y NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.656
2vhx NADAlanine dehydrogenase 1.4.1.1 0.656
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.655
4j49 NAIUncharacterized protein / 0.655
5fwn NAPPutative dehydrogenase / 0.655
1t2a NDPGDP-mannose 4,6 dehydratase 4.2.1.47 0.654
4dlb NADS-(hydroxymethyl)glutathione dehydrogenase / 0.654
4e5k NADPhosphonate dehydrogenase 1.20.1.1 0.654
1ur5 NADMalate dehydrogenase / 0.653
2iyp NAP6-phosphogluconate dehydrogenase, decarboxylating 1.1.1.44 0.653
2xlt NA0Putative flavin-containing monooxygenase / 0.653
3keo NADRedox-sensing transcriptional repressor Rex / 0.653
4b7x NAPProbable oxidoreductase / 0.653
1n5d NDPCarbonyl reductase [NADPH] 1 / 0.652
2wba NDPTrypanothione reductase 1.8.1.12 0.652
3ngl NAPBifunctional protein FolD / 0.652
4hfm NAP2-alkenal reductase (NADP(+)-dependent) / 0.652
4wji NAPPutative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase / 0.652
5doz NDPJamJ / 0.652
1u5a BIKL-lactate dehydrogenase 1.1.1.27 0.651
4qed NAPElxO / 0.651
1a71 NADAlcohol dehydrogenase E chain 1.1.1.1 0.650
1f9a ATPNicotinamide-nucleotide adenylyltransferase / 0.650
2y05 NAPProstaglandin reductase 1 / 0.650