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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
2gsd NAD Formate dehydrogenase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2gsd NADFormate dehydrogenase / 1.298
2nad NADFormate dehydrogenase / 1.252
4xyb NDPFormate dehydrogenase / 0.980
4xye NADFormate dehydrogenase / 0.937
3n7u NADFormate dehydrogenase, chloroplastic/mitochondrial / 0.848
4e5n NADPhosphonate dehydrogenase 1.20.1.1 0.807
4e5k NADPhosphonate dehydrogenase 1.20.1.1 0.788
4nu5 NADPhosphonate dehydrogenase 1.20.1.1 0.788
2dt5 NADRedox-sensing transcriptional repressor Rex / 0.786
4tvb NADHomospermidine synthase 2.5.1.44 0.767
4j49 NADUncharacterized protein / 0.763
3wv7 ADPHmd co-occurring protein HcgE / 0.762
3wv8 ATPHmd co-occurring protein HcgE / 0.761
4j43 NADUncharacterized protein / 0.759
4e5m NAPPhosphonate dehydrogenase 1.20.1.1 0.758
3baz NAPHydroxyphenylpyruvate reductase 1.1.1.237 0.754
4nu6 NADPhosphonate dehydrogenase 1.20.1.1 0.749
2o4c NADErythronate-4-phosphate dehydrogenase / 0.747
1hku NADC-terminal-binding protein 1 1.1.1 0.746
4j49 NAIUncharacterized protein / 0.744
1j5p NADL-aspartate dehydrogenase 1.4.1.21 0.743
2ixb NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.735
3kb6 NADD-lactate dehydrogenase / 0.729
1p1h NADInositol-3-phosphate synthase 5.5.1.4 0.728
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.727
4gkv NADAlcohol dehydrogenase, propanol-preferring 1.1.1.1 0.726
4z0p NDPNAD-dependent dehydrogenase / 0.726
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.725
4jbi NDPAlcohol dehydrogenase (Zinc) / 0.721
1r37 NADNAD-dependent alcohol dehydrogenase 1.1.1.1 0.716
2ekl NADD-3-phosphoglycerate dehydrogenase / 0.716
4weq NAPNAD-dependent dehydrogenase / 0.712
1kol NADGlutathione-independent formaldehyde dehydrogenase / 0.711
4plp NADHomospermidine synthase 2.5.1.44 0.708
1sow NADL-lactate dehydrogenase 1.1.1.27 0.707
3d64 NADAdenosylhomocysteinase / 0.707
1o6z NADMalate dehydrogenase / 0.705
1x7d NADPutative ornithine cyclodeaminase / 0.702
1kvr NADUDP-glucose 4-epimerase 5.1.3.2 0.700
4jk3 NADUncharacterized protein / 0.700
2dfv NADL-threonine 3-dehydrogenase / 0.696
4xrg NADHomospermidine synthase 2.5.1.44 0.696
1nai NADUDP-glucose 4-epimerase 5.1.3.2 0.695
2dc1 NADProbable L-aspartate dehydrogenase / 0.695
2fkn NADUrocanate hydratase 4.2.1.49 0.694
4xwz FADFructosyl amine:oxygen oxidoreductase / 0.693
1yba NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.692
3oq6 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.691
4xqc NADHomospermidine synthase 2.5.1.44 0.691
1p31 EPUUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.690
4k28 NADShikimate dehydrogenase family protein / 0.690
2yg5 FADPutrescine oxidase / 0.689
5bqf NAPProbable hydroxyacid dehydrogenase protein / 0.689
1wwk NAD307aa long hypothetical phosphoglycerate dehydrogenase / 0.688
4wct FADFructosyl amine:oxygen oxidoreductase / 0.688
1c1d NAIPhenylalanine dehydrogenase / 0.687
2vou FAD2,6-dihydroxypyridine 3-monooxygenase 1.14.13.10 0.687
4wlu NADMalate dehydrogenase, mitochondrial 1.1.1.37 0.687
1u7h NADPutative ornithine cyclodeaminase / 0.686
2dbr NAPGlyoxylate reductase 1.1.1.26 0.686
2fn7 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.685
2hu2 NADC-terminal binding protein 1 / 0.685
1lld NADL-lactate dehydrogenase 2 1.1.1.27 0.684
3kbo NDPGlyoxylate/hydroxypyruvate reductase A / 0.684
3pgx NADUncharacterized NAD-dependent oxidoreductase MAP_4146 / 0.684
4c4o NADSADH / 0.684
1sc6 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.683
1uxj NADMalate dehydrogenase / 0.683
4njo NADD-3-phosphoglycerate dehydrogenase, putative / 0.683
2xve FADPutative flavin-containing monooxygenase / 0.681
4dwv NAJAlcohol dehydrogenase E chain 1.1.1.1 0.681
3g5q FADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO / 0.680
4nfs NAJAlcohol dehydrogenase E chain 1.1.1.1 0.680
1t2d NADL-lactate dehydrogenase 1.1.1.27 0.679
4lcj NADC-terminal-binding protein 2 / 0.679
4twr NADNAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase / 0.679
1b8v NADMalate dehydrogenase / 0.678
4jnk NAIL-lactate dehydrogenase A chain 1.1.1.27 0.678
1a71 NADAlcohol dehydrogenase E chain 1.1.1.1 0.677
2jb2 FADL-amino acid oxidase / 0.677
4yac NAIC alpha-dehydrogenase / 0.677
1hld NADAlcohol dehydrogenase E chain 1.1.1.1 0.676
1pl6 NADSorbitol dehydrogenase 1.1.1.14 0.676
5doz NDPJamJ / 0.676
2i9k SAHModification methylase HhaI 2.1.1.37 0.675
3jyo NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.675
2vyn NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.674
4cuk NAID-lactate dehydrogenase / 0.672
1yqd NAPSinapyl alcohol dehydrogenase / 0.671
3jv7 NADSecondary alcohol dehydrogenase / 0.671
4xba 5GPAprataxin-like protein 3 0.670
1bw9 NADPhenylalanine dehydrogenase / 0.669
1pl8 NADSorbitol dehydrogenase 1.1.1.14 0.669
2q1s NAIPutative nucleotide sugar epimerase/ dehydratase / 0.669
5j23 A2RPutative 2-hydroxyacid dehydrogenase / 0.669
1o9b NAIQuinate/shikimate dehydrogenase / 0.668
1wam FADUDP-galactopyranose mutase 5.4.99.9 0.668
1f8w FADNADH peroxidase 1.11.1.1 0.667
1nah NADUDP-glucose 4-epimerase 5.1.3.2 0.667
1nhq FADNADH peroxidase 1.11.1.1 0.667
1nhr FADNADH peroxidase 1.11.1.1 0.667
2dvm NAD439aa long hypothetical malate oxidoreductase (NAD) [malic enzyme] / 0.666
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.666
4ynt FDAGlucose oxidase, putative / 0.666
3tm4 SAMUncharacterized protein / 0.665
4nd2 A3DLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.665
4nd4 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.665
4nfh NAJAlcohol dehydrogenase E chain 1.1.1.1 0.665
5kcz NAJAlcohol dehydrogenase E chain 1.1.1.1 0.665
1i3l NADUDP-glucose 4-epimerase / 0.664
1lde NADAlcohol dehydrogenase E chain 1.1.1.1 0.664
2g76 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.664
4ng5 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.664
2dbq NAPGlyoxylate reductase 1.1.1.26 0.663
3pef NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.663
5cdt NAJAlcohol dehydrogenase E chain 1.1.1.1 0.663
2vhz NAIAlanine dehydrogenase 1.4.1.1 0.662
2zcj SAHModification methylase HhaI 2.1.1.37 0.662
3ish FADThioredoxin reductase 1.8.1.9 0.662
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.662
4e5p NADPhosphonate dehydrogenase 1.20.1.1 0.662
2vhx NADAlanine dehydrogenase 1.4.1.1 0.661
3oet NADErythronate-4-phosphate dehydrogenase / 0.661
3nt4 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.660
4o59 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.660
3m6i NADL-arabinitol 4-dehydrogenase 1.1.1.12 0.659
5kjc NAJAlcohol dehydrogenase E chain 1.1.1.1 0.659
1q0q NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase 1.1.1.267 0.658
2ome NADC-terminal-binding protein 2 / 0.658
2q1w NADPutative nucleotide sugar epimerase/ dehydratase / 0.658
3adp NAILambda-crystallin 1.1.1.45 0.658
3cos NADAlcohol dehydrogenase 4 1.1.1.1 0.658
3ict FADCoenzyme A disulfide reductase / 0.658
3qw2 NADMyo-inositol-1-phosphate synthase (Ino1) / 0.658
3rfx NADUronate dehydrogenase / 0.658
5ig2 NADShort-chain dehydrogenase/reductase SDR / 0.658
6adh NADAlcohol dehydrogenase E chain 1.1.1.1 0.658
2q1t NADPutative nucleotide sugar epimerase/ dehydratase / 0.657
3wsw NADL-lactate dehydrogenase / 0.657
1npd NADQuinate/shikimate dehydrogenase / 0.656
2vhv NAIAlanine dehydrogenase 1.4.1.1 0.655
4emw FADCoenzyme A disulfide reductase / 0.655
4ywj NAD4-hydroxy-tetrahydrodipicolinate reductase / 0.655
1hdg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.654
1xcb NADRedox-sensing transcriptional repressor Rex / 0.654
4rtk SAHDNA adenine methylase 2.1.1.72 0.654
3ikt NADRedox-sensing transcriptional repressor Rex / 0.653
3tnl NADShikimate dehydrogenase (NADP(+)) / 0.653
1ib6 NADMalate dehydrogenase / 0.652
1ie3 NADMalate dehydrogenase / 0.652
2gcg NDPGlyoxylate reductase/hydroxypyruvate reductase 1.1.1.79 0.652
3nta FADFAD-dependent pyridine nucleotide-disulphide oxidoreductase / 0.652
3o9z NADLipopolysaccaride biosynthesis protein wbpB / 0.652
5c7o NADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific 1.2.1.12 0.652
1h6d NDPGlucose--fructose oxidoreductase 1.1.99.28 0.651
3gvi ADPMalate dehydrogenase / 0.651
4cr8 NADN-acylmannosamine 1-dehydrogenase 1.1.1.233 0.651
4j4b NAIUncharacterized protein / 0.651
5mdh NADMalate dehydrogenase, cytoplasmic 1.1.1.37 0.651
1h2h NADL-aspartate dehydrogenase 1.4.1.21 0.650
1yqx NAPSinapyl alcohol dehydrogenase / 0.650
3m2t NADProbable dehydrogenase / 0.650
4w6z 8IDAlcohol dehydrogenase 1 1.1.1.1 0.650