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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
2nad NAD Formate dehydrogenase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2nad NADFormate dehydrogenase / 1.266
2gsd NADFormate dehydrogenase / 1.252
4xyb NDPFormate dehydrogenase / 1.069
4xye NADFormate dehydrogenase / 1.040
3n7u NADFormate dehydrogenase, chloroplastic/mitochondrial / 0.878
4e5k NADPhosphonate dehydrogenase 1.20.1.1 0.782
4e5m NAPPhosphonate dehydrogenase 1.20.1.1 0.756
4e5n NADPhosphonate dehydrogenase 1.20.1.1 0.756
4nu6 NADPhosphonate dehydrogenase 1.20.1.1 0.752
3baz NAPHydroxyphenylpyruvate reductase 1.1.1.237 0.748
2o4c NADErythronate-4-phosphate dehydrogenase / 0.743
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.740
4z0p NDPNAD-dependent dehydrogenase / 0.740
1r37 NADNAD-dependent alcohol dehydrogenase 1.1.1.1 0.738
3kb6 NADD-lactate dehydrogenase / 0.735
3wv7 ADPHmd co-occurring protein HcgE / 0.735
2dt5 NADRedox-sensing transcriptional repressor Rex / 0.729
2ixb NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.726
4jbi NDPAlcohol dehydrogenase (Zinc) / 0.721
4j43 NADUncharacterized protein / 0.718
4j49 NADUncharacterized protein / 0.718
2dbq NAPGlyoxylate reductase 1.1.1.26 0.715
4gkv NADAlcohol dehydrogenase, propanol-preferring 1.1.1.1 0.715
4tvb NADHomospermidine synthase 2.5.1.44 0.715
1pzh NADLactate dehydrogenase / 0.713
4xq9 NADHomospermidine synthase 2.5.1.44 0.711
4jk3 NADUncharacterized protein / 0.710
4weq NAPNAD-dependent dehydrogenase / 0.709
4xcv NDPProbable hydroxyacid dehydrogenase protein / 0.709
1j5p NADL-aspartate dehydrogenase 1.4.1.21 0.708
1sow NADL-lactate dehydrogenase 1.1.1.27 0.708
1p1h NADInositol-3-phosphate synthase 5.5.1.4 0.707
5bqf NAPProbable hydroxyacid dehydrogenase protein / 0.703
1t2d NADL-lactate dehydrogenase 1.1.1.27 0.701
4plp NADHomospermidine synthase 2.5.1.44 0.701
1kvr NADUDP-glucose 4-epimerase 5.1.3.2 0.699
1wwk NAD307aa long hypothetical phosphoglycerate dehydrogenase / 0.698
2dfd NADMalate dehydrogenase, mitochondrial 1.1.1.37 0.698
4j4b NAIUncharacterized protein / 0.698
1nai NADUDP-glucose 4-epimerase 5.1.3.2 0.695
3o9z NADLipopolysaccaride biosynthesis protein wbpB / 0.695
4xqc NADHomospermidine synthase 2.5.1.44 0.695
5a1t NAIL-lactate dehydrogenase / 0.694
2ekl NADD-3-phosphoglycerate dehydrogenase / 0.693
4j49 NAIUncharacterized protein / 0.693
2dc1 NADProbable L-aspartate dehydrogenase / 0.692
2fn7 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.692
4k28 NADShikimate dehydrogenase family protein / 0.692
4xrg NADHomospermidine synthase 2.5.1.44 0.691
3oet NADErythronate-4-phosphate dehydrogenase / 0.690
1c1d NAIPhenylalanine dehydrogenase / 0.686
4wlv NADMalate dehydrogenase, mitochondrial 1.1.1.37 0.686
2x0r NADMalate dehydrogenase / 0.684
4e5p NADPhosphonate dehydrogenase 1.20.1.1 0.683
1u7h NADPutative ornithine cyclodeaminase / 0.680
1kol NADGlutathione-independent formaldehyde dehydrogenase / 0.679
1dss NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.678
4nd3 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.677
3kbo NDPGlyoxylate/hydroxypyruvate reductase A / 0.676
3aw9 NADNAD-dependent epimerase/dehydratase / 0.675
3jyo NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.675
4i1i NADMalate dehydrogenase / 0.675
4jnk NAIL-lactate dehydrogenase A chain 1.1.1.27 0.674
1lld NADL-lactate dehydrogenase 2 1.1.1.27 0.673
2pa3 NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.673
2vhx NADAlanine dehydrogenase 1.4.1.1 0.673
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.673
4w6z 8IDAlcohol dehydrogenase 1 1.1.1.1 0.673
2pv7 NADT-protein 1.3.1.12 0.672
1pl8 NADSorbitol dehydrogenase 1.1.1.14 0.671
1ie3 NADMalate dehydrogenase / 0.670
2g76 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.670
3m6i NADL-arabinitol 4-dehydrogenase 1.1.1.12 0.670
2vhv NAIAlanine dehydrogenase 1.4.1.1 0.669
4c4o NADSADH / 0.669
5ig2 NADShort-chain dehydrogenase/reductase SDR / 0.669
2dfv NADL-threonine 3-dehydrogenase / 0.668
2dvm NAD439aa long hypothetical malate oxidoreductase (NAD) [malic enzyme] / 0.668
4nd4 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.668
5doz NDPJamJ / 0.668
1pl6 NADSorbitol dehydrogenase 1.1.1.14 0.667
3jyp NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.667
3dmt NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.665
3phi NDPShikimate dehydrogenase (NADP(+)) / 0.665
4njo NADD-3-phosphoglycerate dehydrogenase, putative / 0.665
2voj NADAlanine dehydrogenase 1.4.1.1 0.664
3cif NADGlyceraldehyde-3-phosphate dehydrogenase / 0.664
3rfx NADUronate dehydrogenase / 0.664
1mp0 NADAlcohol dehydrogenase class-3 1.1.1.1 0.662
3cmc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.661
1sc6 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.660
2dbr NAPGlyoxylate reductase 1.1.1.26 0.660
3g5s FADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO / 0.659
1h6d NDPGlucose--fructose oxidoreductase 1.1.99.28 0.658
3zdf NADGlyceraldehyde-3-phosphate dehydrogenase / 0.658
1psd NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.657
3jv7 NADSecondary alcohol dehydrogenase / 0.657
3mvq NDPGlutamate dehydrogenase 1, mitochondrial 1.4.1.3 0.657
1lde NADAlcohol dehydrogenase E chain 1.1.1.1 0.656
3b1j NADGlyceraldehyde-3-phosphate dehydrogenase / 0.656
3wsw NADL-lactate dehydrogenase / 0.656
1j0x NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.655
1orr NADCDP-paratose 2-epimerase / 0.655
2x0i NAIMalate dehydrogenase / 0.655
2p9g NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.654
1p31 EPUUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.653
1x7d NADPutative ornithine cyclodeaminase / 0.653
3cin NADMyo-inositol-1-phosphate synthase-related protein / 0.653
3cps NADGlyceraldehyde-3-phosphate dehydrogenase / 0.653
4o63 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.653
5c7o NADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific 1.2.1.12 0.653
1o6z NADMalate dehydrogenase / 0.652
2fkn NADUrocanate hydratase 4.2.1.49 0.652
3tnl NADShikimate dehydrogenase (NADP(+)) / 0.652
4cr8 NADN-acylmannosamine 1-dehydrogenase 1.1.1.233 0.652
4xba 5GPAprataxin-like protein 3 0.652
1ib6 NADMalate dehydrogenase / 0.651
2vhz NAIAlanine dehydrogenase 1.4.1.1 0.650
3pef NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.650
3qw2 NADMyo-inositol-1-phosphate synthase (Ino1) / 0.650