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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
4tvb NAD Homospermidine synthase 2.5.1.44

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4tvb NADHomospermidine synthase 2.5.1.44 1.320
4xqc NADHomospermidine synthase 2.5.1.44 1.270
4plp NADHomospermidine synthase 2.5.1.44 1.261
4xrg NADHomospermidine synthase 2.5.1.44 1.255
4xq9 NADHomospermidine synthase 2.5.1.44 1.232
2gsd NADFormate dehydrogenase / 0.767
1hyh NADL-2-hydroxyisocaproate dehydrogenase / 0.756
3abi NADUncharacterized protein / 0.753
3oet NADErythronate-4-phosphate dehydrogenase / 0.752
2o4c NADErythronate-4-phosphate dehydrogenase / 0.749
1u7h NADPutative ornithine cyclodeaminase / 0.748
1x7d NADPutative ornithine cyclodeaminase / 0.741
4jk3 NADUncharacterized protein / 0.732
3pdu NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.731
5lc1 NADL-threonine 3-dehydrogenase / 0.727
2ekl NADD-3-phosphoglycerate dehydrogenase / 0.726
2ph5 NADHomospermidine synthase / 0.726
1e5q NDPSaccharopine dehydrogenase [NADP(+), L-glutamate-forming] 1.5.1.10 0.725
4e5n NADPhosphonate dehydrogenase 1.20.1.1 0.724
1gv0 NADMalate dehydrogenase / 0.723
4ng5 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.723
1guy NADMalate dehydrogenase / 0.722
4nfs NAJAlcohol dehydrogenase E chain 1.1.1.1 0.720
2g76 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.719
4j43 NADUncharacterized protein / 0.718
4e5m NAPPhosphonate dehydrogenase 1.20.1.1 0.717
1gd1 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.715
2nad NADFormate dehydrogenase / 0.715
2ixb NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.713
1i2b NADUDP-sulfoquinovose synthase, chloroplastic 3.13.1.1 0.711
1pjc NADAlanine dehydrogenase / 0.710
4oaq NDPR-specific carbonyl reductase / 0.708
4j49 NADUncharacterized protein / 0.707
3aw9 NADNAD-dependent epimerase/dehydratase / 0.706
4b7x NAPProbable oxidoreductase / 0.706
3qvs NADMyo-inositol-1-phosphate synthase (Ino1) / 0.705
5kjf NAJAlcohol dehydrogenase E chain 1.1.1.1 0.705
1o6z NADMalate dehydrogenase / 0.704
4dwv NAJAlcohol dehydrogenase E chain 1.1.1.1 0.704
4gkv NADAlcohol dehydrogenase, propanol-preferring 1.1.1.1 0.704
5kcz NAJAlcohol dehydrogenase E chain 1.1.1.1 0.704
1lld NADL-lactate dehydrogenase 2 1.1.1.27 0.703
5cdg NAJAlcohol dehydrogenase E chain 1.1.1.1 0.703
2dc1 NADProbable L-aspartate dehydrogenase / 0.702
1yqd NAPSinapyl alcohol dehydrogenase / 0.701
3cmc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.701
4xb2 NDP319aa long hypothetical homoserine dehydrogenase / 0.701
2vyv NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.700
3w6u NAP6-phosphogluconate dehydrogenase, NAD-binding protein / 0.696
4y0k NAPAntE / 0.696
4y1b NAPAntE / 0.696
1p1h NADInositol-3-phosphate synthase 5.5.1.4 0.695
2ohx NADAlcohol dehydrogenase E chain 1.1.1.1 0.695
3ggp NADPrephenate dehydrogenase / 0.695
4bv9 NDPKetimine reductase mu-crystallin 1.5.1.25 0.695
4w6z 8IDAlcohol dehydrogenase 1 1.1.1.1 0.695
4hfm NAP2-alkenal reductase (NADP(+)-dependent) / 0.694
4jbi NDPAlcohol dehydrogenase (Zinc) / 0.694
4nfh NAJAlcohol dehydrogenase E chain 1.1.1.1 0.693
1nqa NADGlyceraldehyde-3-phosphate dehydrogenase / 0.692
1yb5 NAPQuinone oxidoreductase 1.6.5.5 0.692
2ome NADC-terminal-binding protein 2 / 0.692
3l8k ADPDihydrolipoamide dehydrogenase (PdhD-3) / 0.692
5cdt NAJAlcohol dehydrogenase E chain 1.1.1.1 0.692
3jyq NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.691
3n7u NADFormate dehydrogenase, chloroplastic/mitochondrial / 0.691
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.690
1ur5 NADMalate dehydrogenase / 0.689
5kcp NAJAlcohol dehydrogenase E chain 1.1.1.1 0.689
1nyt NAPShikimate dehydrogenase (NADP(+)) / 0.688
3cin NADMyo-inositol-1-phosphate synthase-related protein / 0.688
1mgo NADAlcohol dehydrogenase E chain 1.1.1.1 0.687
3oc4 FADOxidoreductase, pyridine nucleotide-disulfide family / 0.687
5kjc NAJAlcohol dehydrogenase E chain 1.1.1.1 0.687
5kje NAJAlcohol dehydrogenase E chain 1.1.1.1 0.686
2x6t NAPADP-L-glycero-D-manno-heptose-6-epimerase / 0.685
3qvx NADMyo-inositol-1-phosphate synthase (Ino1) / 0.685
1hld NADAlcohol dehydrogenase E chain 1.1.1.1 0.684
3d4p NADL-lactate dehydrogenase 1 1.1.1.27 0.684
3rfx NADUronate dehydrogenase / 0.684
1a71 NADAlcohol dehydrogenase E chain 1.1.1.1 0.682
1hku NADC-terminal-binding protein 1 1.1.1 0.682
1c1d NAIPhenylalanine dehydrogenase / 0.681
1geg NADDiacetyl reductase [(S)-acetoin forming] 1.1.1.304 0.681
1la2 NADInositol-3-phosphate synthase 5.5.1.4 0.681
3kve FADL-amino-acid oxidase / 0.680
4e5k NADPhosphonate dehydrogenase 1.20.1.1 0.679
4xb1 NDP319aa long hypothetical homoserine dehydrogenase / 0.679
3nt4 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.678
2vyn NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.677
3tqh NDPQuinone oxidoreductase / 0.677
1cdo NADAlcohol dehydrogenase 1 1.1.1.1 0.676
3had NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.676
3w8e NAD3-hydroxybutyrate dehydrogenase / 0.676
2oxi NADAlcohol dehydrogenase E chain 1.1.1.1 0.675
3wv8 ATPHmd co-occurring protein HcgE / 0.675
4yr9 NADL-threonine 3-dehydrogenase, mitochondrial 1.1.1.103 0.675
3oq6 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.674
3pef NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.674
3doc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.673
5kj1 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.673
4bk3 FADProbable salicylate monooxygenase / 0.672
4dxh NAJAlcohol dehydrogenase E chain 1.1.1.1 0.672
4xd2 NAIAlcohol dehydrogenase E chain 1.1.1.1 0.672
5kj6 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.672
1agn NADAlcohol dehydrogenase class 4 mu/sigma chain 1.1.1.1 0.671
1lde NADAlcohol dehydrogenase E chain 1.1.1.1 0.671
4j49 NAIUncharacterized protein / 0.671
1wwk NAD307aa long hypothetical phosphoglycerate dehydrogenase / 0.670
2rgj FADFlavin-containing monooxygenase / 0.670
2fkn NADUrocanate hydratase 4.2.1.49 0.669
3cos NADAlcohol dehydrogenase 4 1.1.1.1 0.669
4njo NADD-3-phosphoglycerate dehydrogenase, putative / 0.669
4okn NAIL-lactate dehydrogenase A chain 1.1.1.27 0.669
5cds NAJAlcohol dehydrogenase E chain 1.1.1.1 0.669
1uxk NADMalate dehydrogenase / 0.668
2vhv NAIAlanine dehydrogenase 1.4.1.1 0.668
2x0r NADMalate dehydrogenase / 0.668
4b69 FADL-ornithine N(5)-monooxygenase / 0.667
1h2b NAJNAD-dependent alcohol dehydrogenase / 0.666
1h6d NDPGlucose--fructose oxidoreductase 1.1.99.28 0.666
4j4b NAIUncharacterized protein / 0.666
4xgi NADGlutamate dehydrogenase / 0.666
5ijz NAPNADP-specific glutamate dehydrogenase 1.4.1.4 0.666
1szj NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.665
1u3v NADAlcohol dehydrogenase 1B 1.1.1.1 0.665
3cgd FADCoenzyme A disulfide reductase / 0.665
3nx4 NAPPutative oxidoreductase / 0.665
1kc1 NDPdTDP-4-dehydrorhamnose reductase 1.1.1.133 0.664
1u8f NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.664
3qvt NAIMyo-inositol-1-phosphate synthase (Ino1) / 0.664
3wle NAD(R)-specific carbonyl reductase / 0.664
4egb NADdTDP-glucose 4,6-dehydratase / 0.664
1edo NAP3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic 1.1.1.100 0.663
3v1y NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.663
4nd2 A3DLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.663
1het NADAlcohol dehydrogenase E chain 1.1.1.1 0.662
3pym NADGlyceraldehyde-3-phosphate dehydrogenase 3 1.2.1.12 0.662
5dt9 NADErythronate-4-phosphate dehydrogenase / 0.662
2voj NADAlanine dehydrogenase 1.4.1.1 0.661
3a4v NADNDP-sugar epimerase / 0.661
4b79 NADProbable short-chain dehydrogenase / 0.661
5env NADAlcohol dehydrogenase 1 1.1.1.1 0.661
1bw9 NADPhenylalanine dehydrogenase / 0.660
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.660
3oa2 NADUDP-N-acetyl-2-amino-2-deoxy-D-glucuronate oxidase / 0.660
1gad NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.659
4p8r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.659
4rvu NDPProbable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein) / 0.659
1axe NADAlcohol dehydrogenase E chain 1.1.1.1 0.658
1efk NADNAD-dependent malic enzyme, mitochondrial 1.1.1.38 0.658
1lso NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.658
2wsb NADGalactitol dehydrogenase / 0.658
6adh NADAlcohol dehydrogenase E chain 1.1.1.1 0.658
1h6c NDPGlucose--fructose oxidoreductase 1.1.99.28 0.657
1rp0 AHZThiamine thiazole synthase, chloroplastic / 0.657
2pv7 NADT-protein 1.3.1.12 0.657
3mvq NDPGlutamate dehydrogenase 1, mitochondrial 1.4.1.3 0.657
4rls NAIL-lactate dehydrogenase A chain 1.1.1.27 0.657
4wji NAPPutative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase / 0.657
1hf3 NADAlcohol dehydrogenase E chain 1.1.1.1 0.656
2e1m FADL-glutamate oxidase / 0.656
3nug NADPyridoxal 4-dehydrogenase 1.1.1.107 0.656
1ht0 NADAlcohol dehydrogenase 1C 1.1.1.1 0.655
1p0f NAPNADP-dependent alcohol dehydrogenase 1.1.1.2 0.655
1p1i NADInositol-3-phosphate synthase 5.5.1.4 0.655
1yqx NAPSinapyl alcohol dehydrogenase / 0.655
1fxs NAPGDP-L-fucose synthase / 0.654
2p9e NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.654
3cps NADGlyceraldehyde-3-phosphate dehydrogenase / 0.654
4o63 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.654
1hdz NADAlcohol dehydrogenase 1B 1.1.1.1 0.653
1w4x FADPhenylacetone monooxygenase 1.14.13.92 0.653
2fn7 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.653
3l4s NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.653
3o9z NADLipopolysaccaride biosynthesis protein wbpB / 0.653
3pqf NADL-lactate dehydrogenase 1.1.1.27 0.653
1sc6 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.652
3ggo NAIPrephenate dehydrogenase / 0.652
1kol NADGlutathione-independent formaldehyde dehydrogenase / 0.651
1ryi FADGlycine oxidase 1.4.3.19 0.651
2dt5 NADRedox-sensing transcriptional repressor Rex / 0.651
2j3k NAPNADPH-dependent oxidoreductase 2-alkenal reductase 1.3.1.74 0.651
1g1a NADdTDP-glucose 4,6-dehydratase / 0.650
1i36 NAPConserved protein / 0.650
1n2s NAIdTDP-4-dehydrorhamnose reductase 1.1.1.133 0.650
2dbz NAPGlyoxylate reductase 1.1.1.26 0.650
3w8d NAD3-hydroxybutyrate dehydrogenase / 0.650
3w8f NAD3-hydroxybutyrate dehydrogenase / 0.650
3wsw NADL-lactate dehydrogenase / 0.650
4rf2 NAPNADPH dependent R-specific alcohol dehydrogenase / 0.650