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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
3d64 NAD Adenosylhomocysteinase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3d64 NADAdenosylhomocysteinase / 1.001
1b3r NADAdenosylhomocysteinase 3.3.1.1 0.890
3x2f NAIAdenosylhomocysteinase / 0.822
1ky4 NADAdenosylhomocysteinase 3.3.1.1 0.819
1lld NADL-lactate dehydrogenase 2 1.1.1.27 0.732
3jyo NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.722
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.720
3ec7 NADInositol 2-dehydrogenase / 0.715
3h3j NADL-lactate dehydrogenase 1 1.1.1.27 0.715
1x7d NADPutative ornithine cyclodeaminase / 0.714
2o4c NADErythronate-4-phosphate dehydrogenase / 0.711
4k28 NADShikimate dehydrogenase family protein / 0.708
2gsd NADFormate dehydrogenase / 0.707
2vhx NADAlanine dehydrogenase 1.4.1.1 0.707
3lov FADProtoporphyrinogen oxidase / 0.706
1u7h NADPutative ornithine cyclodeaminase / 0.705
2vhw NAIAlanine dehydrogenase 1.4.1.1 0.705
3wv7 ADPHmd co-occurring protein HcgE / 0.704
3nt4 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.702
3qw2 NADMyo-inositol-1-phosphate synthase (Ino1) / 0.702
3x2e NAIAdenosylhomocysteinase / 0.702
4j49 NADUncharacterized protein / 0.701
1m76 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.699
1pj3 NADNAD-dependent malic enzyme, mitochondrial 1.1.1.38 0.699
4jk3 NADUncharacterized protein / 0.698
3d4p NADL-lactate dehydrogenase 1 1.1.1.27 0.697
1hku NADC-terminal-binding protein 1 1.1.1 0.695
1efk NADNAD-dependent malic enzyme, mitochondrial 1.1.1.38 0.693
3cos NADAlcohol dehydrogenase 4 1.1.1.1 0.691
1o6z NADMalate dehydrogenase / 0.690
1r37 NADNAD-dependent alcohol dehydrogenase 1.1.1.1 0.690
1do8 NADNAD-dependent malic enzyme, mitochondrial 1.1.1.38 0.689
3qvt NAIMyo-inositol-1-phosphate synthase (Ino1) / 0.689
1lde NADAlcohol dehydrogenase E chain 1.1.1.1 0.685
1p1h NADInositol-3-phosphate synthase 5.5.1.4 0.685
3wsw NADL-lactate dehydrogenase / 0.685
1la2 NADInositol-3-phosphate synthase 5.5.1.4 0.684
3jyp NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.684
3wv8 ATPHmd co-occurring protein HcgE / 0.684
4j43 NADUncharacterized protein / 0.684
5g3t FDAFlavin-dependent L-tryptophan oxidase VioA / 0.683
1hf3 NADAlcohol dehydrogenase E chain 1.1.1.1 0.682
1ywg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.682
2dt5 NADRedox-sensing transcriptional repressor Rex / 0.681
3cps NADGlyceraldehyde-3-phosphate dehydrogenase / 0.681
4j4b NAIUncharacterized protein / 0.680
4plp NADHomospermidine synthase 2.5.1.44 0.680
2x0r NADMalate dehydrogenase / 0.679
1dxy NADD-2-hydroxyisocaproate dehydrogenase 1.1.1 0.678
1kol NADGlutathione-independent formaldehyde dehydrogenase / 0.678
2ohx NADAlcohol dehydrogenase E chain 1.1.1.1 0.678
3g5q FADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO / 0.678
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.678
1uxj NADMalate dehydrogenase / 0.677
1d7l RFLp-hydroxybenzoate hydroxylase / 0.675
4okn NAIL-lactate dehydrogenase A chain 1.1.1.27 0.673
3qvs NADMyo-inositol-1-phosphate synthase (Ino1) / 0.672
3pqf NADL-lactate dehydrogenase 1.1.1.27 0.671
3pym NADGlyceraldehyde-3-phosphate dehydrogenase 3 1.2.1.12 0.671
1hyh NADL-2-hydroxyisocaproate dehydrogenase / 0.670
1nbo NADGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.669
3ggo NAIPrephenate dehydrogenase / 0.669
3qvx NADMyo-inositol-1-phosphate synthase (Ino1) / 0.669
4jnk NAIL-lactate dehydrogenase A chain 1.1.1.27 0.669
4nfs NAJAlcohol dehydrogenase E chain 1.1.1.1 0.669
5kjc NAJAlcohol dehydrogenase E chain 1.1.1.1 0.669
1a71 NADAlcohol dehydrogenase E chain 1.1.1.1 0.668
2g5c NADPrephenate dehydrogenase / 0.668
4wlu NADMalate dehydrogenase, mitochondrial 1.1.1.37 0.668
1ie3 NADMalate dehydrogenase / 0.667
2dfv NADL-threonine 3-dehydrogenase / 0.666
2g76 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.666
4e5k NADPhosphonate dehydrogenase 1.20.1.1 0.666
1mgo NADAlcohol dehydrogenase E chain 1.1.1.1 0.665
1uxk NADMalate dehydrogenase / 0.665
3oq6 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.665
4dwv NAJAlcohol dehydrogenase E chain 1.1.1.1 0.665
5cds NAJAlcohol dehydrogenase E chain 1.1.1.1 0.665
5cdt NAJAlcohol dehydrogenase E chain 1.1.1.1 0.665
5kcp NAJAlcohol dehydrogenase E chain 1.1.1.1 0.665
5kcz NAJAlcohol dehydrogenase E chain 1.1.1.1 0.665
5kj6 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.665
5kje NAJAlcohol dehydrogenase E chain 1.1.1.1 0.665
1zmd NAIDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.664
4j2w FADKynurenine 3-monooxygenase / 0.664
4nfh NAJAlcohol dehydrogenase E chain 1.1.1.1 0.664
5cdg NAJAlcohol dehydrogenase E chain 1.1.1.1 0.664
5kj1 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.664
1f8f NADBenzyl alcohol dehydrogenase / 0.663
1ma0 NADAlcohol dehydrogenase class-3 1.1.1.1 0.663
1sc6 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.663
4dxh NAJAlcohol dehydrogenase E chain 1.1.1.1 0.663
4i1i NADMalate dehydrogenase / 0.663
4lcj NADC-terminal-binding protein 2 / 0.663
4pzd NAD3-Hydroxyacyl-CoA dehydrogenase / 0.663
2ome NADC-terminal-binding protein 2 / 0.662
4cpd NADAlcohol dehydrogenase / 0.662
3cin NADMyo-inositol-1-phosphate synthase-related protein / 0.661
3oet NADErythronate-4-phosphate dehydrogenase / 0.661
4j49 NAIUncharacterized protein / 0.661
5env NADAlcohol dehydrogenase 1 1.1.1.1 0.661
6adh NADAlcohol dehydrogenase E chain 1.1.1.1 0.661
1c1d NAIPhenylalanine dehydrogenase / 0.660
3doc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.660
3uko NADAlcohol dehydrogenase class-3 / 0.660
4ywj NAD4-hydroxy-tetrahydrodipicolinate reductase / 0.660
1f0y NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.659
1k0l FADp-hydroxybenzoate hydroxylase / 0.659
1pl8 NADSorbitol dehydrogenase 1.1.1.14 0.659
2qg4 NADUDP-glucose 6-dehydrogenase 1.1.1.22 0.659
4nd2 A3DLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.659
4xwz FADFructosyl amine:oxygen oxidoreductase / 0.659
1pdh FASp-hydroxybenzoate hydroxylase / 0.658
1pl6 NADSorbitol dehydrogenase 1.1.1.14 0.658
1u3v NADAlcohol dehydrogenase 1B 1.1.1.1 0.658
2dph NADFormaldehyde dismutase / 0.658
2dvm NAD439aa long hypothetical malate oxidoreductase (NAD) [malic enzyme] / 0.658
2x6t NAPADP-L-glycero-D-manno-heptose-6-epimerase / 0.658
5mdh NADMalate dehydrogenase, cytoplasmic 1.1.1.37 0.658
1gv0 NADMalate dehydrogenase / 0.657
1pj2 NAINAD-dependent malic enzyme, mitochondrial 1.1.1.38 0.657
1u8f NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.657
2vhz NAIAlanine dehydrogenase 1.4.1.1 0.657
4gkv NADAlcohol dehydrogenase, propanol-preferring 1.1.1.1 0.657
4o59 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.657
1pzg A3DLactate dehydrogenase / 0.656
3nt2 NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.656
4k9d NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.656
3nt2 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.655
4cr8 NADN-acylmannosamine 1-dehydrogenase 1.1.1.233 0.655
4ng5 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.655
4wct FADFructosyl amine:oxygen oxidoreductase / 0.655
1p1i NADInositol-3-phosphate synthase 5.5.1.4 0.654
2q7v FADThioredoxin reductase / 0.654
1j5p NADL-aspartate dehydrogenase 1.4.1.21 0.653
2fze APRAlcohol dehydrogenase class-3 1.1.1.1 0.653
2oxi NADAlcohol dehydrogenase E chain 1.1.1.1 0.653
2voj NADAlanine dehydrogenase 1.4.1.1 0.653
3l4s NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.653
3tsc NADUncharacterized protein / 0.653
2ekl NADD-3-phosphoglycerate dehydrogenase / 0.652
5kjf NAJAlcohol dehydrogenase E chain 1.1.1.1 0.652
1h2h NADL-aspartate dehydrogenase 1.4.1.21 0.651
1mp0 NADAlcohol dehydrogenase class-3 1.1.1.1 0.651
2q3e NAIUDP-glucose 6-dehydrogenase 1.1.1.22 0.651
3dmt NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.651
3ish FADThioredoxin reductase 1.8.1.9 0.651
3oa2 NADUDP-N-acetyl-2-amino-2-deoxy-D-glucuronate oxidase / 0.651
5g3s FDAFlavin-dependent L-tryptophan oxidase VioA / 0.651
1efl NADNAD-dependent malic enzyme, mitochondrial 1.1.1.38 0.650
1vc2 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.650