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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
1o6z NAD Malate dehydrogenase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity
Align
1o6z NADMalate dehydrogenase / 1.221
2x0r NADMalate dehydrogenase / 0.829
1hyh NADL-2-hydroxyisocaproate dehydrogenase / 0.816
4nfh NAJAlcohol dehydrogenase E chain 1.1.1.1 0.813
4jnk NAIL-lactate dehydrogenase A chain 1.1.1.27 0.810
5kje NAJAlcohol dehydrogenase E chain 1.1.1.1 0.809
1r37 NADNAD-dependent alcohol dehydrogenase 1.1.1.1 0.802
4gkv NADAlcohol dehydrogenase, propanol-preferring 1.1.1.1 0.802
5kcp NAJAlcohol dehydrogenase E chain 1.1.1.1 0.795
3d4p NADL-lactate dehydrogenase 1 1.1.1.27 0.794
4dwv NAJAlcohol dehydrogenase E chain 1.1.1.1 0.794
2x0i NAIMalate dehydrogenase / 0.787
5kcz NAJAlcohol dehydrogenase E chain 1.1.1.1 0.785
3cos NADAlcohol dehydrogenase 4 1.1.1.1 0.781
4nd4 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.780
4c4o NADSADH / 0.779
2dt5 NADRedox-sensing transcriptional repressor Rex / 0.775
2oxi NADAlcohol dehydrogenase E chain 1.1.1.1 0.774
5kj6 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.774
1t2d NADL-lactate dehydrogenase 1.1.1.27 0.773
4ng5 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.772
1axe NADAlcohol dehydrogenase E chain 1.1.1.1 0.770
2o4c NADErythronate-4-phosphate dehydrogenase / 0.770
3h3j NADL-lactate dehydrogenase 1 1.1.1.27 0.769
2dfd NADMalate dehydrogenase, mitochondrial 1.1.1.37 0.767
4nfs NAJAlcohol dehydrogenase E chain 1.1.1.1 0.767
5cdt NAJAlcohol dehydrogenase E chain 1.1.1.1 0.766
1h2b NAJNAD-dependent alcohol dehydrogenase / 0.765
5kj1 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.765
1mgo NADAlcohol dehydrogenase E chain 1.1.1.1 0.764
1uxj NADMalate dehydrogenase / 0.764
5cds NAJAlcohol dehydrogenase E chain 1.1.1.1 0.764
1uxk NADMalate dehydrogenase / 0.762
1lld NADL-lactate dehydrogenase 2 1.1.1.27 0.761
5cdg NAJAlcohol dehydrogenase E chain 1.1.1.1 0.759
5kjf NAJAlcohol dehydrogenase E chain 1.1.1.1 0.758
1u3v NADAlcohol dehydrogenase 1B 1.1.1.1 0.755
5a1t NAIL-lactate dehydrogenase / 0.755
4okn NAIL-lactate dehydrogenase A chain 1.1.1.27 0.751
3jv7 NADSecondary alcohol dehydrogenase / 0.748
2g82 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.747
5kjc NAJAlcohol dehydrogenase E chain 1.1.1.1 0.746
1hdz NADAlcohol dehydrogenase 1B 1.1.1.1 0.742
1ib6 NADMalate dehydrogenase / 0.740
2fn7 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.739
4ywj NAD4-hydroxy-tetrahydrodipicolinate reductase / 0.739
1pzh NADLactate dehydrogenase / 0.738
2a92 NAIL-lactate dehydrogenase / 0.737
6adh NADAlcohol dehydrogenase E chain 1.1.1.1 0.737
1ie3 NADMalate dehydrogenase / 0.736
5mdh NADMalate dehydrogenase, cytoplasmic 1.1.1.37 0.736
4w6z 8IDAlcohol dehydrogenase 1 1.1.1.1 0.735
4wlu NADMalate dehydrogenase, mitochondrial 1.1.1.37 0.734
3oq6 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.730
1ez4 NADL-lactate dehydrogenase 1.1.1.27 0.729
3cif NADGlyceraldehyde-3-phosphate dehydrogenase / 0.727
4lsm NADGlyceraldehyde-3-phosphate dehydrogenase / 0.726
1pzf A3DLactate dehydrogenase / 0.724
1t2c NAIL-lactate dehydrogenase 1.1.1.27 0.723
1yl7 NAI4-hydroxy-tetrahydrodipicolinate reductase / 0.723
2vhz NAIAlanine dehydrogenase 1.4.1.1 0.723
4nd2 A3DLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.723
4nd3 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.722
2eer NADNAD-dependent alcohol dehydrogenase 1.1.1.1 0.721
2g76 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.721
2y05 NAPProstaglandin reductase 1 / 0.721
4j43 NADUncharacterized protein / 0.721
2a94 AP0L-lactate dehydrogenase 1.1.1.27 0.720
2vhx NADAlanine dehydrogenase 1.4.1.1 0.720
4k28 NADShikimate dehydrogenase family protein / 0.719
3two NDPMannitol dehydrogenase / 0.718
5ees NAP4-hydroxy-tetrahydrodipicolinate reductase / 0.718
4plp NADHomospermidine synthase 2.5.1.44 0.717
1agn NADAlcohol dehydrogenase class 4 mu/sigma chain 1.1.1.1 0.716
3wle NAD(R)-specific carbonyl reductase / 0.715
1adc PADAlcohol dehydrogenase E chain 1.1.1.1 0.713
1gd1 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.713
4wlv NADMalate dehydrogenase, mitochondrial 1.1.1.37 0.713
4xrg NADHomospermidine synthase 2.5.1.44 0.712
4l4s NAIL-lactate dehydrogenase A chain 1.1.1.27 0.711
1heu NADAlcohol dehydrogenase E chain 1.1.1.1 0.708
1nqa NADGlyceraldehyde-3-phosphate dehydrogenase / 0.707
1nqo NADGlyceraldehyde-3-phosphate dehydrogenase / 0.707
2q3e NAIUDP-glucose 6-dehydrogenase 1.1.1.22 0.706
4b7x NAPProbable oxidoreductase / 0.706
4xqc NADHomospermidine synthase 2.5.1.44 0.706
1ht0 NADAlcohol dehydrogenase 1C 1.1.1.1 0.705
2gsd NADFormate dehydrogenase / 0.705
1guy NADMalate dehydrogenase / 0.704
4mdh NADMalate dehydrogenase, cytoplasmic 1.1.1.37 0.704
4tvb NADHomospermidine synthase 2.5.1.44 0.704
2vhv NAIAlanine dehydrogenase 1.4.1.1 0.703
3oet NADErythronate-4-phosphate dehydrogenase / 0.703
1sow NADL-lactate dehydrogenase 1.1.1.27 0.702
1ur5 NADMalate dehydrogenase / 0.702
1yqd NAPSinapyl alcohol dehydrogenase / 0.702
2xaa NADSecondary alcohol dehydrogenase / 0.702
2fzw NADAlcohol dehydrogenase class-3 1.1.1.1 0.701
2ohx NADAlcohol dehydrogenase E chain 1.1.1.1 0.701
4i1i NADMalate dehydrogenase / 0.699
4oaq NDPR-specific carbonyl reductase / 0.699
3lvf NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.698
1nvm NADAcetaldehyde dehydrogenase 1.2.1.10 0.697
3hja NADGlyceraldehyde-3-phosphate dehydrogenase / 0.697
4xd2 NAIAlcohol dehydrogenase E chain 1.1.1.1 0.697
5env NADAlcohol dehydrogenase 1 1.1.1.1 0.697
1e3s NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.695
1hsz NADAlcohol dehydrogenase 1B 1.1.1.1 0.695
3uko NADAlcohol dehydrogenase class-3 / 0.695
3adp NAILambda-crystallin 1.1.1.45 0.694
4rqu NADAlcohol dehydrogenase class-P / 0.694
4dlb NADS-(hydroxymethyl)glutathione dehydrogenase / 0.693
4dxh NAJAlcohol dehydrogenase E chain 1.1.1.1 0.693
1bdm NAXMalate dehydrogenase / 0.692
2ldb NADL-lactate dehydrogenase 1.1.1.27 0.692
1i36 NAPConserved protein / 0.691
2vhw NAIAlanine dehydrogenase 1.4.1.1 0.690
3d64 NADAdenosylhomocysteinase / 0.690
4xwz FADFructosyl amine:oxygen oxidoreductase / 0.690
1nq5 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.689
1wzi NDPMalate dehydrogenase / 0.689
1mp0 NADAlcohol dehydrogenase class-3 1.1.1.1 0.688
1u7h NADPutative ornithine cyclodeaminase / 0.688
2ekl NADD-3-phosphoglycerate dehydrogenase / 0.688
2p9g NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.688
3x2e NAIAdenosylhomocysteinase / 0.688
1b3r NADAdenosylhomocysteinase 3.3.1.1 0.687
3o9z NADLipopolysaccaride biosynthesis protein wbpB / 0.687
1hf3 NADAlcohol dehydrogenase E chain 1.1.1.1 0.686
4hfm NAP2-alkenal reductase (NADP(+)-dependent) / 0.686
1gv0 NADMalate dehydrogenase / 0.685
1vsv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.685
1yqx NAPSinapyl alcohol dehydrogenase / 0.685
1i2b NADUDP-sulfoquinovose synthase, chloroplastic 3.13.1.1 0.684
2vyv NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.684
3abi NADUncharacterized protein / 0.684
3h3f NAIL-lactate dehydrogenase A chain 1.1.1.27 0.684
1nbo NADGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.683
3pdu NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.683
3zdf NADGlyceraldehyde-3-phosphate dehydrogenase / 0.683
4j49 NADUncharacterized protein / 0.683
1gad NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.682
4cpd NADAlcohol dehydrogenase / 0.681
2aa3 AP0L-lactate dehydrogenase / 0.679
3jyo NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.679
3nt4 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.679
4jji NADAlcohol dehydrogenase class-3 / 0.679
2ep7 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.678
3v1y NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.678
1het NADAlcohol dehydrogenase E chain 1.1.1.1 0.677
1yb5 NAPQuinone oxidoreductase 1.6.5.5 0.677
3ruc NADUDP-N-acetylglucosamine 4-epimerase / 0.677
4xq9 NADHomospermidine synthase 2.5.1.44 0.677
1bdb NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase / 0.676
1kol NADGlutathione-independent formaldehyde dehydrogenase / 0.676
1u8f NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.676
3wsw NADL-lactate dehydrogenase / 0.676
3b1j NADGlyceraldehyde-3-phosphate dehydrogenase / 0.674
3cin NADMyo-inositol-1-phosphate synthase-related protein / 0.674
4wct FADFructosyl amine:oxygen oxidoreductase / 0.674
1axg NADAlcohol dehydrogenase E chain 1.1.1.1 0.673
1vc2 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.673
2jhf NADAlcohol dehydrogenase E chain 1.1.1.1 0.672
3doc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.672
1la2 NADInositol-3-phosphate synthase 5.5.1.4 0.671
1y7t NDPMalate dehydrogenase / 0.671
1ywg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.671
3ggp NADPrephenate dehydrogenase / 0.671
1dhr NADDihydropteridine reductase 1.5.1.34 0.670
1f0y NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.670
1llu NADAlcohol dehydrogenase / 0.669
1sc6 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.669
2q1w NADPutative nucleotide sugar epimerase/ dehydratase / 0.669
1bw9 NADPhenylalanine dehydrogenase / 0.668
1hld NADAlcohol dehydrogenase E chain 1.1.1.1 0.668
1pl6 NADSorbitol dehydrogenase 1.1.1.14 0.668
2dvm NAD439aa long hypothetical malate oxidoreductase (NAD) [malic enzyme] / 0.668
3gvh NADMalate dehydrogenase / 0.668
3qv1 NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.668
1p0f NAPNADP-dependent alcohol dehydrogenase 1.1.1.2 0.667
1pzg A3DLactate dehydrogenase / 0.667
1wwk NAD307aa long hypothetical phosphoglycerate dehydrogenase / 0.667
3ikt NADRedox-sensing transcriptional repressor Rex / 0.667
4k9d NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.667
4wji NAPPutative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase / 0.667
3cmc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.666
2vna NAPProstaglandin reductase 2 1.3.1.48 0.665
2pa3 NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.663
4j49 NAIUncharacterized protein / 0.663
2i9p NAD3-hydroxyisobutyrate dehydrogenase, mitochondrial 1.1.1.31 0.662
3rfx NADUronate dehydrogenase / 0.662
3w6u NAP6-phosphogluconate dehydrogenase, NAD-binding protein / 0.662
4jk3 NADUncharacterized protein / 0.662
1zem NADXylitol dehydrogenase / 0.661
3cps NADGlyceraldehyde-3-phosphate dehydrogenase / 0.661
3qw2 NADMyo-inositol-1-phosphate synthase (Ino1) / 0.661
4o59 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.661
1up7 NAD6-phospho-beta-glucosidase BglT 3.2.1.86 0.660
3pef NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.660
3ruf NADUDP-N-acetylglucosamine 4-epimerase / 0.660
3tri NAPPyrroline-5-carboxylate reductase / 0.660
1u28 NADNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.659
3pym NADGlyceraldehyde-3-phosphate dehydrogenase 3 1.2.1.12 0.659
4p8r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.659
1efk NADNAD-dependent malic enzyme, mitochondrial 1.1.1.38 0.658
1ky4 NADAdenosylhomocysteinase 3.3.1.1 0.658
1wze NADMalate dehydrogenase / 0.658
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.658
2q1s NAIPutative nucleotide sugar epimerase/ dehydratase / 0.658
3ggo NAIPrephenate dehydrogenase / 0.658
2cvz NDP3-hydroxyisobutyrate dehydrogenase / 0.657
2vwq NAPGlucose 1-dehydrogenase / 0.657
1n2s NAIdTDP-4-dehydrorhamnose reductase 1.1.1.133 0.656
1e5q NDPSaccharopine dehydrogenase [NADP(+), L-glutamate-forming] 1.5.1.10 0.655
1lsj NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.654
2vwh NAPGlucose 1-dehydrogenase / 0.654
2zb3 NDPProstaglandin reductase 2 1.3.1.48 0.654
4dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.654
2gv8 NDPThiol-specific monooxygenase 1.14.13 0.653
1e3w NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.652
1emd NADMalate dehydrogenase / 0.652
2nad NADFormate dehydrogenase / 0.652
2vyn NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.651
2yut NAPPutative short-chain oxidoreductase / 0.651
4uun NAIL-lactate dehydrogenase / 0.651
1bmd NADMalate dehydrogenase / 0.650
1o0s NAINAD-dependent malic enzyme, mitochondrial 1.1.1.38 0.650
1pj2 NAINAD-dependent malic enzyme, mitochondrial 1.1.1.38 0.650
1xq6 NAPUncharacterized protein At5g02240 / 0.650
2gdz NAD15-hydroxyprostaglandin dehydrogenase [NAD(+)] 1.1.1.141 0.650
2qg4 NADUDP-glucose 6-dehydrogenase 1.1.1.22 0.650
3ggg NADPrephenate dehydrogenase / 0.650