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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
1guy NAD Malate dehydrogenase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1guy NADMalate dehydrogenase / 0.972
1uxk NADMalate dehydrogenase / 0.824
1ur5 NADMalate dehydrogenase / 0.819
1uxj NADMalate dehydrogenase / 0.798
1hyh NADL-2-hydroxyisocaproate dehydrogenase / 0.770
3d4p NADL-lactate dehydrogenase 1 1.1.1.27 0.767
4okn NAIL-lactate dehydrogenase A chain 1.1.1.27 0.759
4xq9 NADHomospermidine synthase 2.5.1.44 0.753
1gv0 NADMalate dehydrogenase / 0.752
2g5c NADPrephenate dehydrogenase / 0.745
4jnk NAIL-lactate dehydrogenase A chain 1.1.1.27 0.741
5kje NAJAlcohol dehydrogenase E chain 1.1.1.1 0.732
1t2c NAIL-lactate dehydrogenase 1.1.1.27 0.731
4nd4 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.729
4dwv NAJAlcohol dehydrogenase E chain 1.1.1.1 0.727
4nfh NAJAlcohol dehydrogenase E chain 1.1.1.1 0.727
5kcz NAJAlcohol dehydrogenase E chain 1.1.1.1 0.727
5cdg NAJAlcohol dehydrogenase E chain 1.1.1.1 0.726
1lld NADL-lactate dehydrogenase 2 1.1.1.27 0.724
4tvb NADHomospermidine synthase 2.5.1.44 0.722
5kj6 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.722
3oq6 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.721
5cds NAJAlcohol dehydrogenase E chain 1.1.1.1 0.721
5kj1 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.721
4xqc NADHomospermidine synthase 2.5.1.44 0.719
2x0i NAIMalate dehydrogenase / 0.718
4xrg NADHomospermidine synthase 2.5.1.44 0.718
1f0y NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.717
3abi NADUncharacterized protein / 0.717
2o4c NADErythronate-4-phosphate dehydrogenase / 0.716
4o63 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.715
2vyv NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.714
2hjr APRMalate dehydrogenase, adjacent gene encodes predicted lactate dehydrogenase / 0.711
4nfs NAJAlcohol dehydrogenase E chain 1.1.1.1 0.711
1axe NADAlcohol dehydrogenase E chain 1.1.1.1 0.710
2vhx NADAlanine dehydrogenase 1.4.1.1 0.710
1hld NADAlcohol dehydrogenase E chain 1.1.1.1 0.707
4plp NADHomospermidine synthase 2.5.1.44 0.707
4xd2 NAIAlcohol dehydrogenase E chain 1.1.1.1 0.707
1c1d NAIPhenylalanine dehydrogenase / 0.706
2ohx NADAlcohol dehydrogenase E chain 1.1.1.1 0.706
5kjc NAJAlcohol dehydrogenase E chain 1.1.1.1 0.705
1o6z NADMalate dehydrogenase / 0.704
4pzd NAD3-Hydroxyacyl-CoA dehydrogenase / 0.703
1u8f NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.699
4o59 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.698
1lsj NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.697
1vsv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.697
3h3j NADL-lactate dehydrogenase 1 1.1.1.27 0.697
3wsw NADL-lactate dehydrogenase / 0.697
3ggp NADPrephenate dehydrogenase / 0.696
1nq5 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.695
2ep7 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.695
4k28 NADShikimate dehydrogenase family protein / 0.695
3cos NADAlcohol dehydrogenase 4 1.1.1.1 0.694
3uko NADAlcohol dehydrogenase class-3 / 0.694
1il0 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.692
1mgo NADAlcohol dehydrogenase E chain 1.1.1.1 0.692
4l4s NAIL-lactate dehydrogenase A chain 1.1.1.27 0.692
2a94 AP0L-lactate dehydrogenase 1.1.1.27 0.691
1a71 NADAlcohol dehydrogenase E chain 1.1.1.1 0.690
3ggo NAIPrephenate dehydrogenase / 0.690
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.690
3anm NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase 1.1.1.267 0.688
4k9d NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.688
1adc PADAlcohol dehydrogenase E chain 1.1.1.1 0.687
2jhf NADAlcohol dehydrogenase E chain 1.1.1.1 0.687
3pqf NADL-lactate dehydrogenase 1.1.1.27 0.686
3zcx NADGlyceraldehyde-3-phosphate dehydrogenase / 0.686
1cer NADGlyceraldehyde-3-phosphate dehydrogenase / 0.685
1nbo NADGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.685
2vhv NAIAlanine dehydrogenase 1.4.1.1 0.685
2vhz NAIAlanine dehydrogenase 1.4.1.1 0.685
1ib6 NADMalate dehydrogenase / 0.682
4dl9 NADS-(hydroxymethyl)glutathione dehydrogenase / 0.682
4rqu NADAlcohol dehydrogenase class-P / 0.682
1ywg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.681
1hku NADC-terminal-binding protein 1 1.1.1 0.678
1pjc NADAlanine dehydrogenase / 0.677
2fzw NADAlcohol dehydrogenase class-3 1.1.1.1 0.677
3pym NADGlyceraldehyde-3-phosphate dehydrogenase 3 1.2.1.12 0.677
1hdg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.676
1lde NADAlcohol dehydrogenase E chain 1.1.1.1 0.676
2ph5 NADHomospermidine synthase / 0.676
3l4s NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.676
3zw9 NADPeroxisomal bifunctional enzyme 1.1.1.35 0.676
3jyq NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.675
3keq NADRedox-sensing transcriptional repressor Rex / 0.675
5c7o NADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific 1.2.1.12 0.675
1pzh NADLactate dehydrogenase / 0.674
1sc6 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.674
2b4r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.674
4gkv NADAlcohol dehydrogenase, propanol-preferring 1.1.1.1 0.674
4xgi NADGlutamate dehydrogenase / 0.674
1agn NADAlcohol dehydrogenase class 4 mu/sigma chain 1.1.1.1 0.673
3oet NADErythronate-4-phosphate dehydrogenase / 0.673
3wle NAD(R)-specific carbonyl reductase / 0.673
4boy NADGlyceraldehyde-3-phosphate dehydrogenase / 0.673
1adb CNDAlcohol dehydrogenase E chain 1.1.1.1 0.672
2aa3 AP0L-lactate dehydrogenase / 0.672
4nd2 A3DLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.672
2vhw NAIAlanine dehydrogenase 1.4.1.1 0.671
3cin NADMyo-inositol-1-phosphate synthase-related protein / 0.671
3jyo NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.671
3nt4 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.671
1e5q NDPSaccharopine dehydrogenase [NADP(+), L-glutamate-forming] 1.5.1.10 0.670
1i2b NADUDP-sulfoquinovose synthase, chloroplastic 3.13.1.1 0.670
3x2e NAIAdenosylhomocysteinase / 0.668
1dc6 NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.667
1het NADAlcohol dehydrogenase E chain 1.1.1.1 0.667
4e5n NADPhosphonate dehydrogenase 1.20.1.1 0.667
1vc2 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.666
2voj NADAlanine dehydrogenase 1.4.1.1 0.666
3hja NADGlyceraldehyde-3-phosphate dehydrogenase / 0.666
1axg NADAlcohol dehydrogenase E chain 1.1.1.1 0.665
1bw9 NADPhenylalanine dehydrogenase / 0.665
1gae NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.665
1heu NADAlcohol dehydrogenase E chain 1.1.1.1 0.665
3had NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.665
3m2t NADProbable dehydrogenase / 0.665
1f8f NADBenzyl alcohol dehydrogenase / 0.664
3pdu NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.663
4kug NAD3-hydroxybutyryl-CoA dehydrogenase / 0.663
2d2i NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.661
4j49 NAIUncharacterized protein / 0.661
1j0x NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.660
1hdz NADAlcohol dehydrogenase 1B 1.1.1.1 0.659
1llq NADNAD-dependent malic enzyme, mitochondrial 1.1.1.38 0.659
1xcb NADRedox-sensing transcriptional repressor Rex / 0.659
2dfd NADMalate dehydrogenase, mitochondrial 1.1.1.37 0.659
2npx NADNADH peroxidase 1.11.1.1 0.659
3f3s NADLambda-crystallin homolog / 0.659
1a7k NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.658
1hsz NADAlcohol dehydrogenase 1B 1.1.1.1 0.658
1u3v NADAlcohol dehydrogenase 1B 1.1.1.1 0.658
4j49 NADUncharacterized protein / 0.657
1lso NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.656
2ldb NADL-lactate dehydrogenase 1.1.1.27 0.656
2qg4 NADUDP-glucose 6-dehydrogenase 1.1.1.22 0.656
3gvi ADPMalate dehydrogenase / 0.656
3tri NAPPyrroline-5-carboxylate reductase / 0.654
1f17 NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.653
1h2b NAJNAD-dependent alcohol dehydrogenase / 0.653
5bsg NAPPyrroline-5-carboxylate reductase / 0.653
3nx4 NAPPutative oxidoreductase / 0.652
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.652
4jk3 NADUncharacterized protein / 0.652
5ein NAP[LysW]-L-2-aminoadipate 6-phosphate reductase / 0.652
1kol NADGlutathione-independent formaldehyde dehydrogenase / 0.651
1nqo NADGlyceraldehyde-3-phosphate dehydrogenase / 0.651
3qw2 NADMyo-inositol-1-phosphate synthase (Ino1) / 0.651
4j43 NADUncharacterized protein / 0.651
4j4b NAIUncharacterized protein / 0.651
4oaq NDPR-specific carbonyl reductase / 0.651
1ma0 NADAlcohol dehydrogenase class-3 1.1.1.1 0.650
1yb5 NAPQuinone oxidoreductase 1.6.5.5 0.650
4dlb NADS-(hydroxymethyl)glutathione dehydrogenase / 0.650