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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
1bdm NAX Malate dehydrogenase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1bdm NAXMalate dehydrogenase / 1.118
1bmd NADMalate dehydrogenase / 0.926
1b8v NADMalate dehydrogenase / 0.916
4i1i NADMalate dehydrogenase / 0.840
1wze NADMalate dehydrogenase / 0.831
1wzi NDPMalate dehydrogenase / 0.831
1t2c NAIL-lactate dehydrogenase 1.1.1.27 0.827
5a1t NAIL-lactate dehydrogenase / 0.797
2a92 NAIL-lactate dehydrogenase / 0.796
1t2d NADL-lactate dehydrogenase 1.1.1.27 0.787
1pzh NADLactate dehydrogenase / 0.780
1sow NADL-lactate dehydrogenase 1.1.1.27 0.777
2dfd NADMalate dehydrogenase, mitochondrial 1.1.1.37 0.771
1y7t NDPMalate dehydrogenase / 0.767
4nd3 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.765
4nd4 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.763
2fn7 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.759
1b8u NADMalate dehydrogenase / 0.757
4uun NAIL-lactate dehydrogenase / 0.756
4ros APRMalate dehydrogenase / 0.753
2a94 AP0L-lactate dehydrogenase 1.1.1.27 0.748
4wlv NADMalate dehydrogenase, mitochondrial 1.1.1.37 0.745
4nd2 A3DLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.744
2aa3 AP0L-lactate dehydrogenase / 0.738
1pl6 NADSorbitol dehydrogenase 1.1.1.14 0.737
4mdh NADMalate dehydrogenase, cytoplasmic 1.1.1.37 0.737
4wlu NADMalate dehydrogenase, mitochondrial 1.1.1.37 0.737
1pzg A3DLactate dehydrogenase / 0.730
1pl8 NADSorbitol dehydrogenase 1.1.1.14 0.718
1x7d NADPutative ornithine cyclodeaminase / 0.712
1mp0 NADAlcohol dehydrogenase class-3 1.1.1.1 0.706
2d8a NADL-threonine 3-dehydrogenase / 0.706
1uxk NADMalate dehydrogenase / 0.705
4okn NAIL-lactate dehydrogenase A chain 1.1.1.27 0.701
1ib6 NADMalate dehydrogenase / 0.700
1kol NADGlutathione-independent formaldehyde dehydrogenase / 0.697
2x0i NAIMalate dehydrogenase / 0.694
4j43 NADUncharacterized protein / 0.694
1o6z NADMalate dehydrogenase / 0.692
4jji NADAlcohol dehydrogenase class-3 / 0.691
2ekl NADD-3-phosphoglycerate dehydrogenase / 0.689
2fzw NADAlcohol dehydrogenase class-3 1.1.1.1 0.689
3m6i NADL-arabinitol 4-dehydrogenase 1.1.1.12 0.685
4wlo NAIMalate dehydrogenase, mitochondrial 1.1.1.37 0.684
2hjr APRMalate dehydrogenase, adjacent gene encodes predicted lactate dehydrogenase / 0.682
4jnk NAIL-lactate dehydrogenase A chain 1.1.1.27 0.681
4nfs NAJAlcohol dehydrogenase E chain 1.1.1.1 0.679
2p9e NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.677
1ma0 NADAlcohol dehydrogenase class-3 1.1.1.1 0.676
2pa3 NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.676
3d4p NADL-lactate dehydrogenase 1 1.1.1.27 0.676
6adh NADAlcohol dehydrogenase E chain 1.1.1.1 0.676
2dfv NADL-threonine 3-dehydrogenase / 0.674
3kbo NDPGlyoxylate/hydroxypyruvate reductase A / 0.674
1ez4 NADL-lactate dehydrogenase 1.1.1.27 0.671
2vhw NAIAlanine dehydrogenase 1.4.1.1 0.671
5kjc NAJAlcohol dehydrogenase E chain 1.1.1.1 0.671
1h2h NADL-aspartate dehydrogenase 1.4.1.21 0.670
3qvx NADMyo-inositol-1-phosphate synthase (Ino1) / 0.670
4l4s NAIL-lactate dehydrogenase A chain 1.1.1.27 0.670
1llu NADAlcohol dehydrogenase / 0.669
2cvq NDPMalate dehydrogenase / 0.669
5mdh NADMalate dehydrogenase, cytoplasmic 1.1.1.37 0.669
3qvt NAIMyo-inositol-1-phosphate synthase (Ino1) / 0.668
4cpd NADAlcohol dehydrogenase / 0.667
1hyh NADL-2-hydroxyisocaproate dehydrogenase / 0.666
1u7h NADPutative ornithine cyclodeaminase / 0.666
3cos NADAlcohol dehydrogenase 4 1.1.1.1 0.666
4weq NAPNAD-dependent dehydrogenase / 0.665
1xcb NADRedox-sensing transcriptional repressor Rex / 0.664
3nt4 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.664
1adc PADAlcohol dehydrogenase E chain 1.1.1.1 0.663
1e3l NADAlcohol dehydrogenase 4 1.1.1.1 0.663
3n7u NADFormate dehydrogenase, chloroplastic/mitochondrial / 0.662
4rqu NADAlcohol dehydrogenase class-P / 0.662
3gvh NADMalate dehydrogenase / 0.661
4ejm NAPPutative zinc-binding dehydrogenase / 0.661
1b3r NADAdenosylhomocysteinase 3.3.1.1 0.657
1yba NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.657
3cps NADGlyceraldehyde-3-phosphate dehydrogenase / 0.657
3h3f NAIL-lactate dehydrogenase A chain 1.1.1.27 0.657
3qvs NADMyo-inositol-1-phosphate synthase (Ino1) / 0.657
1mgo NADAlcohol dehydrogenase E chain 1.1.1.1 0.656
1ie3 NADMalate dehydrogenase / 0.655
1uxj NADMalate dehydrogenase / 0.655
2ohx NADAlcohol dehydrogenase E chain 1.1.1.1 0.655
5kjf NAJAlcohol dehydrogenase E chain 1.1.1.1 0.655
2dc1 NADProbable L-aspartate dehydrogenase / 0.654
2p9g NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.653
2vhz NAIAlanine dehydrogenase 1.4.1.1 0.653
1axg NADAlcohol dehydrogenase E chain 1.1.1.1 0.652
4dl9 NADS-(hydroxymethyl)glutathione dehydrogenase / 0.652
4xd2 NAIAlcohol dehydrogenase E chain 1.1.1.1 0.652
4gl4 NAIAlcohol dehydrogenase class-3 / 0.651
1gv0 NADMalate dehydrogenase / 0.650
4ng5 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.650
4w6z 8IDAlcohol dehydrogenase 1 1.1.1.1 0.650