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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
2x0i NAI Malate dehydrogenase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2x0i NAIMalate dehydrogenase / 1.150
3d4p NADL-lactate dehydrogenase 1 1.1.1.27 0.867
4nd4 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.859
2fn7 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.851
1sow NADL-lactate dehydrogenase 1.1.1.27 0.828
4nd3 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.827
1t2d NADL-lactate dehydrogenase 1.1.1.27 0.813
1uxj NADMalate dehydrogenase / 0.804
1pzh NADLactate dehydrogenase / 0.800
2dt5 NADRedox-sensing transcriptional repressor Rex / 0.796
4l4s NAIL-lactate dehydrogenase A chain 1.1.1.27 0.794
1hyh NADL-2-hydroxyisocaproate dehydrogenase / 0.793
1o6z NADMalate dehydrogenase / 0.787
1r37 NADNAD-dependent alcohol dehydrogenase 1.1.1.1 0.786
4nd2 A3DLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.786
3h3j NADL-lactate dehydrogenase 1 1.1.1.27 0.784
1uxk NADMalate dehydrogenase / 0.773
4ros APRMalate dehydrogenase / 0.772
4jnk NAIL-lactate dehydrogenase A chain 1.1.1.27 0.767
4okn NAIL-lactate dehydrogenase A chain 1.1.1.27 0.763
1f8f NADBenzyl alcohol dehydrogenase / 0.762
1h2b NAJNAD-dependent alcohol dehydrogenase / 0.762
1t2c NAIL-lactate dehydrogenase 1.1.1.27 0.760
3wle NAD(R)-specific carbonyl reductase / 0.759
4gkv NADAlcohol dehydrogenase, propanol-preferring 1.1.1.1 0.758
5a1t NAIL-lactate dehydrogenase / 0.756
1pzg A3DLactate dehydrogenase / 0.753
1ib6 NADMalate dehydrogenase / 0.748
4c4o NADSADH / 0.742
2a94 AP0L-lactate dehydrogenase 1.1.1.27 0.741
4wlu NADMalate dehydrogenase, mitochondrial 1.1.1.37 0.741
4xd2 NAIAlcohol dehydrogenase E chain 1.1.1.1 0.740
1gv0 NADMalate dehydrogenase / 0.738
1axe NADAlcohol dehydrogenase E chain 1.1.1.1 0.737
2ohx NADAlcohol dehydrogenase E chain 1.1.1.1 0.737
2a92 NAIL-lactate dehydrogenase / 0.732
3jv7 NADSecondary alcohol dehydrogenase / 0.731
1ht0 NADAlcohol dehydrogenase 1C 1.1.1.1 0.729
2dfd NADMalate dehydrogenase, mitochondrial 1.1.1.37 0.728
3h3f NAIL-lactate dehydrogenase A chain 1.1.1.27 0.728
2o4c NADErythronate-4-phosphate dehydrogenase / 0.726
1a71 NADAlcohol dehydrogenase E chain 1.1.1.1 0.725
1het NADAlcohol dehydrogenase E chain 1.1.1.1 0.725
2jhf NADAlcohol dehydrogenase E chain 1.1.1.1 0.724
4j49 NADUncharacterized protein / 0.722
5kjc NAJAlcohol dehydrogenase E chain 1.1.1.1 0.722
2aa3 AP0L-lactate dehydrogenase / 0.721
1heu NADAlcohol dehydrogenase E chain 1.1.1.1 0.720
1hf3 NADAlcohol dehydrogenase E chain 1.1.1.1 0.719
4wlv NADMalate dehydrogenase, mitochondrial 1.1.1.37 0.719
1guy NADMalate dehydrogenase / 0.718
1yqd NAPSinapyl alcohol dehydrogenase / 0.718
4j43 NADUncharacterized protein / 0.718
1b8v NADMalate dehydrogenase / 0.717
1u7h NADPutative ornithine cyclodeaminase / 0.716
2p9g NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.716
1ma0 NADAlcohol dehydrogenase class-3 1.1.1.1 0.715
1x7d NADPutative ornithine cyclodeaminase / 0.714
4rls NAIL-lactate dehydrogenase A chain 1.1.1.27 0.714
1lld NADL-lactate dehydrogenase 2 1.1.1.27 0.712
2vhv NAIAlanine dehydrogenase 1.4.1.1 0.712
1pzf A3DLactate dehydrogenase / 0.709
1mgo NADAlcohol dehydrogenase E chain 1.1.1.1 0.708
5cdg NAJAlcohol dehydrogenase E chain 1.1.1.1 0.708
5kjf NAJAlcohol dehydrogenase E chain 1.1.1.1 0.708
1hld NADAlcohol dehydrogenase E chain 1.1.1.1 0.707
1lde NADAlcohol dehydrogenase E chain 1.1.1.1 0.707
2eer NADNAD-dependent alcohol dehydrogenase 1.1.1.1 0.707
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.706
1mp0 NADAlcohol dehydrogenase class-3 1.1.1.1 0.704
2xaa NADSecondary alcohol dehydrogenase / 0.703
4ywj NAD4-hydroxy-tetrahydrodipicolinate reductase / 0.701
1wwk NAD307aa long hypothetical phosphoglycerate dehydrogenase / 0.700
1zem NADXylitol dehydrogenase / 0.700
2fze APRAlcohol dehydrogenase class-3 1.1.1.1 0.700
3tri NAPPyrroline-5-carboxylate reductase / 0.700
3wsw NADL-lactate dehydrogenase / 0.699
4e5n NADPhosphonate dehydrogenase 1.20.1.1 0.699
4gl4 NAIAlcohol dehydrogenase class-3 / 0.699
1psd NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.698
3oet NADErythronate-4-phosphate dehydrogenase / 0.698
1agn NADAlcohol dehydrogenase class 4 mu/sigma chain 1.1.1.1 0.697
1e3s NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.697
4jk3 NADUncharacterized protein / 0.696
5mdh NADMalate dehydrogenase, cytoplasmic 1.1.1.37 0.696
1wze NADMalate dehydrogenase / 0.695
1bdm NAXMalate dehydrogenase / 0.694
1yl7 NAI4-hydroxy-tetrahydrodipicolinate reductase / 0.694
3qvx NADMyo-inositol-1-phosphate synthase (Ino1) / 0.694
4cpd NADAlcohol dehydrogenase / 0.694
4dlb NADS-(hydroxymethyl)glutathione dehydrogenase / 0.693
4dxh NAJAlcohol dehydrogenase E chain 1.1.1.1 0.693
4mdh NADMalate dehydrogenase, cytoplasmic 1.1.1.37 0.693
1hsz NADAlcohol dehydrogenase 1B 1.1.1.1 0.692
1u3v NADAlcohol dehydrogenase 1B 1.1.1.1 0.692
2ldb NADL-lactate dehydrogenase 1.1.1.27 0.692
3two NDPMannitol dehydrogenase / 0.692
5kj1 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.692
5kj6 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.692
5kje NAJAlcohol dehydrogenase E chain 1.1.1.1 0.692
1sc6 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.691
2oxi NADAlcohol dehydrogenase E chain 1.1.1.1 0.691
5kcp NAJAlcohol dehydrogenase E chain 1.1.1.1 0.691
3uxy NADShort-chain dehydrogenase/reductase SDR / 0.690
4jji NADAlcohol dehydrogenase class-3 / 0.690
2q1w NADPutative nucleotide sugar epimerase/ dehydratase / 0.689
2dvm NAD439aa long hypothetical malate oxidoreductase (NAD) [malic enzyme] / 0.688
5ees NAP4-hydroxy-tetrahydrodipicolinate reductase / 0.688
1yon A2R2-dehydropantoate 2-reductase 1.1.1.169 0.686
1hdz NADAlcohol dehydrogenase 1B 1.1.1.1 0.685
2pa3 NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.685
1llu NADAlcohol dehydrogenase / 0.684
4idg NADPutative UDP-glucose 4-epimerase / 0.683
5env NADAlcohol dehydrogenase 1 1.1.1.1 0.683
1b8u NADMalate dehydrogenase / 0.682
1yba NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.682
2ekl NADD-3-phosphoglycerate dehydrogenase / 0.682
1ie3 NADMalate dehydrogenase / 0.681
4oaq NDPR-specific carbonyl reductase / 0.681
1dxy NADD-2-hydroxyisocaproate dehydrogenase 1.1.1 0.680
2vwh NAPGlucose 1-dehydrogenase / 0.680
4nfs NAJAlcohol dehydrogenase E chain 1.1.1.1 0.680
3jyo NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.679
5bsg NAPPyrroline-5-carboxylate reductase / 0.679
2c59 NADGDP-mannose 3,5-epimerase 5.1.3.18 0.678
2g82 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.678
5kcz NAJAlcohol dehydrogenase E chain 1.1.1.1 0.678
4dwv NAJAlcohol dehydrogenase E chain 1.1.1.1 0.677
4nfh NAJAlcohol dehydrogenase E chain 1.1.1.1 0.677
5cds NAJAlcohol dehydrogenase E chain 1.1.1.1 0.677
2fkn NADUrocanate hydratase 4.2.1.49 0.676
3oq6 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.676
4rqu NADAlcohol dehydrogenase class-P / 0.676
5cdt NAJAlcohol dehydrogenase E chain 1.1.1.1 0.676
1y7t NDPMalate dehydrogenase / 0.675
2fzw NADAlcohol dehydrogenase class-3 1.1.1.1 0.675
2p9e NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.675
1c1d NAIPhenylalanine dehydrogenase / 0.674
1e6w NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.674
3nt2 NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.674
4cr8 NADN-acylmannosamine 1-dehydrogenase 1.1.1.233 0.674
4l0q NADAlcohol dehydrogenase class-3 / 0.674
2hjr APRMalate dehydrogenase, adjacent gene encodes predicted lactate dehydrogenase / 0.673
4i1i NADMalate dehydrogenase / 0.673
4j49 NAIUncharacterized protein / 0.673
1j5p NADL-aspartate dehydrogenase 1.4.1.21 0.672
3uko NADAlcohol dehydrogenase class-3 / 0.672
2g5c NADPrephenate dehydrogenase / 0.671
2p9c NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.671
4dl9 NADS-(hydroxymethyl)glutathione dehydrogenase / 0.671
1q7g NHOHomoserine dehydrogenase 1.1.1.3 0.670
2vhz NAIAlanine dehydrogenase 1.4.1.1 0.670
3abi NADUncharacterized protein / 0.670
1kvr NADUDP-glucose 4-epimerase 5.1.3.2 0.669
1n2s NAIdTDP-4-dehydrorhamnose reductase 1.1.1.133 0.669
2o23 NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.669
3m2t NADProbable dehydrogenase / 0.669
1up7 NAD6-phospho-beta-glucosidase BglT 3.2.1.86 0.668
1wp4 NDP3-hydroxyisobutyrate dehydrogenase / 0.667
2x0r NADMalate dehydrogenase / 0.667
1j0x NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.666
1xcb NADRedox-sensing transcriptional repressor Rex / 0.666
3sxp NADADP-L-glycero-D-mannoheptose-6-epimerase / 0.666
1bws NDPGDP-L-fucose synthase / 0.665
2zb3 NDPProstaglandin reductase 2 1.3.1.48 0.665
4b7x NAPProbable oxidoreductase / 0.665
1emd NADMalate dehydrogenase / 0.662
1gad NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.662
2vwq NAPGlucose 1-dehydrogenase / 0.662
2vyv NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.662
4yr9 NADL-threonine 3-dehydrogenase, mitochondrial 1.1.1.103 0.662
3ggp NADPrephenate dehydrogenase / 0.661
4lcj NADC-terminal-binding protein 2 / 0.661
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.660
2ep7 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.660
3rfx NADUronate dehydrogenase / 0.660
3mje NDPAmphB / 0.659
4j4b NAIUncharacterized protein / 0.659
1pjc NADAlanine dehydrogenase / 0.658
1f17 NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.657
4hxy NDPPlm1 / 0.657
3pym NADGlyceraldehyde-3-phosphate dehydrogenase 3 1.2.1.12 0.656
4e5k NADPhosphonate dehydrogenase 1.20.1.1 0.656
5dt9 NADErythronate-4-phosphate dehydrogenase / 0.656
2nad NADFormate dehydrogenase / 0.655
3b1j NADGlyceraldehyde-3-phosphate dehydrogenase / 0.654
3uce NDPDehydrogenase / 0.654
1adc PADAlcohol dehydrogenase E chain 1.1.1.1 0.653
1bmd NADMalate dehydrogenase / 0.653
3cos NADAlcohol dehydrogenase 4 1.1.1.1 0.653
3f3s NADLambda-crystallin homolog / 0.653
4njo NADD-3-phosphoglycerate dehydrogenase, putative / 0.653
1il0 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.652
2c29 NAPDihydroflavonol 4-reductase / 0.652
3hja NADGlyceraldehyde-3-phosphate dehydrogenase / 0.652
4id9 NADPutative UDP-glucose 4-epimerase / 0.652
1g1a NADdTDP-glucose 4,6-dehydratase / 0.651
3ehe NADUDP-glucose 4-epimerase (GalE-1) / 0.651
1i36 NAPConserved protein / 0.650
3gvh NADMalate dehydrogenase / 0.650
3icp NADNAD-dependent epimerase/dehydratase / 0.650
3nx4 NAPPutative oxidoreductase / 0.650
4k9d NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.650