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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
4nd2 A3D Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4nd2 A3DLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 1.119
4nd4 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 1.073
4nd3 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 1.054
2fn7 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 1.029
1pzh NADLactate dehydrogenase / 0.943
1pzg A3DLactate dehydrogenase / 0.936
1t2d NADL-lactate dehydrogenase 1.1.1.27 0.919
2a94 AP0L-lactate dehydrogenase 1.1.1.27 0.918
1pzf A3DLactate dehydrogenase / 0.916
1sow NADL-lactate dehydrogenase 1.1.1.27 0.902
4ros APRMalate dehydrogenase / 0.865
5a1t NAIL-lactate dehydrogenase / 0.848
1r37 NADNAD-dependent alcohol dehydrogenase 1.1.1.1 0.840
2aa3 AP0L-lactate dehydrogenase / 0.824
1gv0 NADMalate dehydrogenase / 0.813
1t2c NAIL-lactate dehydrogenase 1.1.1.27 0.806
1hyh NADL-2-hydroxyisocaproate dehydrogenase / 0.802
1uxk NADMalate dehydrogenase / 0.799
3d4p NADL-lactate dehydrogenase 1 1.1.1.27 0.797
2a92 NAIL-lactate dehydrogenase / 0.792
2voj NADAlanine dehydrogenase 1.4.1.1 0.790
4okn NAIL-lactate dehydrogenase A chain 1.1.1.27 0.789
2dfd NADMalate dehydrogenase, mitochondrial 1.1.1.37 0.786
2x0i NAIMalate dehydrogenase / 0.786
4wlv NADMalate dehydrogenase, mitochondrial 1.1.1.37 0.782
1ib6 NADMalate dehydrogenase / 0.780
1h2b NAJNAD-dependent alcohol dehydrogenase / 0.777
4wlu NADMalate dehydrogenase, mitochondrial 1.1.1.37 0.775
1wze NADMalate dehydrogenase / 0.774
2hjr APRMalate dehydrogenase, adjacent gene encodes predicted lactate dehydrogenase / 0.766
4mdh NADMalate dehydrogenase, cytoplasmic 1.1.1.37 0.766
1uxj NADMalate dehydrogenase / 0.765
1bmd NADMalate dehydrogenase / 0.764
4l4s NAIL-lactate dehydrogenase A chain 1.1.1.27 0.759
5kjf NAJAlcohol dehydrogenase E chain 1.1.1.1 0.757
3h3j NADL-lactate dehydrogenase 1 1.1.1.27 0.756
2vhv NAIAlanine dehydrogenase 1.4.1.1 0.753
4jnk NAIL-lactate dehydrogenase A chain 1.1.1.27 0.753
1psd NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.752
4i1i NADMalate dehydrogenase / 0.752
2g76 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.751
1dxy NADD-2-hydroxyisocaproate dehydrogenase 1.1.1 0.747
1axe NADAlcohol dehydrogenase E chain 1.1.1.1 0.744
1bdm NAXMalate dehydrogenase / 0.744
1wzi NDPMalate dehydrogenase / 0.743
5env NADAlcohol dehydrogenase 1 1.1.1.1 0.740
3oet NADErythronate-4-phosphate dehydrogenase / 0.739
2ekl NADD-3-phosphoglycerate dehydrogenase / 0.738
1lde NADAlcohol dehydrogenase E chain 1.1.1.1 0.737
2ohx NADAlcohol dehydrogenase E chain 1.1.1.1 0.737
5kjc NAJAlcohol dehydrogenase E chain 1.1.1.1 0.737
4nfs NAJAlcohol dehydrogenase E chain 1.1.1.1 0.736
5kje NAJAlcohol dehydrogenase E chain 1.1.1.1 0.736
2oxi NADAlcohol dehydrogenase E chain 1.1.1.1 0.734
1b8v NADMalate dehydrogenase / 0.731
1lld NADL-lactate dehydrogenase 2 1.1.1.27 0.728
1wwk NAD307aa long hypothetical phosphoglycerate dehydrogenase / 0.728
1het NADAlcohol dehydrogenase E chain 1.1.1.1 0.725
1ht0 NADAlcohol dehydrogenase 1C 1.1.1.1 0.725
4c4o NADSADH / 0.724
1o6z NADMalate dehydrogenase / 0.723
1u3v NADAlcohol dehydrogenase 1B 1.1.1.1 0.723
2vhx NADAlanine dehydrogenase 1.4.1.1 0.723
2vhz NAIAlanine dehydrogenase 1.4.1.1 0.722
4ng5 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.722
1hld NADAlcohol dehydrogenase E chain 1.1.1.1 0.720
5mdh NADMalate dehydrogenase, cytoplasmic 1.1.1.37 0.715
1ur5 NADMalate dehydrogenase / 0.711
4w6z 8IDAlcohol dehydrogenase 1 1.1.1.1 0.711
3cos NADAlcohol dehydrogenase 4 1.1.1.1 0.709
3gvh NADMalate dehydrogenase / 0.708
4dlb NADS-(hydroxymethyl)glutathione dehydrogenase / 0.708
5cdt NAJAlcohol dehydrogenase E chain 1.1.1.1 0.706
5kcp NAJAlcohol dehydrogenase E chain 1.1.1.1 0.706
1c1d NAIPhenylalanine dehydrogenase / 0.705
3h3f NAIL-lactate dehydrogenase A chain 1.1.1.27 0.705
1pjc NADAlanine dehydrogenase / 0.704
1yqd NAPSinapyl alcohol dehydrogenase / 0.704
1ie3 NADMalate dehydrogenase / 0.702
3n7u NADFormate dehydrogenase, chloroplastic/mitochondrial / 0.702
2vhw NAIAlanine dehydrogenase 1.4.1.1 0.700
1pl6 NADSorbitol dehydrogenase 1.1.1.14 0.699
1yqx NAPSinapyl alcohol dehydrogenase / 0.699
1u7h NADPutative ornithine cyclodeaminase / 0.696
4jk3 NADUncharacterized protein / 0.696
3ggp NADPrephenate dehydrogenase / 0.695
4dwv NAJAlcohol dehydrogenase E chain 1.1.1.1 0.695
1agn NADAlcohol dehydrogenase class 4 mu/sigma chain 1.1.1.1 0.694
1hf3 NADAlcohol dehydrogenase E chain 1.1.1.1 0.694
1f8f NADBenzyl alcohol dehydrogenase / 0.693
1x7d NADPutative ornithine cyclodeaminase / 0.693
4j43 NADUncharacterized protein / 0.693
3wsw NADL-lactate dehydrogenase / 0.692
2pa3 NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.691
1mgo NADAlcohol dehydrogenase E chain 1.1.1.1 0.690
4j4b NAIUncharacterized protein / 0.690
3qvx NADMyo-inositol-1-phosphate synthase (Ino1) / 0.688
4j49 NAIUncharacterized protein / 0.687
1obb NADAlpha-glucosidase 3.2.1.20 0.685
2dvm NAD439aa long hypothetical malate oxidoreductase (NAD) [malic enzyme] / 0.685
2ldb NADL-lactate dehydrogenase 1.1.1.27 0.683
4e5k NADPhosphonate dehydrogenase 1.20.1.1 0.682
4xq9 NADHomospermidine synthase 2.5.1.44 0.682
1pl8 NADSorbitol dehydrogenase 1.1.1.14 0.680
1emd NADMalate dehydrogenase / 0.678
2p9e NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.674
3gvi ADPMalate dehydrogenase / 0.674
1guy NADMalate dehydrogenase / 0.672
1mp0 NADAlcohol dehydrogenase class-3 1.1.1.1 0.672
3wle NAD(R)-specific carbonyl reductase / 0.672
2xaa NADSecondary alcohol dehydrogenase / 0.671
1hdz NADAlcohol dehydrogenase 1B 1.1.1.1 0.670
3anm NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase 1.1.1.267 0.669
3jyp NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.668
2p9c NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.667
1b8u NADMalate dehydrogenase / 0.666
3ggg NADPrephenate dehydrogenase / 0.666
2gsd NADFormate dehydrogenase / 0.665
1ez4 NADL-lactate dehydrogenase 1.1.1.27 0.664
1f17 NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.664
3uko NADAlcohol dehydrogenase class-3 / 0.664
4e5p NADPhosphonate dehydrogenase 1.20.1.1 0.664
4l0q NADAlcohol dehydrogenase class-3 / 0.664
4tvb NADHomospermidine synthase 2.5.1.44 0.663
1a71 NADAlcohol dehydrogenase E chain 1.1.1.1 0.662
4dl9 NADS-(hydroxymethyl)glutathione dehydrogenase / 0.662
1f0y NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.661
2yjz NAPMetalloreductase STEAP4 1.16.1 0.661
4ej0 NAPADP-L-glycero-D-manno-heptose-6-epimerase / 0.661
4gkv NADAlcohol dehydrogenase, propanol-preferring 1.1.1.1 0.661
1p1h NADInositol-3-phosphate synthase 5.5.1.4 0.660
2yy7 NADL-threonine dehydrogenase / 0.660
3d64 NADAdenosylhomocysteinase / 0.659
2c20 NADUDP-glucose 4-epimerase / 0.658
2pv7 NADT-protein 1.3.1.12 0.658
2ag5 NAD3-hydroxybutyrate dehydrogenase type 2 / 0.657
4xcv NDPProbable hydroxyacid dehydrogenase protein / 0.657
2hdh NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.656
2nnl NAPDihydroflavonol 4-reductase 1.1.1.219 0.656
3m2t NADProbable dehydrogenase / 0.656
4kug NAD3-hydroxybutyryl-CoA dehydrogenase / 0.656
2x0r NADMalate dehydrogenase / 0.655
1nfr NAD3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase 1.1.1.53 0.654
2p5y NADUDP-glucose 4-epimerase / 0.654
4y1b NAPAntE / 0.654
3kb6 NADD-lactate dehydrogenase / 0.653
1kol NADGlutathione-independent formaldehyde dehydrogenase / 0.652
2c29 NAPDihydroflavonol 4-reductase / 0.652
3f3s NADLambda-crystallin homolog / 0.651
1omo NADAlanine dehydrogenase / 0.650
3wmx NADNAD dependent epimerase/dehydratase / 0.650
4j49 NADUncharacterized protein / 0.650
4xd2 NAIAlcohol dehydrogenase E chain 1.1.1.1 0.650