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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
4nd3 NAD Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4nd3 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 1.116
4nd4 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 1.107
2fn7 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 1.063
4nd2 A3DLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 1.054
1sow NADL-lactate dehydrogenase 1.1.1.27 1.001
1pzh NADLactate dehydrogenase / 0.999
1t2d NADL-lactate dehydrogenase 1.1.1.27 0.988
2a94 AP0L-lactate dehydrogenase 1.1.1.27 0.918
1pzf A3DLactate dehydrogenase / 0.917
1pzg A3DLactate dehydrogenase / 0.905
5a1t NAIL-lactate dehydrogenase / 0.873
4ros APRMalate dehydrogenase / 0.868
1t2c NAIL-lactate dehydrogenase 1.1.1.27 0.864
2a92 NAIL-lactate dehydrogenase / 0.863
1gv0 NADMalate dehydrogenase / 0.853
1uxk NADMalate dehydrogenase / 0.853
1r37 NADNAD-dependent alcohol dehydrogenase 1.1.1.1 0.848
2aa3 AP0L-lactate dehydrogenase / 0.836
2x0i NAIMalate dehydrogenase / 0.827
2dfd NADMalate dehydrogenase, mitochondrial 1.1.1.37 0.826
1hyh NADL-2-hydroxyisocaproate dehydrogenase / 0.825
1uxj NADMalate dehydrogenase / 0.824
4wlv NADMalate dehydrogenase, mitochondrial 1.1.1.37 0.823
1b8v NADMalate dehydrogenase / 0.817
1wze NADMalate dehydrogenase / 0.812
4wlu NADMalate dehydrogenase, mitochondrial 1.1.1.37 0.805
1yba NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.803
3d4p NADL-lactate dehydrogenase 1 1.1.1.27 0.801
1ib6 NADMalate dehydrogenase / 0.795
4i1i NADMalate dehydrogenase / 0.788
4okn NAIL-lactate dehydrogenase A chain 1.1.1.27 0.787
2hjr APRMalate dehydrogenase, adjacent gene encodes predicted lactate dehydrogenase / 0.784
2vhx NADAlanine dehydrogenase 1.4.1.1 0.781
4jnk NAIL-lactate dehydrogenase A chain 1.1.1.27 0.780
4mdh NADMalate dehydrogenase, cytoplasmic 1.1.1.37 0.779
1bmd NADMalate dehydrogenase / 0.775
1h2b NAJNAD-dependent alcohol dehydrogenase / 0.766
4j43 NADUncharacterized protein / 0.766
1bdm NAXMalate dehydrogenase / 0.765
2eer NADNAD-dependent alcohol dehydrogenase 1.1.1.1 0.763
3h3j NADL-lactate dehydrogenase 1 1.1.1.27 0.763
2vhv NAIAlanine dehydrogenase 1.4.1.1 0.761
1axe NADAlcohol dehydrogenase E chain 1.1.1.1 0.759
3h3f NAIL-lactate dehydrogenase A chain 1.1.1.27 0.759
1lld NADL-lactate dehydrogenase 2 1.1.1.27 0.757
4c4o NADSADH / 0.754
1wzi NDPMalate dehydrogenase / 0.753
4j49 NADUncharacterized protein / 0.752
5kjc NAJAlcohol dehydrogenase E chain 1.1.1.1 0.752
1wwk NAD307aa long hypothetical phosphoglycerate dehydrogenase / 0.749
1lde NADAlcohol dehydrogenase E chain 1.1.1.1 0.747
3jv7 NADSecondary alcohol dehydrogenase / 0.740
1psd NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.739
4l4s NAIL-lactate dehydrogenase A chain 1.1.1.27 0.739
1ie3 NADMalate dehydrogenase / 0.738
3gvh NADMalate dehydrogenase / 0.738
4gkv NADAlcohol dehydrogenase, propanol-preferring 1.1.1.1 0.737
4j4b NAIUncharacterized protein / 0.732
1f8f NADBenzyl alcohol dehydrogenase / 0.731
4j49 NAIUncharacterized protein / 0.731
1hld NADAlcohol dehydrogenase E chain 1.1.1.1 0.730
2vhz NAIAlanine dehydrogenase 1.4.1.1 0.730
2voj NADAlanine dehydrogenase 1.4.1.1 0.727
4dl9 NADS-(hydroxymethyl)glutathione dehydrogenase / 0.726
1u8x NADMaltose-6'-phosphate glucosidase 3.2.1.122 0.725
1u7h NADPutative ornithine cyclodeaminase / 0.724
3two NDPMannitol dehydrogenase / 0.723
4jji NADAlcohol dehydrogenase class-3 / 0.723
1o6z NADMalate dehydrogenase / 0.722
5mdh NADMalate dehydrogenase, cytoplasmic 1.1.1.37 0.720
4oaq NDPR-specific carbonyl reductase / 0.718
1hdz NADAlcohol dehydrogenase 1B 1.1.1.1 0.717
3oet NADErythronate-4-phosphate dehydrogenase / 0.716
4dlb NADS-(hydroxymethyl)glutathione dehydrogenase / 0.716
1pjc NADAlanine dehydrogenase / 0.715
2pa3 NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.714
1e3l NADAlcohol dehydrogenase 4 1.1.1.1 0.713
2dt5 NADRedox-sensing transcriptional repressor Rex / 0.713
4nfs NAJAlcohol dehydrogenase E chain 1.1.1.1 0.713
1mgo NADAlcohol dehydrogenase E chain 1.1.1.1 0.711
4ng5 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.711
5kcp NAJAlcohol dehydrogenase E chain 1.1.1.1 0.711
5kcz NAJAlcohol dehydrogenase E chain 1.1.1.1 0.711
5kj6 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.711
5kje NAJAlcohol dehydrogenase E chain 1.1.1.1 0.711
1pl8 NADSorbitol dehydrogenase 1.1.1.14 0.710
2oxi NADAlcohol dehydrogenase E chain 1.1.1.1 0.710
4nfh NAJAlcohol dehydrogenase E chain 1.1.1.1 0.710
5kjf NAJAlcohol dehydrogenase E chain 1.1.1.1 0.707
1axg NADAlcohol dehydrogenase E chain 1.1.1.1 0.706
1hsz NADAlcohol dehydrogenase 1B 1.1.1.1 0.706
1yqd NAPSinapyl alcohol dehydrogenase / 0.706
4w6z 8IDAlcohol dehydrogenase 1 1.1.1.1 0.706
1ht0 NADAlcohol dehydrogenase 1C 1.1.1.1 0.705
2g76 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.705
2ome NADC-terminal-binding protein 2 / 0.705
2vhw NAIAlanine dehydrogenase 1.4.1.1 0.702
2p9g NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.701
5cdt NAJAlcohol dehydrogenase E chain 1.1.1.1 0.700
4jk3 NADUncharacterized protein / 0.699
2ohx NADAlcohol dehydrogenase E chain 1.1.1.1 0.697
1pl6 NADSorbitol dehydrogenase 1.1.1.14 0.696
1u3v NADAlcohol dehydrogenase 1B 1.1.1.1 0.696
1b8u NADMalate dehydrogenase / 0.695
1yqx NAPSinapyl alcohol dehydrogenase / 0.695
3oq6 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.695
4dwv NAJAlcohol dehydrogenase E chain 1.1.1.1 0.695
5cdg NAJAlcohol dehydrogenase E chain 1.1.1.1 0.695
5cds NAJAlcohol dehydrogenase E chain 1.1.1.1 0.695
5kj1 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.695
6adh NADAlcohol dehydrogenase E chain 1.1.1.1 0.695
1j5p NADL-aspartate dehydrogenase 1.4.1.21 0.692
4dxh NAJAlcohol dehydrogenase E chain 1.1.1.1 0.691
2hu2 NADC-terminal binding protein 1 / 0.689
4pvd NDPNADPH-dependent methylglyoxal reductase GRE2 / 0.689
5ees NAP4-hydroxy-tetrahydrodipicolinate reductase / 0.689
1kol NADGlutathione-independent formaldehyde dehydrogenase / 0.688
1n2s NAIdTDP-4-dehydrorhamnose reductase 1.1.1.133 0.688
5env NADAlcohol dehydrogenase 1 1.1.1.1 0.687
2x0r NADMalate dehydrogenase / 0.686
3wle NAD(R)-specific carbonyl reductase / 0.686
1mp0 NADAlcohol dehydrogenase class-3 1.1.1.1 0.684
2fzw NADAlcohol dehydrogenase class-3 1.1.1.1 0.684
1ma0 NADAlcohol dehydrogenase class-3 1.1.1.1 0.683
1ur5 NADMalate dehydrogenase / 0.683
4e5k NADPhosphonate dehydrogenase 1.20.1.1 0.683
4wlo NAIMalate dehydrogenase, mitochondrial 1.1.1.37 0.683
1hf3 NADAlcohol dehydrogenase E chain 1.1.1.1 0.682
2ldb NADL-lactate dehydrogenase 1.1.1.27 0.682
3cif NADGlyceraldehyde-3-phosphate dehydrogenase / 0.682
1sc6 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.680
3kbo NDPGlyoxylate/hydroxypyruvate reductase A / 0.680
4l0q NADAlcohol dehydrogenase class-3 / 0.680
2nad NADFormate dehydrogenase / 0.677
1a71 NADAlcohol dehydrogenase E chain 1.1.1.1 0.676
2d8a NADL-threonine 3-dehydrogenase / 0.675
2p9c NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.675
4ejm NAPPutative zinc-binding dehydrogenase / 0.675
2ejv NADL-threonine 3-dehydrogenase / 0.673
3qvx NADMyo-inositol-1-phosphate synthase (Ino1) / 0.673
1ez4 NADL-lactate dehydrogenase 1.1.1.27 0.671
2o4c NADErythronate-4-phosphate dehydrogenase / 0.671
3kb6 NADD-lactate dehydrogenase / 0.671
4z0p NDPNAD-dependent dehydrogenase / 0.671
2ekl NADD-3-phosphoglycerate dehydrogenase / 0.670
3uko NADAlcohol dehydrogenase class-3 / 0.670
2dc1 NADProbable L-aspartate dehydrogenase / 0.667
4ej0 NAPADP-L-glycero-D-manno-heptose-6-epimerase / 0.667
4lis NADUDP-glucose 4-epimerase (Eurofung) / 0.667
2c29 NAPDihydroflavonol 4-reductase / 0.666
2xaa NADSecondary alcohol dehydrogenase / 0.666
3gvi ADPMalate dehydrogenase / 0.666
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.666
3wsw NADL-lactate dehydrogenase / 0.665
1c1d NAIPhenylalanine dehydrogenase / 0.664
4b7x NAPProbable oxidoreductase / 0.664
2e37 NADL-lactate dehydrogenase / 0.663
4xcv NDPProbable hydroxyacid dehydrogenase protein / 0.663
2dph NADFormaldehyde dismutase / 0.662
3abi NADUncharacterized protein / 0.662
4hfm NAP2-alkenal reductase (NADP(+)-dependent) / 0.662
1hku NADC-terminal-binding protein 1 1.1.1 0.661
2bbw GP5Adenylate kinase 4, mitochondrial / 0.661
3ggg NADPrephenate dehydrogenase / 0.661
3wmx NADNAD dependent epimerase/dehydratase / 0.661
4e5n NADPhosphonate dehydrogenase 1.20.1.1 0.661
1fk8 NAD3-alpha-hydroxysteroid dehydrogenase/carbonyl reductase 1.1.1.50 0.660
2vwh NAPGlucose 1-dehydrogenase / 0.660
3tqh NDPQuinone oxidoreductase / 0.660
3wfj NAD2-dehydropantoate 2-reductase / 0.660
1p1h NADInositol-3-phosphate synthase 5.5.1.4 0.659
3m6i NADL-arabinitol 4-dehydrogenase 1.1.1.12 0.659
2c20 NADUDP-glucose 4-epimerase / 0.658
4cpd NADAlcohol dehydrogenase / 0.658
2cdc NAPGlucose 1-dehydrogenase / 0.656
3wid NAPGlucose 1-dehydrogenase / 0.656
2hdh NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.655
3gy0 NAPNAD(P)-dependent oxidoreductase / 0.654
4xye NADFormate dehydrogenase / 0.654
4rvu NDPProbable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein) / 0.653
2dvm NAD439aa long hypothetical malate oxidoreductase (NAD) [malic enzyme] / 0.652
4e5p NADPhosphonate dehydrogenase 1.20.1.1 0.652
1agn NADAlcohol dehydrogenase class 4 mu/sigma chain 1.1.1.1 0.651
1m75 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.651
1x7d NADPutative ornithine cyclodeaminase / 0.651
2yy7 NADL-threonine dehydrogenase / 0.651
3pdu NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.651
4weq NAPNAD-dependent dehydrogenase / 0.650