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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
4nd4 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
4nd4 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 1.134
4nd3 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 1.107
4nd2 A3DLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 1.073
2fn7 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 1.055
1pzh NADLactate dehydrogenase / 0.978
1sow NADL-lactate dehydrogenase 1.1.1.27 0.971
1t2d NADL-lactate dehydrogenase 1.1.1.27 0.968
1hyh NADL-2-hydroxyisocaproate dehydrogenase / 0.877
2a94 AP0L-lactate dehydrogenase 1.1.1.27 0.868
1pzg A3DLactate dehydrogenase / 0.864
1pzf A3DLactate dehydrogenase / 0.863
1r37 NADNAD-dependent alcohol dehydrogenase 1.1.1.1 0.861
2x0i NAIMalate dehydrogenase / 0.859
1t2c NAIL-lactate dehydrogenase 1.1.1.27 0.857
1uxk NADMalate dehydrogenase / 0.855
1gv0 NADMalate dehydrogenase / 0.853
3d4p NADL-lactate dehydrogenase 1 1.1.1.27 0.847
2dfd NADMalate dehydrogenase, mitochondrial 1.1.1.37 0.844
4ros APRMalate dehydrogenase / 0.843
4wlv NADMalate dehydrogenase, mitochondrial 1.1.1.37 0.841
5a1t NAIL-lactate dehydrogenase / 0.830
1uxj NADMalate dehydrogenase / 0.826
1ib6 NADMalate dehydrogenase / 0.823
4wlu NADMalate dehydrogenase, mitochondrial 1.1.1.37 0.819
1wze NADMalate dehydrogenase / 0.818
2vhx NADAlanine dehydrogenase 1.4.1.1 0.813
1h2b NAJNAD-dependent alcohol dehydrogenase / 0.809
2vhv NAIAlanine dehydrogenase 1.4.1.1 0.808
2a92 NAIL-lactate dehydrogenase / 0.806
2hjr APRMalate dehydrogenase, adjacent gene encodes predicted lactate dehydrogenase / 0.805
1b8v NADMalate dehydrogenase / 0.802
5kjc NAJAlcohol dehydrogenase E chain 1.1.1.1 0.797
4l4s NAIL-lactate dehydrogenase A chain 1.1.1.27 0.794
2aa3 AP0L-lactate dehydrogenase / 0.789
4jnk NAIL-lactate dehydrogenase A chain 1.1.1.27 0.788
4i1i NADMalate dehydrogenase / 0.787
2voj NADAlanine dehydrogenase 1.4.1.1 0.786
1lld NADL-lactate dehydrogenase 2 1.1.1.27 0.781
4j43 NADUncharacterized protein / 0.781
1o6z NADMalate dehydrogenase / 0.780
2g76 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.778
3two NDPMannitol dehydrogenase / 0.775
1bmd NADMalate dehydrogenase / 0.772
5kjf NAJAlcohol dehydrogenase E chain 1.1.1.1 0.770
4okn NAIL-lactate dehydrogenase A chain 1.1.1.27 0.769
1psd NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.765
1bdm NAXMalate dehydrogenase / 0.763
3h3j NADL-lactate dehydrogenase 1 1.1.1.27 0.762
1pjc NADAlanine dehydrogenase / 0.761
4c4o NADSADH / 0.761
1wzi NDPMalate dehydrogenase / 0.759
4nfh NAJAlcohol dehydrogenase E chain 1.1.1.1 0.759
1axe NADAlcohol dehydrogenase E chain 1.1.1.1 0.757
4j49 NADUncharacterized protein / 0.757
2vhz NAIAlanine dehydrogenase 1.4.1.1 0.756
4xd2 NAIAlcohol dehydrogenase E chain 1.1.1.1 0.756
5kje NAJAlcohol dehydrogenase E chain 1.1.1.1 0.756
2ohx NADAlcohol dehydrogenase E chain 1.1.1.1 0.753
1ie3 NADMalate dehydrogenase / 0.752
1yba NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.749
5mdh NADMalate dehydrogenase, cytoplasmic 1.1.1.37 0.746
1wwk NAD307aa long hypothetical phosphoglycerate dehydrogenase / 0.744
3wsw NADL-lactate dehydrogenase / 0.741
4mdh NADMalate dehydrogenase, cytoplasmic 1.1.1.37 0.740
5kj6 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.740
2p9g NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.739
4dxh NAJAlcohol dehydrogenase E chain 1.1.1.1 0.739
3h3f NAIL-lactate dehydrogenase A chain 1.1.1.27 0.738
3jv7 NADSecondary alcohol dehydrogenase / 0.738
4j4b NAIUncharacterized protein / 0.738
1u3v NADAlcohol dehydrogenase 1B 1.1.1.1 0.737
4j49 NAIUncharacterized protein / 0.737
4w6z 8IDAlcohol dehydrogenase 1 1.1.1.1 0.734
4dwv NAJAlcohol dehydrogenase E chain 1.1.1.1 0.733
2oxi NADAlcohol dehydrogenase E chain 1.1.1.1 0.732
3cos NADAlcohol dehydrogenase 4 1.1.1.1 0.732
1hld NADAlcohol dehydrogenase E chain 1.1.1.1 0.731
1ht0 NADAlcohol dehydrogenase 1C 1.1.1.1 0.731
4gkv NADAlcohol dehydrogenase, propanol-preferring 1.1.1.1 0.730
1guy NADMalate dehydrogenase / 0.729
1f8f NADBenzyl alcohol dehydrogenase / 0.728
2eer NADNAD-dependent alcohol dehydrogenase 1.1.1.1 0.728
3oq6 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.728
4dl9 NADS-(hydroxymethyl)glutathione dehydrogenase / 0.728
4dlb NADS-(hydroxymethyl)glutathione dehydrogenase / 0.728
5kcp NAJAlcohol dehydrogenase E chain 1.1.1.1 0.728
5kj1 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.728
1axg NADAlcohol dehydrogenase E chain 1.1.1.1 0.727
4jji NADAlcohol dehydrogenase class-3 / 0.727
2dt5 NADRedox-sensing transcriptional repressor Rex / 0.725
4ng5 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.725
1het NADAlcohol dehydrogenase E chain 1.1.1.1 0.722
3oet NADErythronate-4-phosphate dehydrogenase / 0.722
1llu NADAlcohol dehydrogenase / 0.720
1mgo NADAlcohol dehydrogenase E chain 1.1.1.1 0.719
2vhw NAIAlanine dehydrogenase 1.4.1.1 0.719
3n7u NADFormate dehydrogenase, chloroplastic/mitochondrial / 0.719
2x0r NADMalate dehydrogenase / 0.718
3gvh NADMalate dehydrogenase / 0.718
5cds NAJAlcohol dehydrogenase E chain 1.1.1.1 0.718
1ma0 NADAlcohol dehydrogenase class-3 1.1.1.1 0.717
1agn NADAlcohol dehydrogenase class 4 mu/sigma chain 1.1.1.1 0.716
4jk3 NADUncharacterized protein / 0.716
1lde NADAlcohol dehydrogenase E chain 1.1.1.1 0.715
2pa3 NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.715
4l0q NADAlcohol dehydrogenase class-3 / 0.715
4nfs NAJAlcohol dehydrogenase E chain 1.1.1.1 0.715
1hf3 NADAlcohol dehydrogenase E chain 1.1.1.1 0.714
1yqx NAPSinapyl alcohol dehydrogenase / 0.714
1hdz NADAlcohol dehydrogenase 1B 1.1.1.1 0.713
2ldb NADL-lactate dehydrogenase 1.1.1.27 0.713
4ywj NAD4-hydroxy-tetrahydrodipicolinate reductase / 0.713
5kcz NAJAlcohol dehydrogenase E chain 1.1.1.1 0.713
1pl6 NADSorbitol dehydrogenase 1.1.1.14 0.712
5cdt NAJAlcohol dehydrogenase E chain 1.1.1.1 0.712
1hsz NADAlcohol dehydrogenase 1B 1.1.1.1 0.709
1emd NADMalate dehydrogenase / 0.700
1pl8 NADSorbitol dehydrogenase 1.1.1.14 0.700
2dvm NAD439aa long hypothetical malate oxidoreductase (NAD) [malic enzyme] / 0.700
1e3l NADAlcohol dehydrogenase 4 1.1.1.1 0.699
1ur5 NADMalate dehydrogenase / 0.698
2jhf NADAlcohol dehydrogenase E chain 1.1.1.1 0.697
3kbo NDPGlyoxylate/hydroxypyruvate reductase A / 0.697
1c1d NAIPhenylalanine dehydrogenase / 0.695
3uko NADAlcohol dehydrogenase class-3 / 0.695
5cdg NAJAlcohol dehydrogenase E chain 1.1.1.1 0.694
4e5k NADPhosphonate dehydrogenase 1.20.1.1 0.693
1a71 NADAlcohol dehydrogenase E chain 1.1.1.1 0.692
2xaa NADSecondary alcohol dehydrogenase / 0.691
4e5n NADPhosphonate dehydrogenase 1.20.1.1 0.691
1dxy NADD-2-hydroxyisocaproate dehydrogenase 1.1.1 0.689
2ekl NADD-3-phosphoglycerate dehydrogenase / 0.687
1yqd NAPSinapyl alcohol dehydrogenase / 0.686
2p9c NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.686
1b8u NADMalate dehydrogenase / 0.685
1mp0 NADAlcohol dehydrogenase class-3 1.1.1.1 0.685
5env NADAlcohol dehydrogenase 1 1.1.1.1 0.685
1u7h NADPutative ornithine cyclodeaminase / 0.684
4z0p NDPNAD-dependent dehydrogenase / 0.683
4wlo NAIMalate dehydrogenase, mitochondrial 1.1.1.37 0.682
1f17 NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.681
4b7x NAPProbable oxidoreductase / 0.681
3q3c NADNAD-dependent L-serine dehydrogenase / 0.680
1adb CNDAlcohol dehydrogenase E chain 1.1.1.1 0.679
1adc PADAlcohol dehydrogenase E chain 1.1.1.1 0.679
2ome NADC-terminal-binding protein 2 / 0.679
3ggg NADPrephenate dehydrogenase / 0.679
4hfm NAP2-alkenal reductase (NADP(+)-dependent) / 0.679
1ez4 NADL-lactate dehydrogenase 1.1.1.27 0.676
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.676
1nyt NAPShikimate dehydrogenase (NADP(+)) / 0.675
1yb5 NAPQuinone oxidoreductase 1.6.5.5 0.675
3kb6 NADD-lactate dehydrogenase / 0.675
3uxy NADShort-chain dehydrogenase/reductase SDR / 0.675
2d8a NADL-threonine 3-dehydrogenase / 0.674
2p9e NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.674
4e5p NADPhosphonate dehydrogenase 1.20.1.1 0.674
2hu2 NADC-terminal binding protein 1 / 0.673
3qvx NADMyo-inositol-1-phosphate synthase (Ino1) / 0.672
1x7d NADPutative ornithine cyclodeaminase / 0.671
1kol NADGlutathione-independent formaldehyde dehydrogenase / 0.670
3pdu NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.670
4oaq NDPR-specific carbonyl reductase / 0.669
1o8c NDPProbable acrylyl-CoA reductase AcuI 1.3.1.84 0.668
2nad NADFormate dehydrogenase / 0.668
3gvi ADPMalate dehydrogenase / 0.667
2fzw NADAlcohol dehydrogenase class-3 1.1.1.1 0.666
2gsd NADFormate dehydrogenase / 0.665
2q3e NAIUDP-glucose 6-dehydrogenase 1.1.1.22 0.665
2e37 NADL-lactate dehydrogenase / 0.664
2vwh NAPGlucose 1-dehydrogenase / 0.663
3anm NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase 1.1.1.267 0.663
4y0k NAPAntE / 0.663
1hku NADC-terminal-binding protein 1 1.1.1 0.662
3qvs NADMyo-inositol-1-phosphate synthase (Ino1) / 0.661
3x2f NAIAdenosylhomocysteinase / 0.661
1p1h NADInositol-3-phosphate synthase 5.5.1.4 0.660
3abi NADUncharacterized protein / 0.660
3tqh NDPQuinone oxidoreductase / 0.660
1il0 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.659
2cdc NAPGlucose 1-dehydrogenase / 0.659
4y1b NAPAntE / 0.659
2c20 NADUDP-glucose 4-epimerase / 0.658
3cps NADGlyceraldehyde-3-phosphate dehydrogenase / 0.658
2bbw GP5Adenylate kinase 4, mitochondrial / 0.657
1n2s NAIdTDP-4-dehydrorhamnose reductase 1.1.1.133 0.656
3nt4 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.655
2c29 NAPDihydroflavonol 4-reductase / 0.654
2dc1 NADProbable L-aspartate dehydrogenase / 0.654
2ejv NADL-threonine 3-dehydrogenase / 0.654
2q1u NADPutative nucleotide sugar epimerase/ dehydratase / 0.654
4rvu NDPProbable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein) / 0.654
5ijz NAPNADP-specific glutamate dehydrogenase 1.4.1.4 0.654
1fk8 NAD3-alpha-hydroxysteroid dehydrogenase/carbonyl reductase 1.1.1.50 0.653
1geg NADDiacetyl reductase [(S)-acetoin forming] 1.1.1.304 0.653
1i2b NADUDP-sulfoquinovose synthase, chloroplastic 3.13.1.1 0.653
3jyp NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.653
4ej0 NAPADP-L-glycero-D-manno-heptose-6-epimerase / 0.653
1o0s NAINAD-dependent malic enzyme, mitochondrial 1.1.1.38 0.652
2p5y NADUDP-glucose 4-epimerase / 0.652
3ru7 NADUDP-N-acetylglucosamine 4-epimerase / 0.652
1sc6 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.651
2b5v NAPGlucose 1-dehydrogenase / 0.651
3hdh NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.651
3wle NAD(R)-specific carbonyl reductase / 0.651
3wmx NADNAD dependent epimerase/dehydratase / 0.651
4pvd NDPNADPH-dependent methylglyoxal reductase GRE2 / 0.651
2ggs NDPdTDP-4-dehydrorhamnose reductase / 0.650
3cif NADGlyceraldehyde-3-phosphate dehydrogenase / 0.650
5c7o NADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific 1.2.1.12 0.650