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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
3d4p NAD L-lactate dehydrogenase 1 1.1.1.27

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3d4p NADL-lactate dehydrogenase 1 1.1.1.27 1.131
3h3j NADL-lactate dehydrogenase 1 1.1.1.27 1.029
1hyh NADL-2-hydroxyisocaproate dehydrogenase / 0.908
4okn NAIL-lactate dehydrogenase A chain 1.1.1.27 0.903
2x0i NAIMalate dehydrogenase / 0.867
1lld NADL-lactate dehydrogenase 2 1.1.1.27 0.851
4nd4 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.847
4jnk NAIL-lactate dehydrogenase A chain 1.1.1.27 0.839
1uxk NADMalate dehydrogenase / 0.833
4l4s NAIL-lactate dehydrogenase A chain 1.1.1.27 0.831
1ib6 NADMalate dehydrogenase / 0.822
5kjf NAJAlcohol dehydrogenase E chain 1.1.1.1 0.819
2fn7 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.818
1pzh NADLactate dehydrogenase / 0.815
2dfd NADMalate dehydrogenase, mitochondrial 1.1.1.37 0.813
5kcp NAJAlcohol dehydrogenase E chain 1.1.1.1 0.813
4dxh NAJAlcohol dehydrogenase E chain 1.1.1.1 0.812
5kcz NAJAlcohol dehydrogenase E chain 1.1.1.1 0.809
5kj6 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.804
2ohx NADAlcohol dehydrogenase E chain 1.1.1.1 0.803
4nd3 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.801
1hdz NADAlcohol dehydrogenase 1B 1.1.1.1 0.799
4nd2 A3DLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.797
1h2b NAJNAD-dependent alcohol dehydrogenase / 0.795
1t2d NADL-lactate dehydrogenase 1.1.1.27 0.795
1o6z NADMalate dehydrogenase / 0.794
5kj1 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.793
1u3v NADAlcohol dehydrogenase 1B 1.1.1.1 0.788
5kjc NAJAlcohol dehydrogenase E chain 1.1.1.1 0.788
4j43 NADUncharacterized protein / 0.782
1ht0 NADAlcohol dehydrogenase 1C 1.1.1.1 0.781
4wlu NADMalate dehydrogenase, mitochondrial 1.1.1.37 0.778
1hsz NADAlcohol dehydrogenase 1B 1.1.1.1 0.777
1mgo NADAlcohol dehydrogenase E chain 1.1.1.1 0.777
1ma0 NADAlcohol dehydrogenase class-3 1.1.1.1 0.775
1het NADAlcohol dehydrogenase E chain 1.1.1.1 0.774
4cpd NADAlcohol dehydrogenase / 0.774
1yqd NAPSinapyl alcohol dehydrogenase / 0.772
1ie3 NADMalate dehydrogenase / 0.770
1hf3 NADAlcohol dehydrogenase E chain 1.1.1.1 0.768
1guy NADMalate dehydrogenase / 0.767
1lde NADAlcohol dehydrogenase E chain 1.1.1.1 0.766
4gkv NADAlcohol dehydrogenase, propanol-preferring 1.1.1.1 0.766
2vhv NAIAlanine dehydrogenase 1.4.1.1 0.765
4j49 NADUncharacterized protein / 0.762
4ros APRMalate dehydrogenase / 0.761
4oaq NDPR-specific carbonyl reductase / 0.759
5cds NAJAlcohol dehydrogenase E chain 1.1.1.1 0.759
1mp0 NADAlcohol dehydrogenase class-3 1.1.1.1 0.756
1uxj NADMalate dehydrogenase / 0.755
2a94 AP0L-lactate dehydrogenase 1.1.1.27 0.753
3wsw NADL-lactate dehydrogenase / 0.753
1r37 NADNAD-dependent alcohol dehydrogenase 1.1.1.1 0.752
2voj NADAlanine dehydrogenase 1.4.1.1 0.750
3jv7 NADSecondary alcohol dehydrogenase / 0.749
1sow NADL-lactate dehydrogenase 1.1.1.27 0.748
4xd2 NAIAlcohol dehydrogenase E chain 1.1.1.1 0.748
2fze APRAlcohol dehydrogenase class-3 1.1.1.1 0.747
4jk3 NADUncharacterized protein / 0.747
1f8f NADBenzyl alcohol dehydrogenase / 0.746
1f0y NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.745
4dl9 NADS-(hydroxymethyl)glutathione dehydrogenase / 0.744
4c4o NADSADH / 0.743
5cdg NAJAlcohol dehydrogenase E chain 1.1.1.1 0.743
5kje NAJAlcohol dehydrogenase E chain 1.1.1.1 0.743
4nfh NAJAlcohol dehydrogenase E chain 1.1.1.1 0.742
1gv0 NADMalate dehydrogenase / 0.741
4j4b NAIUncharacterized protein / 0.741
4nfs NAJAlcohol dehydrogenase E chain 1.1.1.1 0.741
4w6z 8IDAlcohol dehydrogenase 1 1.1.1.1 0.740
3oq6 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.739
4dwv NAJAlcohol dehydrogenase E chain 1.1.1.1 0.739
1hld NADAlcohol dehydrogenase E chain 1.1.1.1 0.738
2o4c NADErythronate-4-phosphate dehydrogenase / 0.738
3wle NAD(R)-specific carbonyl reductase / 0.736
1axe NADAlcohol dehydrogenase E chain 1.1.1.1 0.734
3h3f NAIL-lactate dehydrogenase A chain 1.1.1.27 0.734
4j49 NAIUncharacterized protein / 0.734
4wlv NADMalate dehydrogenase, mitochondrial 1.1.1.37 0.733
1il0 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.732
3pef NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.731
3nt2 NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.730
1teh NADAlcohol dehydrogenase class-3 1.1.1.1 0.729
2fzw NADAlcohol dehydrogenase class-3 1.1.1.1 0.729
4ywj NAD4-hydroxy-tetrahydrodipicolinate reductase / 0.729
2oxi NADAlcohol dehydrogenase E chain 1.1.1.1 0.728
1bws NDPGDP-L-fucose synthase / 0.727
2vhx NADAlanine dehydrogenase 1.4.1.1 0.727
3two NDPMannitol dehydrogenase / 0.727
5cdt NAJAlcohol dehydrogenase E chain 1.1.1.1 0.727
1pjc NADAlanine dehydrogenase / 0.725
2g5c NADPrephenate dehydrogenase / 0.724
5a1t NAIL-lactate dehydrogenase / 0.724
1x7d NADPutative ornithine cyclodeaminase / 0.722
1kol NADGlutathione-independent formaldehyde dehydrogenase / 0.721
4ng5 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.721
4gl4 NAIAlcohol dehydrogenase class-3 / 0.720
4mdh NADMalate dehydrogenase, cytoplasmic 1.1.1.37 0.720
2x0r NADMalate dehydrogenase / 0.719
4b7x NAPProbable oxidoreductase / 0.719
4jji NADAlcohol dehydrogenase class-3 / 0.719
3cos NADAlcohol dehydrogenase 4 1.1.1.1 0.718
4l0q NADAlcohol dehydrogenase class-3 / 0.718
1wp4 NDP3-hydroxyisobutyrate dehydrogenase / 0.717
3tri NAPPyrroline-5-carboxylate reductase / 0.717
3uko NADAlcohol dehydrogenase class-3 / 0.716
2eer NADNAD-dependent alcohol dehydrogenase 1.1.1.1 0.714
1zem NADXylitol dehydrogenase / 0.712
4dlb NADS-(hydroxymethyl)glutathione dehydrogenase / 0.712
1pzf A3DLactate dehydrogenase / 0.711
3qvx NADMyo-inositol-1-phosphate synthase (Ino1) / 0.711
4xgi NADGlutamate dehydrogenase / 0.711
1heu NADAlcohol dehydrogenase E chain 1.1.1.1 0.710
4rqu NADAlcohol dehydrogenase class-P / 0.710
1yba NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.709
2y05 NAPProstaglandin reductase 1 / 0.709
4i1i NADMalate dehydrogenase / 0.709
1u7h NADPutative ornithine cyclodeaminase / 0.708
1adb CNDAlcohol dehydrogenase E chain 1.1.1.1 0.707
1t2c NAIL-lactate dehydrogenase 1.1.1.27 0.707
1yqx NAPSinapyl alcohol dehydrogenase / 0.707
3ggp NADPrephenate dehydrogenase / 0.707
3oet NADErythronate-4-phosphate dehydrogenase / 0.707
1m76 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.706
2a92 NAIL-lactate dehydrogenase / 0.706
1yb5 NAPQuinone oxidoreductase 1.6.5.5 0.705
1emd NADMalate dehydrogenase / 0.702
1sc6 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.702
3tqh NDPQuinone oxidoreductase / 0.702
5mdh NADMalate dehydrogenase, cytoplasmic 1.1.1.37 0.701
1a71 NADAlcohol dehydrogenase E chain 1.1.1.1 0.700
1b3r NADAdenosylhomocysteinase 3.3.1.1 0.700
2jhf NADAlcohol dehydrogenase E chain 1.1.1.1 0.699
2q3e NAIUDP-glucose 6-dehydrogenase 1.1.1.22 0.699
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.699
4rls NAIL-lactate dehydrogenase A chain 1.1.1.27 0.699
1ez4 NADL-lactate dehydrogenase 1.1.1.27 0.697
1llu NADAlcohol dehydrogenase / 0.697
3adp NAILambda-crystallin 1.1.1.45 0.697
3d64 NADAdenosylhomocysteinase / 0.697
3f3s NADLambda-crystallin homolog / 0.697
3qvs NADMyo-inositol-1-phosphate synthase (Ino1) / 0.696
6adh NADAlcohol dehydrogenase E chain 1.1.1.1 0.696
1ur5 NADMalate dehydrogenase / 0.695
2ldb NADL-lactate dehydrogenase 1.1.1.27 0.695
1m75 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.693
3ggo NAIPrephenate dehydrogenase / 0.693
3ikt NADRedox-sensing transcriptional repressor Rex / 0.693
1yjq NAP2-dehydropantoate 2-reductase 1.1.1.169 0.692
2i9p NAD3-hydroxyisobutyrate dehydrogenase, mitochondrial 1.1.1.31 0.692
3qv1 NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.692
1c1d NAIPhenylalanine dehydrogenase / 0.691
2cvz NDP3-hydroxyisobutyrate dehydrogenase / 0.690
3m2t NADProbable dehydrogenase / 0.689
4hfm NAP2-alkenal reductase (NADP(+)-dependent) / 0.689
1psd NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.688
3pdu NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.688
3cin NADMyo-inositol-1-phosphate synthase-related protein / 0.687
3jyo NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.687
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.686
5a02 NAPGlucose-fructose oxidoreductase / 0.685
1axg NADAlcohol dehydrogenase E chain 1.1.1.1 0.684
3abi NADUncharacterized protein / 0.684
4lcj NADC-terminal-binding protein 2 / 0.684
4tvb NADHomospermidine synthase 2.5.1.44 0.684
1gd1 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.683
4xr9 NADCalS8 / 0.683
5a04 NDPGlucose-fructose oxidoreductase / 0.683
1wze NADMalate dehydrogenase / 0.682
3qvt NAIMyo-inositol-1-phosphate synthase (Ino1) / 0.682
1pzg A3DLactate dehydrogenase / 0.681
3q3c NADNAD-dependent L-serine dehydrogenase / 0.681
4wji NAPPutative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase / 0.681
1p0f NAPNADP-dependent alcohol dehydrogenase 1.1.1.2 0.680
4e5p NADPhosphonate dehydrogenase 1.20.1.1 0.680
1gad NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.679
2dfv NADL-threonine 3-dehydrogenase / 0.679
5a05 NDPGlucose-fructose oxidoreductase / 0.679
5env NADAlcohol dehydrogenase 1 1.1.1.1 0.679
4e5n NADPhosphonate dehydrogenase 1.20.1.1 0.678
4xb2 NDP319aa long hypothetical homoserine dehydrogenase / 0.678
1bdm NAXMalate dehydrogenase / 0.676
1bmd NADMalate dehydrogenase / 0.676
2hdh NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.676
3ulk NDPKetol-acid reductoisomerase (NADP(+)) / 0.676
4pzd NAD3-Hydroxyacyl-CoA dehydrogenase / 0.676
1bw9 NADPhenylalanine dehydrogenase / 0.674
2e37 NADL-lactate dehydrogenase / 0.674
2p9g NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.673
3nx4 NAPPutative oxidoreductase / 0.673
3qw2 NADMyo-inositol-1-phosphate synthase (Ino1) / 0.673
3uxy NADShort-chain dehydrogenase/reductase SDR / 0.673
4kug NAD3-hydroxybutyryl-CoA dehydrogenase / 0.673
1wzi NDPMalate dehydrogenase / 0.672
2dph NADFormaldehyde dismutase / 0.672
3qvw NADMyo-inositol-1-phosphate synthase (Ino1) / 0.672
3w8e NAD3-hydroxybutyrate dehydrogenase / 0.672
4xqc NADHomospermidine synthase 2.5.1.44 0.672
2aa3 AP0L-lactate dehydrogenase / 0.671
3orf NADDihydropteridine reductase 1.5.1.34 0.671
3ru9 NADUDP-N-acetylglucosamine 4-epimerase / 0.671
1i36 NAPConserved protein / 0.670
3nt4 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.670
3wfj NAD2-dehydropantoate 2-reductase / 0.670
1j5p NADL-aspartate dehydrogenase 1.4.1.21 0.669
3a14 NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase / 0.669
3x2e NAIAdenosylhomocysteinase / 0.669
1efk NADNAD-dependent malic enzyme, mitochondrial 1.1.1.38 0.668
1ky4 NADAdenosylhomocysteinase 3.3.1.1 0.668
3ehe NADUDP-glucose 4-epimerase (GalE-1) / 0.668
1agn NADAlcohol dehydrogenase class 4 mu/sigma chain 1.1.1.1 0.667
2vyv NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.667
3gvi ADPMalate dehydrogenase / 0.667
3hja NADGlyceraldehyde-3-phosphate dehydrogenase / 0.667
5a03 NDPGlucose-fructose oxidoreductase / 0.667
2g82 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.666
2npx NADNADH peroxidase 1.11.1.1 0.666
2ztv NADD(-)-3-hydroxybutyrate dehydrogenase / 0.666
1zh8 NAPUncharacterized protein / 0.665
4e5k NADPhosphonate dehydrogenase 1.20.1.1 0.665
1e3l NADAlcohol dehydrogenase 4 1.1.1.1 0.664
1f17 NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.664
3x2f NAIAdenosylhomocysteinase / 0.664
4ejm NAPPutative zinc-binding dehydrogenase / 0.664
1b8v NADMalate dehydrogenase / 0.663
1lso NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.663
1n2s NAIdTDP-4-dehydrorhamnose reductase 1.1.1.133 0.663
1p1h NADInositol-3-phosphate synthase 5.5.1.4 0.663
3jyn NDPQuinone oxidoreductase / 0.663
4k28 NADShikimate dehydrogenase family protein / 0.663
4p8r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.663
5ein NAP[LysW]-L-2-aminoadipate 6-phosphate reductase / 0.662
2xaa NADSecondary alcohol dehydrogenase / 0.660
2zb3 NDPProstaglandin reductase 2 1.3.1.48 0.660
3cif NADGlyceraldehyde-3-phosphate dehydrogenase / 0.660
3l4s NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.660
3ntq NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.660
1zmd NAIDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.659
2ph5 NADHomospermidine synthase / 0.659
3pgx NADUncharacterized NAD-dependent oxidoreductase MAP_4146 / 0.659
1xse NDPCorticosteroid 11-beta-dehydrogenase isozyme 1 1.1.1.146 0.658
1hzz NADNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.657
1pl6 NADSorbitol dehydrogenase 1.1.1.14 0.657
4rvu NDPProbable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein) / 0.657
5d2e NAPMlnE / 0.657
5dt9 NADErythronate-4-phosphate dehydrogenase / 0.657
1h6a NDPGlucose--fructose oxidoreductase 1.1.99.28 0.656
1qor NDPQuinone oxidoreductase 1 / 0.656
2ep7 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.656
3sxp NADADP-L-glycero-D-mannoheptose-6-epimerase / 0.656
4pvd NDPNADPH-dependent methylglyoxal reductase GRE2 / 0.656
1yl7 NAI4-hydroxy-tetrahydrodipicolinate reductase / 0.655
1fdu NAPEstradiol 17-beta-dehydrogenase 1 1.1.1.62 0.654
1nq5 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.654
1szj NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.654
1xcb NADRedox-sensing transcriptional repressor Rex / 0.654
2p9e NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.654
2q2v NADBeta-D-hydroxybutyrate dehydrogenase / 0.653
4idg NADPutative UDP-glucose 4-epimerase / 0.653
1b8u NADMalate dehydrogenase / 0.652
1cdo NADAlcohol dehydrogenase 1 1.1.1.1 0.652
2c29 NAPDihydroflavonol 4-reductase / 0.652
2vhz NAIAlanine dehydrogenase 1.4.1.1 0.652
1orr NADCDP-paratose 2-epimerase / 0.651
2pv7 NADT-protein 1.3.1.12 0.651
3icp NADNAD-dependent epimerase/dehydratase / 0.651
1ywg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.650
3cmc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.650
4o0l NDPNADPH-dependent 3-quinuclidinone reductase / 0.650