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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
4xqc NAD Homospermidine synthase 2.5.1.44

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4xqc NADHomospermidine synthase 2.5.1.44 1.281
4tvb NADHomospermidine synthase 2.5.1.44 1.270
4xrg NADHomospermidine synthase 2.5.1.44 1.258
4xq9 NADHomospermidine synthase 2.5.1.44 1.240
4plp NADHomospermidine synthase 2.5.1.44 1.234
2o4c NADErythronate-4-phosphate dehydrogenase / 0.767
1hyh NADL-2-hydroxyisocaproate dehydrogenase / 0.760
1u7h NADPutative ornithine cyclodeaminase / 0.753
3oet NADErythronate-4-phosphate dehydrogenase / 0.748
3pdu NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.741
5kjc NAJAlcohol dehydrogenase E chain 1.1.1.1 0.741
3pef NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.739
3wmx NADNAD dependent epimerase/dehydratase / 0.732
2ph5 NADHomospermidine synthase / 0.731
4jbi NDPAlcohol dehydrogenase (Zinc) / 0.731
1pjc NADAlanine dehydrogenase / 0.728
1e5q NDPSaccharopine dehydrogenase [NADP(+), L-glutamate-forming] 1.5.1.10 0.724
3abi NADUncharacterized protein / 0.722
1i2b NADUDP-sulfoquinovose synthase, chloroplastic 3.13.1.1 0.721
1lld NADL-lactate dehydrogenase 2 1.1.1.27 0.720
5lc1 NADL-threonine 3-dehydrogenase / 0.720
1guy NADMalate dehydrogenase / 0.719
4jk3 NADUncharacterized protein / 0.719
2ixb NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.717
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.717
4b7x NAPProbable oxidoreductase / 0.717
4y1b NAPAntE / 0.717
4gkv NADAlcohol dehydrogenase, propanol-preferring 1.1.1.1 0.716
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.714
4j43 NADUncharacterized protein / 0.714
5cdg NAJAlcohol dehydrogenase E chain 1.1.1.1 0.714
4nfs NAJAlcohol dehydrogenase E chain 1.1.1.1 0.713
3qvs NADMyo-inositol-1-phosphate synthase (Ino1) / 0.712
4e5n NADPhosphonate dehydrogenase 1.20.1.1 0.712
1yb5 NAPQuinone oxidoreductase 1.6.5.5 0.709
4j49 NADUncharacterized protein / 0.708
4e5k NADPhosphonate dehydrogenase 1.20.1.1 0.707
1o6z NADMalate dehydrogenase / 0.706
3cin NADMyo-inositol-1-phosphate synthase-related protein / 0.706
3qvx NADMyo-inositol-1-phosphate synthase (Ino1) / 0.706
5kjf NAJAlcohol dehydrogenase E chain 1.1.1.1 0.706
2ohx NADAlcohol dehydrogenase E chain 1.1.1.1 0.705
1mgo NADAlcohol dehydrogenase E chain 1.1.1.1 0.704
5kj6 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.704
1gv0 NADMalate dehydrogenase / 0.703
2vhx NADAlanine dehydrogenase 1.4.1.1 0.702
1axe NADAlcohol dehydrogenase E chain 1.1.1.1 0.701
3nx4 NAPPutative oxidoreductase / 0.700
4bv9 NDPKetimine reductase mu-crystallin 1.5.1.25 0.700
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.699
1nyt NAPShikimate dehydrogenase (NADP(+)) / 0.698
1hld NADAlcohol dehydrogenase E chain 1.1.1.1 0.697
3aw9 NADNAD-dependent epimerase/dehydratase / 0.696
1p1h NADInositol-3-phosphate synthase 5.5.1.4 0.695
2nad NADFormate dehydrogenase / 0.695
1het NADAlcohol dehydrogenase E chain 1.1.1.1 0.694
3h3j NADL-lactate dehydrogenase 1 1.1.1.27 0.693
4xd2 NAIAlcohol dehydrogenase E chain 1.1.1.1 0.693
4oaq NDPR-specific carbonyl reductase / 0.692
2gsd NADFormate dehydrogenase / 0.691
2vou FAD2,6-dihydroxypyridine 3-monooxygenase 1.14.13.10 0.691
4nfh NAJAlcohol dehydrogenase E chain 1.1.1.1 0.691
5kcp NAJAlcohol dehydrogenase E chain 1.1.1.1 0.691
1x7d NADPutative ornithine cyclodeaminase / 0.690
3cos NADAlcohol dehydrogenase 4 1.1.1.1 0.690
3o9z NADLipopolysaccaride biosynthesis protein wbpB / 0.690
3qvw NADMyo-inositol-1-phosphate synthase (Ino1) / 0.690
4dwv NAJAlcohol dehydrogenase E chain 1.1.1.1 0.690
4dxh NAJAlcohol dehydrogenase E chain 1.1.1.1 0.689
5cdt NAJAlcohol dehydrogenase E chain 1.1.1.1 0.689
3l4s NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.688
4lsm NADGlyceraldehyde-3-phosphate dehydrogenase / 0.688
5cds NAJAlcohol dehydrogenase E chain 1.1.1.1 0.688
1agn NADAlcohol dehydrogenase class 4 mu/sigma chain 1.1.1.1 0.687
1kol NADGlutathione-independent formaldehyde dehydrogenase / 0.687
2vyv NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.687
3n7u NADFormate dehydrogenase, chloroplastic/mitochondrial / 0.687
1a71 NADAlcohol dehydrogenase E chain 1.1.1.1 0.686
4ysh FADGlycine oxidase / 0.686
1fxs NAPGDP-L-fucose synthase / 0.685
1la2 NADInositol-3-phosphate synthase 5.5.1.4 0.685
1ur5 NADMalate dehydrogenase / 0.684
4o63 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.684
1geg NADDiacetyl reductase [(S)-acetoin forming] 1.1.1.304 0.683
1hku NADC-terminal-binding protein 1 1.1.1 0.683
1yqd NAPSinapyl alcohol dehydrogenase / 0.683
4j4b NAIUncharacterized protein / 0.683
4w6z 8IDAlcohol dehydrogenase 1 1.1.1.1 0.683
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.682
3jyq NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.682
1i36 NAPConserved protein / 0.681
1wp4 NDP3-hydroxyisobutyrate dehydrogenase / 0.681
3qvt NAIMyo-inositol-1-phosphate synthase (Ino1) / 0.681
3wsw NADL-lactate dehydrogenase / 0.681
2oxi NADAlcohol dehydrogenase E chain 1.1.1.1 0.680
5ijz NAPNADP-specific glutamate dehydrogenase 1.4.1.4 0.679
2cvz NDP3-hydroxyisobutyrate dehydrogenase / 0.678
3w8e NAD3-hydroxybutyrate dehydrogenase / 0.678
5bsf NADPyrroline-5-carboxylate reductase / 0.678
1gad NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.677
2vna NAPProstaglandin reductase 2 1.3.1.48 0.677
3oq6 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.677
4k28 NADShikimate dehydrogenase family protein / 0.677
5dt9 NADErythronate-4-phosphate dehydrogenase / 0.677
1cdo NADAlcohol dehydrogenase 1 1.1.1.1 0.676
1n2s NAIdTDP-4-dehydrorhamnose reductase 1.1.1.133 0.676
2vyn NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.676
4e5m NAPPhosphonate dehydrogenase 1.20.1.1 0.676
4xb1 NDP319aa long hypothetical homoserine dehydrogenase / 0.676
5eio NAP[LysW]-L-2-aminoadipate 6-phosphate reductase / 0.676
5kje NAJAlcohol dehydrogenase E chain 1.1.1.1 0.676
1psd NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.675
5kcz NAJAlcohol dehydrogenase E chain 1.1.1.1 0.675
4j49 NAIUncharacterized protein / 0.674
5kj1 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.674
1lde NADAlcohol dehydrogenase E chain 1.1.1.1 0.673
1vc2 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.673
3tqh NDPQuinone oxidoreductase / 0.673
4yr9 NADL-threonine 3-dehydrogenase, mitochondrial 1.1.1.103 0.673
1j5p NADL-aspartate dehydrogenase 1.4.1.21 0.672
1lsj NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.672
3d4p NADL-lactate dehydrogenase 1 1.1.1.27 0.672
3ggp NADPrephenate dehydrogenase / 0.672
2dfd NADMalate dehydrogenase, mitochondrial 1.1.1.37 0.671
4rvu NDPProbable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein) / 0.671
3ras NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase / 0.670
4ng5 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.670
4njo NADD-3-phosphoglycerate dehydrogenase, putative / 0.670
5env NADAlcohol dehydrogenase 1 1.1.1.1 0.670
1p0f NAPNADP-dependent alcohol dehydrogenase 1.1.1.2 0.669
5bsg NAPPyrroline-5-carboxylate reductase / 0.669
1dc6 NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.668
2rgj FADFlavin-containing monooxygenase / 0.668
2vhv NAIAlanine dehydrogenase 1.4.1.1 0.668
3had NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.668
3pym NADGlyceraldehyde-3-phosphate dehydrogenase 3 1.2.1.12 0.668
1up6 NAD6-phospho-beta-glucosidase BglT 3.2.1.86 0.667
4xgi NADGlutamate dehydrogenase / 0.667
1hf3 NADAlcohol dehydrogenase E chain 1.1.1.1 0.666
1u3v NADAlcohol dehydrogenase 1B 1.1.1.1 0.666
3qv1 NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.666
3wbf NAPMeso-diaminopimelate D-dehydrogenase / 0.666
4nu6 NADPhosphonate dehydrogenase 1.20.1.1 0.666
2dc1 NADProbable L-aspartate dehydrogenase / 0.665
2x6t NAPADP-L-glycero-D-manno-heptose-6-epimerase / 0.665
3wle NAD(R)-specific carbonyl reductase / 0.665
4imp NDPPolyketide synthase extender modules 3-4 / 0.665
1u8f NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.664
2dt5 NADRedox-sensing transcriptional repressor Rex / 0.664
3jyo NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.664
5ein NAP[LysW]-L-2-aminoadipate 6-phosphate reductase / 0.664
1o8c NDPProbable acrylyl-CoA reductase AcuI 1.3.1.84 0.663
4k9d NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.663
4yac NAIC alpha-dehydrogenase / 0.663
1bw9 NADPhenylalanine dehydrogenase / 0.662
1kc1 NDPdTDP-4-dehydrorhamnose reductase 1.1.1.133 0.661
3oa2 NADUDP-N-acetyl-2-amino-2-deoxy-D-glucuronate oxidase / 0.661
4cpd NADAlcohol dehydrogenase / 0.661
2fkn NADUrocanate hydratase 4.2.1.49 0.660
2jl1 NAPTriphenylmethane reductase / 0.660
2vhz NAIAlanine dehydrogenase 1.4.1.1 0.660
2y05 NAPProstaglandin reductase 1 / 0.660
1mo9 FAD2-oxopropyl-CoM reductase, carboxylating 1.8.1.5 0.659
1nqo NADGlyceraldehyde-3-phosphate dehydrogenase / 0.659
1rp0 AHZThiamine thiazole synthase, chloroplastic / 0.659
2p5y NADUDP-glucose 4-epimerase / 0.659
2xvi FADPutative flavin-containing monooxygenase / 0.659
3doc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.659
3lu1 NADUDP-N-acetylglucosamine 4-epimerase / 0.659
3rua NADUDP-N-acetylglucosamine 4-epimerase / 0.659
1ky4 NADAdenosylhomocysteinase 3.3.1.1 0.658
3nt4 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.658
4jji NADAlcohol dehydrogenase class-3 / 0.658
1szj NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.657
2ep7 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.657
3keq NADRedox-sensing transcriptional repressor Rex / 0.657
1t2d NADL-lactate dehydrogenase 1.1.1.27 0.656
2dph NADFormaldehyde dismutase / 0.656
2qg4 NADUDP-glucose 6-dehydrogenase 1.1.1.22 0.656
2voj NADAlanine dehydrogenase 1.4.1.1 0.656
1efk NADNAD-dependent malic enzyme, mitochondrial 1.1.1.38 0.655
1i8t FADUDP-galactopyranose mutase 5.4.99.9 0.655
2x0r NADMalate dehydrogenase / 0.655
2j3k NAPNADPH-dependent oxidoreductase 2-alkenal reductase 1.3.1.74 0.654
4lcj NADC-terminal-binding protein 2 / 0.654
1ht0 NADAlcohol dehydrogenase 1C 1.1.1.1 0.653
1vsv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.653
1wzi NDPMalate dehydrogenase / 0.653
5a1t NAIL-lactate dehydrogenase / 0.653
1a7k NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.652
1m75 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.652
2q1w NADPutative nucleotide sugar epimerase/ dehydratase / 0.652
3tnl NADShikimate dehydrogenase (NADP(+)) / 0.652
1ib6 NADMalate dehydrogenase / 0.651
1nvm NADAcetaldehyde dehydrogenase 1.2.1.10 0.651
3a9w NADNDP-sugar epimerase / 0.651
1c0l FADD-amino-acid oxidase 1.4.3.3 0.650
1m76 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.650
1yqx NAPSinapyl alcohol dehydrogenase / 0.650
3ru9 NADUDP-N-acetylglucosamine 4-epimerase / 0.650
3two NDPMannitol dehydrogenase / 0.650
4wji NAPPutative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase / 0.650