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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
3wv8 ATP Hmd co-occurring protein HcgE

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3wv8 ATPHmd co-occurring protein HcgE / 1.020
3wv7 ADPHmd co-occurring protein HcgE / 0.988
2gsd NADFormate dehydrogenase / 0.761
2vhx NADAlanine dehydrogenase 1.4.1.1 0.732
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.725
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.722
2ixb NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.714
2vhz NAIAlanine dehydrogenase 1.4.1.1 0.711
2xyr SFGReplicase polyprotein 1ab 2.1.1 0.705
2fkn NADUrocanate hydratase 4.2.1.49 0.702
4nec SAHPutative SAM-dependent methyltransferase / 0.700
3lcc SAHThiocyanate methyltransferase 1 / 0.699
2vhw NAIAlanine dehydrogenase 1.4.1.1 0.696
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.696
1dss NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.695
2q1t NADPutative nucleotide sugar epimerase/ dehydratase / 0.695
2vhv NAIAlanine dehydrogenase 1.4.1.1 0.695
4yuz S4MSpermidine synthase, putative / 0.694
2pzj NADPutative nucleotide sugar epimerase/ dehydratase / 0.693
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.692
4j49 NADUncharacterized protein / 0.689
2o07 MTASpermidine synthase 2.5.1.16 0.688
3h5n ATPMccB protein / 0.687
3i53 SAH2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase / 0.686
5cku FADL-ornithine N(5)-monooxygenase / 0.686
2v7g NADUrocanate hydratase 4.2.1.49 0.685
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.685
4j43 NADUncharacterized protein / 0.685
3d64 NADAdenosylhomocysteinase / 0.684
3vqr FADPutative oxidoreductase / 0.684
5c7o NADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific 1.2.1.12 0.684
2q1s NAIPutative nucleotide sugar epimerase/ dehydratase / 0.683
4jk3 NADUncharacterized protein / 0.683
1uay ADNOxidoreductase / 0.681
1y56 FAD382aa long hypothetical sarcosine oxidase / 0.680
2vou FAD2,6-dihydroxypyridine 3-monooxygenase 1.14.13.10 0.680
3ec7 NADInositol 2-dehydrogenase / 0.680
4tm3 FADKtzI / 0.680
1u7h NADPutative ornithine cyclodeaminase / 0.679
2dfd NADMalate dehydrogenase, mitochondrial 1.1.1.37 0.679
1g1a NADdTDP-glucose 4,6-dehydratase / 0.678
1nbh SAMGlycine N-methyltransferase 2.1.1.20 0.678
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.678
1p1h NADInositol-3-phosphate synthase 5.5.1.4 0.676
1ptj SNDNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.676
2plw SAMRibosomal RNA methyltransferase, putative / 0.676
4tvb NADHomospermidine synthase 2.5.1.44 0.675
1emd NADMalate dehydrogenase / 0.674
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.674
3jyo NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.673
3jyp NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.673
3l8k ADPDihydrolipoamide dehydrogenase (PdhD-3) / 0.673
3ou6 SAMSAM-dependent methyltransferase / 0.673
3s5w FADL-ornithine N(5)-monooxygenase / 0.673
4j49 NAIUncharacterized protein / 0.673
5hxw FADL-amino acid deaminase / 0.671
4w6z 8IDAlcohol dehydrogenase 1 1.1.1.1 0.670
3tos SAHCalS11 / 0.669
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.669
1vjt NADAlpha-glucosidase, putative / 0.668
3fpf MTAUncharacterized protein / 0.668
3oet NADErythronate-4-phosphate dehydrogenase / 0.668
3ruh NADUDP-N-acetylglucosamine 4-epimerase / 0.668
1pl6 NADSorbitol dehydrogenase 1.1.1.14 0.667
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.667
2q28 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.666
3qvt NAIMyo-inositol-1-phosphate synthase (Ino1) / 0.666
1b3r NADAdenosylhomocysteinase 3.3.1.1 0.665
1pjc NADAlanine dehydrogenase / 0.665
3ru9 NADUDP-N-acetylglucosamine 4-epimerase / 0.665
4gdp FADPolyamine oxidase FMS1 / 0.665
1e3s NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.664
4wlu NADMalate dehydrogenase, mitochondrial 1.1.1.37 0.664
1e6w NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.663
1la2 NADInositol-3-phosphate synthase 5.5.1.4 0.663
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.663
2o23 NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.663
4nzh FADL-ornithine N(5)-monooxygenase / 0.663
4yac NAIC alpha-dehydrogenase / 0.663
1e3w NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.662
1zem NADXylitol dehydrogenase / 0.661
2cdu ADPNADH oxidase / 0.660
2pv7 NADT-protein 1.3.1.12 0.660
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.660
4gf5 SAHCalS11 / 0.660
4yv2 S4MSpermidine synthase, putative / 0.660
5ig2 NADShort-chain dehydrogenase/reductase SDR / 0.660
1kia SAMGlycine N-methyltransferase 2.1.1.20 0.659
2zwa SAHtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.659
1bxk NADdTDP-glucose 4,6-dehydratase 2 / 0.658
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.658
1ywg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.658
4wec NADShort chain dehydrogenase / 0.658
1av5 AP2Histidine triad nucleotide-binding protein 1 3 0.657
3g5q FADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO / 0.657
2g76 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.655
2gvc FADThiol-specific monooxygenase 1.14.13 0.655
3rud NADUDP-N-acetylglucosamine 4-epimerase / 0.654
4ek9 EP4Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.654
1l7e NAINAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.653
1pl8 NADSorbitol dehydrogenase 1.1.1.14 0.653
2i9k SAHModification methylase HhaI 2.1.1.37 0.653
2x1l ADNMethionine--tRNA ligase / 0.653
2yy7 NADL-threonine dehydrogenase / 0.653
3of2 NADEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.653
4yjd FADD-amino-acid oxidase 1.4.3.3 0.653
1u7t TDT3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.652
2hun NAD336aa long hypothetical dTDP-glucose 4,6-dehydratase / 0.652
2pan FADGlyoxylate carboligase 4.1.1.47 0.652
3n1s 5GPPurine nucleoside phosphoramidase / 0.652
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.652
1ib6 NADMalate dehydrogenase / 0.651
3icr FADCoenzyme A disulfide reductase / 0.651
3qvw NADMyo-inositol-1-phosphate synthase (Ino1) / 0.651
4j4b NAIUncharacterized protein / 0.651
4y9d NAIC alpha-dehydrogenase / 0.651
7mht SAHModification methylase HhaI 2.1.1.37 0.651
1m75 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.650
1nw6 SFGModification methylase RsrI 2.1.1.72 0.650
2o4c NADErythronate-4-phosphate dehydrogenase / 0.650
3utf FDAUDP-galactopyranose mutase / 0.650
4b68 FADL-ornithine N(5)-monooxygenase / 0.650
5je2 SAHMethyl transferase / 0.650