sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 1jki | NAI | Inositol-3-phosphate synthase | 5.5.1.4 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 1jki | NAI | Inositol-3-phosphate synthase | 5.5.1.4 | 1.154 | |
| 1p1h | NAD | Inositol-3-phosphate synthase | 5.5.1.4 | 0.842 | |
| 1la2 | NAD | Inositol-3-phosphate synthase | 5.5.1.4 | 0.782 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.772 | |
| 2yg4 | FAD | Putrescine oxidase | / | 0.751 | |
| 1y8q | ATP | SUMO-activating enzyme subunit 2 | 6.3.2 | 0.746 | |
| 2yg6 | FAD | Putrescine oxidase | / | 0.745 | |
| 3qvx | NAD | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.744 | |
| 2yg3 | FAD | Putrescine oxidase | / | 0.734 | |
| 1p1i | NAD | Inositol-3-phosphate synthase | 5.5.1.4 | 0.733 | |
| 2gsd | NAD | Formate dehydrogenase | / | 0.727 | |
| 1lld | NAD | L-lactate dehydrogenase 2 | 1.1.1.27 | 0.725 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.725 | |
| 3wv8 | ATP | Hmd co-occurring protein HcgE | / | 0.725 | |
| 3wv7 | ADP | Hmd co-occurring protein HcgE | / | 0.724 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.724 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.722 | |
| 3d64 | NAD | Adenosylhomocysteinase | / | 0.720 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.719 | |
| 4hb9 | FAD | Uncharacterized protein | / | 0.719 | |
| 3nlc | FAD | Uncharacterized protein | / | 0.718 | |
| 2yg5 | FAD | Putrescine oxidase | / | 0.717 | |
| 2yg7 | FAD | Putrescine oxidase | / | 0.715 | |
| 2x0r | NAD | Malate dehydrogenase | / | 0.713 | |
| 1pdh | FAS | p-hydroxybenzoate hydroxylase | / | 0.712 | |
| 5g3t | FDA | Flavin-dependent L-tryptophan oxidase VioA | / | 0.712 | |
| 2vhx | NAD | Alanine dehydrogenase | 1.4.1.1 | 0.711 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.711 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.708 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.708 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.708 | |
| 5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.708 | |
| 1hyh | NAD | L-2-hydroxyisocaproate dehydrogenase | / | 0.706 | |
| 3rua | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.704 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.703 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.702 | |
| 2dt5 | NAD | Redox-sensing transcriptional repressor Rex | / | 0.701 | |
| 2dw4 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.701 | |
| 4at0 | FAD | Possible succinate dehydrogenase | / | 0.701 | |
| 1b3r | NAD | Adenosylhomocysteinase | 3.3.1.1 | 0.700 | |
| 4d04 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.700 | |
| 3ec7 | NAD | Inositol 2-dehydrogenase | / | 0.699 | |
| 4yac | NAI | C alpha-dehydrogenase | / | 0.699 | |
| 2ji9 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.698 | |
| 3jyo | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.697 | |
| 3cin | NAD | Myo-inositol-1-phosphate synthase-related protein | / | 0.696 | |
| 3nn6 | FB0 | 6-hydroxy-L-nicotine oxidase | / | 0.696 | |
| 3rha | FDA | Putrescine oxidase | / | 0.696 | |
| 1ek5 | NAD | UDP-glucose 4-epimerase | / | 0.695 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.695 | |
| 2vhw | NAI | Alanine dehydrogenase | 1.4.1.1 | 0.695 | |
| 3mj4 | FAD | UDP-galactopyranose mutase | / | 0.695 | |
| 1dss | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.694 | |
| 1k0l | FAD | p-hydroxybenzoate hydroxylase | / | 0.693 | |
| 1lqu | FAD | NADPH-ferredoxin reductase FprA | 1.18.1.2 | 0.693 | |
| 1hku | NAD | C-terminal-binding protein 1 | 1.1.1 | 0.692 | |
| 2g5c | NAD | Prephenate dehydrogenase | / | 0.692 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.692 | |
| 3qvw | NAD | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.692 | |
| 3n7u | NAD | Formate dehydrogenase, chloroplastic/mitochondrial | / | 0.690 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.690 | |
| 3rud | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.690 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.689 | |
| 1nai | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.689 | |
| 1orr | NAD | CDP-paratose 2-epimerase | / | 0.689 | |
| 5i39 | FAD | L-amino acid deaminase | / | 0.689 | |
| 2rgh | FAD | Alpha-Glycerophosphate Oxidase | / | 0.688 | |
| 4fwf | FAD | Lysine-specific histone demethylase 1B | 1 | 0.687 | |
| 1e6e | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.686 | |
| 1jkf | NAD | Inositol-3-phosphate synthase | 5.5.1.4 | 0.686 | |
| 2g1p | SAH | DNA adenine methylase | 2.1.1.72 | 0.683 | |
| 4yuz | S4M | Spermidine synthase, putative | / | 0.683 | |
| 1i8t | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.682 | |
| 3icp | NAD | NAD-dependent epimerase/dehydratase | / | 0.682 | |
| 3qvs | NAD | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.682 | |
| 4pyo | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.682 | |
| 4xqc | NAD | Homospermidine synthase | 2.5.1.44 | 0.682 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.681 | |
| 2ym1 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.681 | |
| 3ids | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.681 | |
| 3k7m | FAD | 6-hydroxy-L-nicotine oxidase | / | 0.681 | |
| 4j43 | NAD | Uncharacterized protein | / | 0.679 | |
| 4xrg | NAD | Homospermidine synthase | 2.5.1.44 | 0.679 | |
| 2igo | FAD | Pyranose 2-oxidase | / | 0.678 | |
| 3zdf | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.678 | |
| 4j49 | NAD | Uncharacterized protein | / | 0.678 | |
| 1hzz | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.677 | |
| 4xbf | FAD | Lysine-specific histone demethylase 1A | 1 | 0.677 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.676 | |
| 2ign | FAD | Pyranose 2-oxidase | / | 0.676 | |
| 2yr4 | FAD | Phenylalanine 2-monooxygenase precursor | 1.13.12.9 | 0.676 | |
| 3k4c | FAD | Pyranose 2-oxidase | / | 0.676 | |
| 1pzg | A3D | Lactate dehydrogenase | / | 0.675 | |
| 3g5s | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.675 | |
| 3qv1 | NAD | Glyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic | 1.2.1.13 | 0.675 | |
| 3u81 | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.675 | |
| 4mok | FAD | Pyranose 2-oxidase | / | 0.675 | |
| 4pyn | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.675 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.674 | |
| 1j5p | NAD | L-aspartate dehydrogenase | 1.4.1.21 | 0.674 | |
| 1c1d | NAI | Phenylalanine dehydrogenase | / | 0.673 | |
| 1nqa | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.673 | |
| 2ep7 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.673 | |
| 2g82 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.673 | |
| 2q28 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.673 | |
| 2vhv | NAI | Alanine dehydrogenase | 1.4.1.1 | 0.673 | |
| 4krh | SAM | Phosphoethanolamine N-methyltransferase 2 | / | 0.673 | |
| 1h83 | FAD | Polyamine oxidase | 1.5.3.14 | 0.672 | |
| 1zmd | NAI | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.672 | |
| 3ikt | NAD | Redox-sensing transcriptional repressor Rex | / | 0.672 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.672 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.671 | |
| 1szj | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.671 | |
| 3nt2 | NAD | Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase | 1.1.1.18 | 0.671 | |
| 1e1k | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.670 | |
| 4xq9 | NAD | Homospermidine synthase | 2.5.1.44 | 0.670 | |
| 5jr3 | SAH | Carminomycin 4-O-methyltransferase DnrK | 2.1.1.292 | 0.670 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.669 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.669 | |
| 3l8k | ADP | Dihydrolipoamide dehydrogenase (PdhD-3) | / | 0.669 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.669 | |
| 4e5p | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.669 | |
| 4i1i | NAD | Malate dehydrogenase | / | 0.669 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.669 | |
| 5fs9 | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.669 | |
| 3fws | ANP | Transcriptional repressor CcpN | / | 0.668 | |
| 4tm1 | FDA | KtzI | / | 0.668 | |
| 1jr4 | CL4 | Catechol O-methyltransferase | 2.1.1.6 | 0.667 | |
| 2oor | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.667 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.667 | |
| 4j49 | NAI | Uncharacterized protein | / | 0.667 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.667 | |
| 1nah | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.666 | |
| 2okc | SAM | Probable type I restriction enzyme BthVORF4518P M protein | 2.1.1.72 | 0.666 | |
| 2p5y | NAD | UDP-glucose 4-epimerase | / | 0.666 | |
| 4plp | NAD | Homospermidine synthase | 2.5.1.44 | 0.666 | |
| 4xcx | SAH | Small RNA 2'-O-methyltransferase | / | 0.666 | |
| 1uxj | NAD | Malate dehydrogenase | / | 0.665 | |
| 3cmc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.665 | |
| 3pqf | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.665 | |
| 1lde | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.664 | |
| 1rjd | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.664 | |
| 1u2d | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.664 | |
| 2hu2 | NAD | C-terminal binding protein 1 | / | 0.664 | |
| 3epp | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.664 | |
| 3qvt | NAI | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.664 | |
| 2ixa | NAD | Alpha-N-acetylgalactosaminidase | 3.2.1.49 | 0.663 | |
| 1nqo | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.662 | |
| 1rp0 | AHZ | Thiamine thiazole synthase, chloroplastic | / | 0.662 | |
| 2bac | FAD | Putative aminooxidase | / | 0.662 | |
| 2e1m | FAD | L-glutamate oxidase | / | 0.662 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.662 | |
| 3nt4 | NAI | Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase | 1.1.1.18 | 0.662 | |
| 1jnz | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.661 | |
| 1y9d | FAD | Pyruvate oxidase | 1.2.3.3 | 0.661 | |
| 2o07 | MTA | Spermidine synthase | 2.5.1.16 | 0.661 | |
| 3gsi | FAD | Dimethylglycine oxidase | 1.5.3.10 | 0.661 | |
| 1lso | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.660 | |
| 1npt | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.660 | |
| 1xcb | NAD | Redox-sensing transcriptional repressor Rex | / | 0.660 | |
| 2x0i | NAI | Malate dehydrogenase | / | 0.660 | |
| 3q9t | FAY | Uncharacterized protein | / | 0.660 | |
| 4tvb | NAD | Homospermidine synthase | 2.5.1.44 | 0.660 | |
| 1l7e | NAI | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.659 | |
| 2o4c | NAD | Erythronate-4-phosphate dehydrogenase | / | 0.659 | |
| 2qe6 | SAM | Uncharacterized protein | / | 0.659 | |
| 3duw | SAH | O-methyltransferase, putative | / | 0.659 | |
| 3ggp | NAD | Prephenate dehydrogenase | / | 0.659 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.659 | |
| 3oet | NAD | Erythronate-4-phosphate dehydrogenase | / | 0.659 | |
| 4c4o | NAD | SADH | / | 0.659 | |
| 4ebf | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.659 | |
| 1bdb | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | / | 0.658 | |
| 1hdr | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.658 | |
| 1sow | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.658 | |
| 3abi | NAD | Uncharacterized protein | / | 0.658 | |
| 3ad9 | NAD | Subunit alpha of sarocosine oxidase | / | 0.658 | |
| 3aw9 | NAD | NAD-dependent epimerase/dehydratase | / | 0.658 | |
| 3cif | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.658 | |
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 0.658 | |
| 4y9d | NAI | C alpha-dehydrogenase | / | 0.658 | |
| 5bsg | NAP | Pyrroline-5-carboxylate reductase | / | 0.658 | |
| 1jnr | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.656 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.656 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.656 | |
| 3adp | NAI | Lambda-crystallin | 1.1.1.45 | 0.656 | |
| 5a1t | NAI | L-lactate dehydrogenase | / | 0.656 | |
| 1pjc | NAD | Alanine dehydrogenase | / | 0.655 | |
| 1ptj | SND | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.655 | |
| 2fjd | SFD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.655 | |
| 2fje | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.655 | |
| 3kkj | FAD | Renalase | / | 0.655 | |
| 3kve | FAD | L-amino-acid oxidase | / | 0.655 | |
| 3pym | NAD | Glyceraldehyde-3-phosphate dehydrogenase 3 | 1.2.1.12 | 0.655 | |
| 3ukf | FDA | UDP-galactopyranose mutase | / | 0.655 | |
| 3v1y | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1, cytosolic | 1.2.1.12 | 0.655 | |
| 4fx9 | FAD | Coenzyme A disulfide reductase | 1.8.1.14 | 0.655 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.655 | |
| 1u2g | APR | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.654 | |
| 3lsm | SFD | Pyranose 2-oxidase | / | 0.654 | |
| 4usr | FAD | Monooxygenase | / | 0.654 | |
| 5c7o | NAD | Glyceraldehyde-3-phosphate dehydrogenase, testis-specific | 1.2.1.12 | 0.654 | |
| 2yr5 | FAD | Phenylalanine 2-monooxygenase precursor | 1.13.12.9 | 0.653 | |
| 3cnt | FAD | Polyamine oxidase FMS1 | / | 0.653 | |
| 3g5q | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.653 | |
| 3k7t | FAD | 6-hydroxy-L-nicotine oxidase | / | 0.653 | |
| 3t37 | FAD | Pyridoxine 4-oxidase | / | 0.653 | |
| 4b63 | FAD | L-ornithine N(5)-monooxygenase | / | 0.653 | |
| 2ome | NAD | C-terminal-binding protein 2 | / | 0.652 | |
| 2voj | NAD | Alanine dehydrogenase | 1.4.1.1 | 0.652 | |
| 3c3y | SAH | O-methyltransferase | / | 0.652 | |
| 3ics | FAD | Coenzyme A disulfide reductase | / | 0.652 | |
| 3p9u | FAD | TetX family tetracycline inactivation enzyme | / | 0.652 | |
| 4gbe | SAH | DNA adenine methylase | 2.1.1.72 | 0.652 | |
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.652 | |
| 1u1i | NAD | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.651 | |
| 1u28 | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.651 | |
| 2b9y | FAD | Putative aminooxidase | / | 0.651 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.651 | |
| 3nt2 | NAI | Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase | 1.1.1.18 | 0.651 | |
| 1e1n | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.650 | |
| 2o06 | MTA | Spermidine synthase | 2.5.1.16 | 0.650 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.650 | |
| 3bwc | SAM | Spermidine synthase, putative | / | 0.650 | |
| 3ksd | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1 | / | 0.650 | |
| 3q2k | NAI | Probable oxidoreductase | / | 0.650 | |
| 3uko | NAD | Alcohol dehydrogenase class-3 | / | 0.650 | |
| 4z0h | NAD | Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic | 1.2.1.12 | 0.650 |