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 Sites are compared using Shaper.
For more information, please see the following publication:
Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 4tmc | FMN | Old yellow enzyme |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4tmc | FMN | Old yellow enzyme | / | 1.000 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.624 | |
| 4rnv | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.622 | |
| 1bwk | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.605 | |
| 4tmb | FMN | Old yellow enzyme | / | 0.602 | |
| 1oyc | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.596 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.590 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.589 | |
| 4e2d | FMN | Dehydrogenase | / | 0.583 | |
| 3p82 | FMN | Pentaerythritol tetranitrate reductase | / | 0.582 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.580 | |
| 1icq | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.580 | |
| 4rnw | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.578 | |
| 1oya | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.577 | |
| 4h6k | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.575 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.569 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.568 | |
| 3hgr | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.568 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.563 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.563 | |
| 4df2 | FMN | NADPH dehydrogenase | / | 0.562 | |
| 1vji | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.560 | |
| 1q45 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.558 | |
| 4e2b | FMN | Dehydrogenase | / | 0.557 | |
| 4k7y | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.557 | |
| 2q3r | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.556 | |
| 4rnx | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.555 | |
| 3hgs | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.553 | |
| 4m5p | FMN | NADPH dehydrogenase | / | 0.551 | |
| 3aty | FMN | Prostaglandin F2a synthase | / | 0.550 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.548 | |
| 1k02 | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.547 | |
| 4jic | FMN | GTN Reductase | / | 0.547 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.544 | |
| 4rnu | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.544 | |
| 3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 0.541 | |
| 4a3u | FMN | NADH:flavin oxidoreductase/NADH oxidase | / | 0.531 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.530 | |
| 4qai | FMN | NADPH dehydrogenase | / | 0.530 | |
| 2hs6 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.529 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.525 | |
| 1icp | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.525 | |
| 3tjl | FMN | NADPH dehydrogenase | / | 0.519 | |
| 3p84 | FMN | Pentaerythritol tetranitrate reductase | / | 0.511 | |
| 2hs8 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.510 | |
| 4awt | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.509 | |
| 3hgo | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.507 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.503 | |
| 3gka | FMN | N-ethylmaleimide reductase | / | 0.499 | |
| 3p8j | FMN | Pentaerythritol tetranitrate reductase | / | 0.499 | |
| 4aws | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.497 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.494 | |
| 4uth | FMN | Xenobiotic reductase | / | 0.492 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.491 | |
| 4b5n | FMN | NAD(P)H:flavin oxidoreductase Sye4 | / | 0.490 | |
| 1kbj | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.484 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.483 | |
| 2gou | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.482 | |
| 4i6g | FAD | Cryptochrome-2 | / | 0.481 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.479 | |
| 1szg | FNS | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.479 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.478 | |
| 3cnd | FAD | Polyamine oxidase FMS1 | / | 0.477 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.475 | |
| 1dxo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.475 | |
| 2rgh | FAD | Alpha-Glycerophosphate Oxidase | / | 0.475 | |
| 4utl | FNR | Xenobiotic reductase | / | 0.475 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.475 | |
| 2nli | FMN | Lactate oxidase | / | 0.474 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.472 | |
| 4qnw | FMN | Chanoclavine-I aldehyde reductase easA | / | 0.472 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.471 | |
| 2fj1 | CTC | Tetracycline repressor protein class D | / | 0.470 | |
| 3il1 | B5D | Glutamate receptor 2 | / | 0.470 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.469 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.469 | |
| 4xq6 | FMN | Dihydroorotate dehydrogenase (quinone) | / | 0.469 | |
| 1qyw | 5SD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.468 | |
| 3ixp | 834 | Ecdysone receptor | / | 0.468 | |
| 3l5l | FMN | Xenobiotic reductase | / | 0.468 | |
| 3n14 | FMN | Xenobiotic reductase | / | 0.468 | |
| 2gqa | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.467 | |
| 2j6x | FMN | Lactate oxidase | / | 0.467 | |
| 3ty3 | GGG | Homoisocitrate dehydrogenase | 1.1.1.87 | 0.467 | |
| 4xiw | AZM | Carbonic anhydrase, alpha type | / | 0.467 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.466 | |
| 4hhz | 15S | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.466 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.465 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.465 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.465 | |
| 4ycp | FMN | tRNA-dihydrouridine(16) synthase | / | 0.465 | |
| 1kbi | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.464 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.464 | |
| 2y8q | ADP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.464 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.463 | |
| 2w6q | OA5 | Biotin carboxylase | 6.3.4.14 | 0.463 | |
| 3ibq | ATP | Pyridoxal kinase | / | 0.463 | |
| 3lgx | ATP | D-alanine--poly(phosphoribitol) ligase subunit 1 | / | 0.463 | |
| 1h72 | ANP | Homoserine kinase | 2.7.1.39 | 0.461 | |
| 1tez | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.460 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.460 | |
| 4hmv | WUB | Phenazine biosynthesis protein PhzG | 1.4 | 0.460 | |
| 2d29 | FAD | Acyl-CoA dehydrogenase | / | 0.459 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.459 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.459 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.459 | |
| 1gox | FMN | Peroxisomal (S)-2-hydroxy-acid oxidase | 1.1.3.15 | 0.458 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.458 | |
| 4yl2 | FMN | Lactate oxidase | / | 0.458 | |
| 1m13 | HYF | Nuclear receptor subfamily 1 group I member 2 | / | 0.457 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.457 | |
| 1zth | ADP | RIO-type serine/threonine-protein kinase Rio1 | 2.7.11.1 | 0.457 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.457 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.457 | |
| 3giy | FMN | (S)-mandelate dehydrogenase | 1.1.99.31 | 0.456 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.456 | |
| 2h8x | FMN | XenA | / | 0.455 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.455 | |
| 4eak | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.455 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.454 | |
| 1z44 | FMN | NADPH dehydrogenase | / | 0.454 | |
| 2fr0 | NDP | 6-deoxyerythronolide-B synthase EryA1, modules 1 and 2 | / | 0.454 | |
| 4e5y | NDP | GDP-L-fucose synthase | 1.1.1.271 | 0.454 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.453 | |
| 2cft | PLP | Pyridoxal phosphate phosphatase | / | 0.453 | |
| 2z9d | FMN | FMN-dependent NADH-azoreductase | / | 0.453 | |
| 3tqh | NDP | Quinone oxidoreductase | / | 0.453 | |
| 1nvt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.452 | |
| 2yyi | FAD | 4-hydroxyphenylacetate 3-monooxygenase oxygenase component | 1.14.14.9 | 0.452 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 4r81 | FMN | Predicted NADH dehydrogenase | / | 0.452 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 3zs7 | ATP | Pyridoxine/pyridoxal/pyridoxamine kinase | / | 0.451 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.450 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.450 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.450 | |
| 2zfa | FMN | Lactate oxidase | / | 0.450 | |
| 3zvm | ADP | Bifunctional polynucleotide phosphatase/kinase | 2.7.1.78 | 0.450 | |
| 4a6n | FAD | TetX family tetracycline inactivation enzyme | / | 0.450 | |
| 4dbc | 3QP | Aspartate aminotransferase | 2.6.1.1 | 0.450 | |
| 4hhy | 15R | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.450 | |
| 5ebu | FMN | Lactate oxidase | / | 0.450 | |
| 1bsv | NDP | GDP-L-fucose synthase | / | 0.449 | |
| 3hyo | ADP | Pyridoxal kinase | / | 0.449 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.449 | |
| 4dpt | AGS | Mevalonate diphosphate decarboxylase | / | 0.449 | |
| 4ge7 | 0K5 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.449 | |
| 1szf | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.448 | |
| 2du2 | FMN | Lactate oxidase | / | 0.448 | |
| 2q3o | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.448 | |
| 2rl1 | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.448 | |
| 2vtb | FAD | Cryptochrome DASH, chloroplastic/mitochondrial | / | 0.448 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.448 | |
| 4g3q | UD1 | Bifunctional protein GlmU | / | 0.448 | |
| 1ygk | RRC | Pyridoxal kinase | 2.7.1.35 | 0.447 | |
| 2cbr | A80 | Cellular retinoic acid-binding protein 1 | / | 0.447 | |
| 2eix | FAD | NADH-cytochrome b5 reductase | / | 0.447 | |
| 2lba | CHO | Fatty acid binding protein 6 | / | 0.447 | |
| 2ok7 | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.447 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.447 | |
| 4fxy | 0W2 | Neurolysin, mitochondrial | 3.4.24.16 | 0.447 | |
| 4gdd | NAI | UDP-galactopyranose mutase | / | 0.447 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.446 | |
| 1dyj | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.446 | |
| 2e77 | FMN | Lactate oxidase | / | 0.446 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.446 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.446 | |
| 2w6z | L21 | Biotin carboxylase | 6.3.4.14 | 0.446 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.446 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.446 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.446 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.446 | |
| 4yco | FMN | tRNA-dihydrouridine(16) synthase | / | 0.446 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.445 | |
| 2v59 | LZK | Biotin carboxylase | 6.3.4.14 | 0.445 | |
| 2y4g | TIR | TamL | / | 0.445 | |
| 3dsz | LIZ | Neutrophil gelatinase-associated lipocalin | / | 0.445 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.445 | |
| 3vwd | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.445 | |
| 3w1r | MRO | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.445 | |
| 4z38 | FMN | MlnA | / | 0.445 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.444 | |
| 2i4p | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.444 | |
| 3gr8 | FMN | NADPH dehydrogenase | / | 0.444 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 3pm1 | ET | HTH-type transcriptional regulator QacR | / | 0.444 | |
| 5cwa | 0GA | Anthranilate synthase component 1 | 4.1.3.27 | 0.444 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.443 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.443 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.443 | |
| 2ylr | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.443 | |
| 3enk | UPG | UDP-glucose 4-epimerase | / | 0.443 | |
| 1dmy | AZM | Carbonic anhydrase 5A, mitochondrial | 4.2.1.1 | 0.442 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 1fcb | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.442 | |
| 1h73 | ANP | Homoserine kinase | 2.7.1.39 | 0.442 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.442 | |
| 3zc3 | NAP | Ferredoxin--NADP reductase | 1.18.1.2 | 0.442 | |
| 4a99 | FAD | TetX family tetracycline inactivation enzyme | / | 0.442 | |
| 1i59 | ANP | Chemotaxis protein CheA | 2.7.13.3 | 0.441 | |
| 1zrz | BI1 | Protein kinase C iota type | 2.7.11.13 | 0.441 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.441 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.441 | |
| 2j4d | FAD | Cryptochrome DASH, chloroplastic/mitochondrial | / | 0.441 | |
| 2ohv | NHL | Glutamate racemase | / | 0.441 | |
| 2q7v | FAD | Thioredoxin reductase | / | 0.441 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.441 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 3cly | ACP | Fibroblast growth factor receptor 2 | / | 0.441 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3n19 | FNR | Xenobiotic reductase | / | 0.441 | |
| 3nl6 | TPS | Uncharacterized protein | / | 0.441 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.441 | |
| 3suf | SUE | Polyprotein | / | 0.441 | |
| 3w1t | WRO | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.441 | |
| 4bge | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 4c0b | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.441 | |
| 4c3f | 7KW | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.441 | |
| 4h8a | NAI | Ureidoglycolate dehydrogenase (NAD(+)) | 1.1.1.350 | 0.441 | |
| 4hbm | 0Y7 | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 | 0.441 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.441 | |
| 1kc1 | NDP | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.440 | |
| 2ch6 | ADP | N-acetyl-D-glucosamine kinase | 2.7.1.59 | 0.440 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.440 | |
| 2q85 | 973 | UDP-N-acetylenolpyruvoylglucosamine reductase | 1.3.1.98 | 0.440 | |
| 2z4s | ADP | Chromosomal replication initiator protein DnaA | / | 0.440 | |
| 3bw4 | FMN | Putative 2-nitropropane dioxygenase | / | 0.440 | |
| 3frk | TQP | QdtB | / | 0.440 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.440 | |
| 3sf6 | FDA | Glutaryl-CoA dehydrogenase | / | 0.440 | |
| 4gdc | NDP | UDP-galactopyranose mutase | / | 0.440 | |
| 4ike | ADP | Adenylate kinase | / | 0.440 | |
| 4rrr | A3T | Threonine--tRNA ligase | 6.1.1.3 | 0.440 |