sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Cavities 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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 1i0s | FMN | Ferric-chelate reductase (NAD(P)H) |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1i0s | FMN | Ferric-chelate reductase (NAD(P)H) | / | 1.000 | |
| 3tr0 | 5GP | Guanylate kinase | / | 0.491 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.488 | |
| 5ein | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.485 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.482 | |
| 3opx | U5P | Suppressor of disruption of TFIIS | / | 0.482 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.480 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.477 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.477 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.477 | |
| 2i3g | NAP | N-acetyl-gamma-glutamyl-phosphate reductase | 1.2.1.38 | 0.476 | |
| 4hyv | PEP | Pyruvate kinase 1 | 2.7.1.40 | 0.474 | |
| 4wzh | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.472 | |
| 2iib | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.471 | |
| 4blr | UTP | NTPase P4 | / | 0.470 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.469 | |
| 1p0p | BCH | Cholinesterase | 3.1.1.8 | 0.469 | |
| 1icp | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.467 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.466 | |
| 2a1h | GBN | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.466 | |
| 1icq | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.465 | |
| 3phi | NDP | Shikimate dehydrogenase (NADP(+)) | / | 0.464 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.463 | |
| 3m2v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.463 | |
| 3rpe | FAD | Putative modulator of drug activity | / | 0.463 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.463 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.462 | |
| 2dft | ADP | Shikimate kinase | 2.7.1.71 | 0.462 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.461 | |
| 1umk | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.461 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.461 | |
| 4j75 | TYM | Tryptophan--tRNA ligase | / | 0.461 | |
| 1npd | NAD | Quinate/shikimate dehydrogenase | / | 0.460 | |
| 2fre | FMN | NAD(P)H-flavin oxidoreductase | / | 0.460 | |
| 3dzi | RGT | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.460 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.459 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.459 | |
| 2ok8 | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.459 | |
| 2vyq | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.459 | |
| 1vi2 | NAD | Quinate/shikimate dehydrogenase | / | 0.458 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.458 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.458 | |
| 1fdr | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.457 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.457 | |
| 1ra8 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.457 | |
| 2q3r | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.457 | |
| 2vq7 | FAD | Putative flavin-containing monooxygenase | / | 0.457 | |
| 4rnu | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.457 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.457 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.456 | |
| 3bnk | FMN | Flavoredoxin | / | 0.456 | |
| 3inr | GDU | UDP-galactopyranose mutase | 5.4.99.9 | 0.456 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.456 | |
| 3toz | NAD | Shikimate dehydrogenase (NADP(+)) | / | 0.456 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.456 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.455 | |
| 1zdw | FLV | Prenyltransferase | / | 0.455 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.455 | |
| 2xvh | FAD | Putative flavin-containing monooxygenase | / | 0.455 | |
| 4rlh | 0WE | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.455 | |
| 1kr2 | TAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.454 | |
| 2zvc | SAH | Precorrin-3 C17-methyltransferase | / | 0.454 | |
| 3h2s | NDP | Putative NADH-flavin reductase | / | 0.454 | |
| 3kjg | ADP | CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC | / | 0.454 | |
| 4yp6 | NAP | Nicotinamide-nucleotide adenylyltransferase | 2.7.7.1 | 0.454 | |
| 1w34 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.453 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.453 | |
| 2yd0 | BES | Endoplasmic reticulum aminopeptidase 1 | 3.4.11 | 0.453 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.453 | |
| 3pft | FMN | Flavin reductase | / | 0.453 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.453 | |
| 2hpv | FMN | FMN-dependent NADH-azoreductase | 1.7 | 0.452 | |
| 2qbm | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 3dzk | NMN | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.452 | |
| 3i0p | NAD | Malate dehydrogenase, putative | / | 0.452 | |
| 4k9o | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.452 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.452 | |
| 4ttc | FMN | Iodotyrosine deiodinase 1 | / | 0.452 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.452 | |
| 1d0l | BLG | Membrane-bound lytic murein transglycosylase B | 4.2.2.n1 | 0.451 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.451 | |
| 2ok7 | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.451 | |
| 4bqz | GNP | Ectonucleoside triphosphate diphosphohydrolase 2 | / | 0.451 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.451 | |
| 1dyi | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1gpu | THD | Transketolase 1 | 2.2.1.1 | 0.450 | |
| 2bb3 | SAH | Cobalamin biosynthesis precorrin-6Y methylase (CbiE) | / | 0.450 | |
| 2hu2 | NAD | C-terminal binding protein 1 | / | 0.450 | |
| 2i65 | NAD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.450 | |
| 3gf4 | UPG | UDP-galactopyranose mutase | 5.4.99.9 | 0.450 | |
| 3wyc | NAP | Meso-diaminopimelate D-dehydrogenase | 1.4.1.16 | 0.450 | |
| 1u1g | BBB | Uridine phosphorylase | 2.4.2.3 | 0.449 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.449 | |
| 3vsw | R31 | Renin | 3.4.23.15 | 0.449 | |
| 4l4e | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.448 | |
| 2abj | CBC | Branched-chain-amino-acid aminotransferase, cytosolic | 2.6.1.42 | 0.448 | |
| 2c9z | QUE | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.448 | |
| 2x06 | NAD | L-sulfolactate dehydrogenase | / | 0.448 | |
| 3hgo | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.448 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.448 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.448 | |
| 4j4n | D44 | Peptidylprolyl isomerase | / | 0.448 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.448 | |
| 5fwn | NAP | Putative dehydrogenase | / | 0.448 | |
| 3gka | FMN | N-ethylmaleimide reductase | / | 0.447 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.446 | |
| 1tco | FK5 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.446 | |
| 1tco | FK5 | Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform | 3.1.3.16 | 0.446 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 3jyq | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.446 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.446 | |
| 3t4e | NAD | Quinate/shikimate dehydrogenase | / | 0.446 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.446 | |
| 5a0y | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.446 | |
| 5a0y | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.446 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 1f20 | FAD | Nitric oxide synthase, brain | 1.14.13.39 | 0.445 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.445 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1owe | 675 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.445 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 2cnd | FAD | Nitrate reductase [NADH] | 1.7.1.1 | 0.445 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.445 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.445 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.445 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.445 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.445 | |
| 3nut | SAH | Precorrin-3 methylase | / | 0.445 | |
| 1d0m | BLG | Membrane-bound lytic murein transglycosylase B | 4.2.2.n1 | 0.444 | |
| 1h73 | ANP | Homoserine kinase | 2.7.1.39 | 0.444 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 1qx4 | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.444 | |
| 3axk | NDP | Ribulose bisphosphate carboxylase large chain | 4.1.1.39 | 0.444 | |
| 3dm6 | 757 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3ids | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.444 | |
| 3jyo | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.444 | |
| 3m30 | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.444 | |
| 3m30 | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.444 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.444 | |
| 4mrm | 2BY | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.444 | |
| 4yj2 | GTP | Tubulin alpha-1B chain | / | 0.444 | |
| 4zu4 | 4TG | WxcM-like protein | / | 0.444 | |
| 1bvr | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 1dhf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1nfy | RTR | Coagulation factor X | 3.4.21.6 | 0.443 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.443 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.443 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.443 | |
| 2dfv | NAD | L-threonine 3-dehydrogenase | / | 0.443 | |
| 2v2z | ADP | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.443 | |
| 2v7q | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.443 | |
| 2v7q | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.443 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 3f63 | GTX | Glutathione transferase GST1-4 | / | 0.443 | |
| 3lxi | CAM | Cytochrome P450 | / | 0.443 | |
| 3vkj | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.443 | |
| 4b77 | 54M | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4u3j | GTP | Tubulin beta chain | / | 0.443 | |
| 4y35 | F90 | Endothiapepsin | 3.4.23.22 | 0.443 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1q45 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.442 | |
| 1qbq | HFP | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.442 | |
| 1qbq | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.442 | |
| 1udb | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.442 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.442 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.442 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.442 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.442 | |
| 3tg4 | SAM | N-lysine methyltransferase SMYD2 | / | 0.442 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.442 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.442 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4gid | 0GH | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4xr9 | NAD | CalS8 | / | 0.442 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.442 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.442 | |
| 1ee9 | NAD | Methylenetetrahydrofolate dehydrogenase [NAD(+)] | 1.5.1.15 | 0.441 | |
| 1lrj | UD1 | UDP-glucose 4-epimerase | 5.1.3.2 | 0.441 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.441 | |
| 2ii6 | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.441 | |
| 2p8h | MY9 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.441 | |
| 4eue | NAI | Trans-2-enoyl-CoA reductase [NADH] | / | 0.441 | |
| 4lut | DCS | Alanine racemase | / | 0.441 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.440 | |
| 1j9z | FAD | NADPH--cytochrome P450 reductase | / | 0.440 | |
| 2p6d | SAH | Diphthine synthase | / | 0.440 | |
| 2zvb | SAH | Precorrin-3 C17-methyltransferase | / | 0.440 | |
| 3bgs | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.440 | |
| 3eku | CY9 | Actin-5C | / | 0.440 | |
| 3hlw | CE3 | Beta-lactamase | / | 0.440 | |
| 3n71 | SFG | Histone-lysine N-methyltransferase Smyd1 | / | 0.440 | |
| 4a0r | DTB | Bifunctional dethiobiotin synthetase/7,8-diamino-pelargonic acid aminotransferase, mitochondrial | 6.3.3.3 | 0.440 | |
| 4a86 | 2AN | Major pollen allergen Bet v 1-A | / | 0.440 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 4ke1 | 1R6 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4z26 | FAD | Putative GMC-type oxidoreductase R135 | 1 | 0.440 |