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 |
|---|---|---|---|
| 1hnh | COA | 3-oxoacyl-[acyl-carrier-protein] synthase 3 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1hnh | COA | 3-oxoacyl-[acyl-carrier-protein] synthase 3 | / | 1.000 | |
| 1hnd | COA | 3-oxoacyl-[acyl-carrier-protein] synthase 3 | / | 0.651 | |
| 2gyo | COA | 3-oxoacyl-[acyl-carrier-protein] synthase 3 | / | 0.565 | |
| 1mzs | 669 | 3-oxoacyl-[acyl-carrier-protein] synthase 3 | / | 0.560 | |
| 2eft | COA | 3-oxoacyl-[acyl-carrier-protein] synthase 3 | / | 0.531 | |
| 1ebl | COA | 3-oxoacyl-[acyl-carrier-protein] synthase 3 | / | 0.500 | |
| 3zu2 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.487 | |
| 3il4 | ACO | 3-oxoacyl-[acyl-carrier-protein] synthase 3 | / | 0.486 | |
| 3i1y | 33N | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.478 | |
| 4g2i | 0VQ | Vitamin D3 receptor | / | 0.476 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.471 | |
| 1fdw | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.469 | |
| 2hb7 | O1C | Vitamin D3 receptor | / | 0.469 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.469 | |
| 2o4r | VD5 | Vitamin D3 receptor | / | 0.468 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.467 | |
| 3vt4 | 5YI | Vitamin D3 receptor | / | 0.467 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.466 | |
| 3w5t | LHP | Vitamin D3 receptor | / | 0.464 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.464 | |
| 4fmx | CNL | 1,8-cineole 2-endo-monooxygenase | 1.14.13.156 | 0.464 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.463 | |
| 4r1f | ADP | DNA topoisomerase 2-alpha | 5.99.1.3 | 0.463 | |
| 3iae | D7K | Benzaldehyde lyase | / | 0.462 | |
| 5c4f | UPG | Histo-blood group ABO system transferase | / | 0.462 | |
| 1piw | NAP | NADP-dependent alcohol dehydrogenase 6 | 1.1.1.2 | 0.461 | |
| 2hc4 | VDX | Vitamin D3 receptor A | / | 0.461 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.461 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.460 | |
| 4euf | NAD | Trans-2-enoyl-CoA reductase [NADH] | / | 0.460 | |
| 1hrv | SDZ | Genome polyprotein | / | 0.459 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.459 | |
| 3w0c | 6DS | Vitamin D3 receptor | / | 0.459 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.459 | |
| 5c4c | UPG | Histo-blood group ABO system transferase | / | 0.459 | |
| 1r6g | 442 | Thyroid hormone receptor beta | / | 0.458 | |
| 1w06 | W05 | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.458 | |
| 4m6j | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 4n4v | 2GY | Tankyrase-1 | 2.4.2.30 | 0.458 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.457 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.457 | |
| 1fdu | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.456 | |
| 1nq7 | ARL | Nuclear receptor ROR-beta | / | 0.456 | |
| 3il6 | B83 | 3-oxoacyl-[acyl-carrier-protein] synthase 3 | / | 0.456 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.456 | |
| 4i4b | 1CV | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.88 | 0.456 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.455 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 5kp2 | COA | 3-oxoacyl-[acyl-carrier-protein] synthase 3 protein 2 | / | 0.455 | |
| 1rsz | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.454 | |
| 3vtc | TK3 | Vitamin D3 receptor | / | 0.454 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.454 | |
| 3clb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.453 | |
| 3cop | ADP | Glycogen synthase | 2.4.1.21 | 0.453 | |
| 4n3c | UD1 | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.453 | |
| 4ozn | ATP | Ammonium transporter | / | 0.453 | |
| 1f5f | DHT | Sex hormone-binding globulin | / | 0.452 | |
| 1n4h | REA | Nuclear receptor ROR-beta | / | 0.452 | |
| 2itu | ITQ | Epidermal growth factor receptor | 2.7.10.1 | 0.452 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 4c71 | 7RD | 3-oxoacyl-ACP synthase | / | 0.452 | |
| 1drf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 1fp2 | HMO | Isoflavone-7-O-methyltransferase 8 | 2.1.1.150 | 0.451 | |
| 1iy8 | NAD | Levodione reductase | / | 0.451 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 2i0z | FAD | NAD(FAD)-utilizing dehydrogenases | / | 0.451 | |
| 2r2n | KYN | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.451 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.451 | |
| 3lfm | 3DT | Alpha-ketoglutarate-dependent dioxygenase FTO | / | 0.451 | |
| 1kt3 | RTL | Retinol-binding protein 4 | / | 0.450 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1uuo | BRF | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.450 | |
| 2bac | FAD | Putative aminooxidase | / | 0.450 | |
| 2gmv | PEP | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] | 4.1.1.32 | 0.450 | |
| 2ylx | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.450 | |
| 2zl9 | VDA | Vitamin D3 receptor | / | 0.450 | |
| 3bej | MUF | Bile acid receptor | / | 0.450 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.450 | |
| 4ceq | QCH | Integrase | / | 0.450 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.450 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.450 | |
| 4itf | TFY | Vitamin D3 receptor | / | 0.450 | |
| 3sn6 | P0G | Beta-2 adrenergic receptor | / | 0.450 | |
| 1kc1 | NDP | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.449 | |
| 1osv | CHC | Bile acid receptor | / | 0.449 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.449 | |
| 3otb | DGT | Probable tRNA(His) guanylyltransferase | 2.7.7.79 | 0.449 | |
| 4g67 | SAH | Uncharacterized ACR, COG1565 superfamily | / | 0.449 | |
| 1mvt | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1ppj | ANY | Cytochrome b | / | 0.448 | |
| 1rx8 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1trg | CB3 | Thymidylate synthase | / | 0.448 | |
| 1u0w | STL | Chalcone synthase 2 | 2.3.1.74 | 0.448 | |
| 1uxj | NAD | Malate dehydrogenase | / | 0.448 | |
| 1zxm | ANP | DNA topoisomerase 2-alpha | 5.99.1.3 | 0.448 | |
| 5cp8 | TCU | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.448 | |
| 5iub | CLR | Adenosine receptor A2a | / | 0.448 | |
| 1dhf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1pyd | TDP | Pyruvate decarboxylase isozyme 1 | / | 0.447 | |
| 2a0w | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.447 | |
| 2hzi | JIN | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.447 | |
| 2yg4 | FAD | Putrescine oxidase | / | 0.447 | |
| 3cuk | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.447 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.447 | |
| 4fhh | 0U3 | Vitamin D3 receptor A | / | 0.447 | |
| 4g21 | 0VP | Vitamin D3 receptor A | / | 0.447 | |
| 4g2h | 0VQ | Vitamin D3 receptor A | / | 0.447 | |
| 1opb | RET | Retinol-binding protein 2 | / | 0.446 | |
| 1pow | FAD | Pyruvate oxidase | 1.2.3.3 | 0.446 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.446 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 2iyg | FMN | AppA, antirepressor of ppsR, sensor of blue light | / | 0.446 | |
| 3ipu | O40 | Oxysterols receptor LXR-alpha | / | 0.446 | |
| 3orf | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.446 | |
| 1efa | NPF | Lactose operon repressor | / | 0.445 | |
| 1equ | EQI | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.445 | |
| 1fnd | A2P | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 0.445 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.445 | |
| 1qyx | ASD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.445 | |
| 2aq7 | TL5 | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.445 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.445 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.445 | |
| 3eku | CY9 | Actin-5C | / | 0.445 | |
| 4an4 | DUD | Putative glycosyl transferase | / | 0.445 | |
| 1diu | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1p0p | BCH | Cholinesterase | 3.1.1.8 | 0.444 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.444 | |
| 1r2j | FAD | FkbI | / | 0.444 | |
| 1z7y | AA5 | Cysteine synthase 1 | 2.5.1.47 | 0.444 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 3cx4 | ADP | Glycogen synthase | 2.4.1.21 | 0.444 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 3gqo | APR | Non-structural polyprotein | / | 0.444 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.444 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.444 | |
| 4kp7 | 1UQ | 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic | 1.1.1.267 | 0.444 | |
| 4kq2 | 1S3 | Glycogen [starch] synthase isoform 2 | 2.4.1.11 | 0.444 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.444 | |
| 1td2 | PXL | Pyridoxal kinase PdxY | / | 0.443 | |
| 2has | C3O | Vitamin D3 receptor | / | 0.443 | |
| 2ieb | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 3a9w | NAD | NDP-sugar epimerase | / | 0.443 | |
| 3dr1 | C5D | Vitamin D3 receptor A | / | 0.443 | |
| 3w0j | T08 | Vitamin D3 receptor | / | 0.443 | |
| 4cj4 | S3G | Integrase | / | 0.443 | |
| 4ure | 1PS | Cyclohexanol dehydrogenase | / | 0.443 | |
| 1db1 | VDX | Vitamin D3 receptor | / | 0.442 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.442 | |
| 1mq4 | ADP | Aurora kinase A | 2.7.11.1 | 0.442 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 2hbh | XE4 | Vitamin D3 receptor A | / | 0.442 | |
| 2qa2 | FAD | Polyketide oxygenase CabE | / | 0.442 | |
| 3ha3 | SAH | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.442 | |
| 3maa | FKP | Adenylate cyclase type 2 | / | 0.442 | |
| 3maa | FKP | Adenylate cyclase type 5 | / | 0.442 | |
| 3v2u | ATP | Protein GAL3 | / | 0.442 | |
| 3vtb | TKA | Vitamin D3 receptor | / | 0.442 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 4bfy | ZVY | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 4wuo | NAD | 3-isopropylmalate dehydrogenase | 1.1.1.85 | 0.442 | |
| 1emd | NAD | Malate dehydrogenase | / | 0.441 | |
| 1pox | FAD | Pyruvate oxidase | 1.2.3.3 | 0.441 | |
| 3ngl | NAP | Bifunctional protein FolD | / | 0.441 | |
| 3pbz | F02 | Endothiapepsin | 3.4.23.22 | 0.441 | |
| 3vru | YS3 | Vitamin D3 receptor | / | 0.441 | |
| 4abk | AR6 | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.441 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 5cb5 | APR | O-acetyl-ADP-ribose deacetylase | / | 0.441 | |
| 1crb | RTL | Retinol-binding protein 1 | / | 0.440 | |
| 1fwk | ADP | Homoserine kinase | 2.7.1.39 | 0.440 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 2pr2 | DG1 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.440 | |
| 2w3b | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.440 | |
| 4c6u | TLG | 3-oxoacyl-ACP synthase | / | 0.440 | |
| 4c72 | TLG | 3-oxoacyl-ACP synthase | / | 0.440 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.440 | |
| 4kq2 | U5P | Glycogen [starch] synthase isoform 2 | 2.4.1.11 | 0.440 |