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 |
|---|---|---|---|
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 1.000 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.492 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.491 | |
| 2rkv | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.484 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.484 | |
| 1ddr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.482 | |
| 4q72 | FAD | Bifunctional protein PutA | / | 0.478 | |
| 1nvt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.477 | |
| 3of2 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.477 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.475 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.474 | |
| 2hrc | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.473 | |
| 3t3r | 9PL | Cytochrome P450 2A6 | 1.14.13 | 0.472 | |
| 2q9f | C3S | Cholesterol 24-hydroxylase | / | 0.471 | |
| 4ejh | 0QA | Cytochrome P450 2A13 | 1.14.14.1 | 0.469 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.468 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.468 | |
| 1m13 | HYF | Nuclear receptor subfamily 1 group I member 2 | / | 0.467 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.467 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.467 | |
| 3qg2 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.466 | |
| 3ruk | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.466 | |
| 3da2 | 4MD | Carbonic anhydrase 13 | 4.2.1.1 | 0.465 | |
| 3ibq | ATP | Pyridoxal kinase | / | 0.465 | |
| 3mdm | FJZ | Cholesterol 24-hydroxylase | / | 0.465 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.465 | |
| 3tnl | NAD | Shikimate dehydrogenase (NADP(+)) | / | 0.465 | |
| 4bge | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.465 | |
| 4dti | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.465 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.465 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.464 | |
| 4o1m | NAD | Enoyl-acyl carrier reductase | / | 0.464 | |
| 5ai5 | BSU | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.464 | |
| 5akk | 1P8 | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.464 | |
| 3t3q | 9PL | Cytochrome P450 2A6 | 1.14.13 | 0.463 | |
| 3oew | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.462 | |
| 3oey | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.462 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.461 | |
| 4kla | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.461 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.460 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.460 | |
| 2qo5 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.460 | |
| 4d0l | 093 | Phosphatidylinositol 4-kinase beta | 2.7.1.67 | 0.460 | |
| 4l4d | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.460 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.459 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.459 | |
| 1iwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.459 | |
| 1t2b | CNL | 1,8-cineole 2-endo-monooxygenase | 1.14.13.156 | 0.459 | |
| 1uyu | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.459 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.459 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.459 | |
| 4j03 | FVS | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.459 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 1phe | PIY | Camphor 5-monooxygenase | 1.14.15.1 | 0.458 | |
| 1v35 | NAI | Enoyl-ACP reductase | / | 0.458 | |
| 2znq | 401 | Peroxisome proliferator-activated receptor delta | / | 0.458 | |
| 3ans | S38 | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.457 | |
| 3cpp | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.457 | |
| 3lxi | CAM | Cytochrome P450 | / | 0.457 | |
| 3mdv | CL6 | Cholesterol 24-hydroxylase | / | 0.457 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.457 | |
| 1t86 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.456 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.456 | |
| 4lxh | C1E | Alpha/beta hydrolase fold | / | 0.456 | |
| 5fwn | NAP | Putative dehydrogenase | / | 0.456 | |
| 1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.455 | |
| 2qd3 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.455 | |
| 3kjr | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.455 | |
| 4dre | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.455 | |
| 4enh | FVX | Cholesterol 24-hydroxylase | / | 0.455 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.455 | |
| 4r20 | AER | Cytochrome P450 family 17 polypeptide 2 | / | 0.455 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.454 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.454 | |
| 4bqp | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.454 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.453 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.453 | |
| 3ics | COA | Coenzyme A disulfide reductase | / | 0.453 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.453 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.453 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.453 | |
| 1eio | GCH | Gastrotropin | / | 0.452 | |
| 1iwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 1x2h | LPA | Lipoate-protein ligase A | 6.3.1.20 | 0.452 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.452 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.452 | |
| 2y3r | TRK | TamL | / | 0.452 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.451 | |
| 3th8 | TH9 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.451 | |
| 4a84 | DXC | Major pollen allergen Bet v 1-A | / | 0.451 | |
| 4l4c | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.451 | |
| 4nkv | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.451 | |
| 1cqp | 803 | Integrin alpha-L | / | 0.450 | |
| 3kjm | 245 | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.450 | |
| 3koo | 24D | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.450 | |
| 3zuy | TCH | Transporter | / | 0.450 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.450 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.450 | |
| 1t85 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 1t88 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.449 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.449 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 3ieu | GDP | GTPase Era | / | 0.449 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 4bgi | I4I | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.449 | |
| 4fjz | 4FJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.449 | |
| 5hs1 | VOR | Lanosterol 14-alpha demethylase | / | 0.449 | |
| 1fpq | SAM | Isoliquiritigenin 2'-O-methyltransferase | / | 0.448 | |
| 1klk | PMD | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1q1r | FAD | Putidaredoxin reductase | 1.18.1.5 | 0.448 | |
| 2pnj | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.448 | |
| 3s79 | ASD | Aromatase | 1.14.14.14 | 0.448 | |
| 3wv9 | FEG | Hmd co-occurring protein HcgE | / | 0.448 | |
| 4l4f | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.448 | |
| 4z64 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.448 | |
| 4zow | CLM | Multidrug transporter MdfA | / | 0.448 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 1osv | CHC | Bile acid receptor | / | 0.447 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 1t87 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 1yrc | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 3fwg | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.447 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.446 | |
| 2a1n | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 2aq8 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.446 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.446 | |
| 3qgt | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.446 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.445 | |
| 1ro6 | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.445 | |
| 1rx8 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 2a1m | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 2a1o | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.445 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.445 | |
| 3pgq | GY3 | Acetyl-CoA carboxylase | / | 0.445 | |
| 4c9p | CAM | Cytochrome P450 | / | 0.445 | |
| 4jx1 | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 4rlh | 0WE | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.445 | |
| 6cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 1bvr | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 1jpa | ANP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.444 | |
| 2npa | MMB | Peroxisome proliferator-activated receptor alpha | / | 0.444 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.444 | |
| 2wpx | ACO | Orf14 | / | 0.444 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.444 | |
| 3tz3 | B36 | Acetyl-CoA carboxylase | / | 0.444 | |
| 4zj8 | SUV | Orexin receptor type 1 | / | 0.444 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.443 | |
| 1nyt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.443 | |
| 1phg | MYT | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 2aqk | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 2ddo | ATP | Pyridoxine/pyridoxal/pyridoxamine kinase | / | 0.443 | |
| 2feu | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.443 | |
| 2hw2 | RFP | Rifampin ADP-ribosyl transferase | / | 0.443 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.443 | |
| 3c0i | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.443 | |
| 3fwf | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 3iqe | H4M | F420-dependent methylenetetrahydromethanopterin dehydrogenase | 1.5.98.1 | 0.443 | |
| 3ixp | 834 | Ecdysone receptor | / | 0.443 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.443 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.443 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.443 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.443 | |
| 4fmx | CNL | 1,8-cineole 2-endo-monooxygenase | 1.14.13.156 | 0.443 | |
| 4y8w | STR | Steroid 21-hydroxylase | / | 0.443 | |
| 1dds | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1drb | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1qyx | ASD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 2aqh | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.442 | |
| 2i40 | BLZ | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.442 | |
| 2z97 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 3d4p | NAD | L-lactate dehydrogenase 1 | 1.1.1.27 | 0.442 | |
| 3d7k | D7K | Benzaldehyde lyase | / | 0.442 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3w1w | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.442 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.442 | |
| 4g47 | TZF | Mycocyclosin synthase | 1.14.21.9 | 0.442 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.442 | |
| 1dhi | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1dhj | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1f17 | NAI | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.441 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1noo | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.441 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.441 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.441 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 4c9o | CAM | Cytochrome P450 | / | 0.441 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.441 | |
| 4g2g | TDH | Mycocyclosin synthase | 1.14.21.9 | 0.441 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.441 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.441 | |
| 1rb3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 2e9d | B76 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.440 | |
| 2ktd | PUC | Prostaglandin-H2 D-isomerase | 5.3.99.2 | 0.440 | |
| 2q5g | 1FA | Peroxisome proliferator-activated receptor delta | / | 0.440 | |
| 2xa4 | AZ5 | Tyrosine-protein kinase JAK2 | / | 0.440 | |
| 2y3s | TIR | TamL | / | 0.440 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2zui | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 3pm0 | BHF | Cytochrome P450 1B1 | / | 0.440 | |
| 3vth | APC | Carbamoyltransferase | / | 0.440 | |
| 3wrh | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 4cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.440 | |
| 4ktl | 1CQ | Cytochrome P450 | / | 0.440 | |
| 4l4a | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 4mvh | 2F5 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 | |
| 4v12 | POG | MaoC like domain protein | / | 0.440 | |
| 5a3b | APR | SIR2 family protein | / | 0.440 |