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 |
|---|---|---|---|
| 2ij7 | TPF | Mycocyclosin synthase | 1.14.21.9 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2ij7 | TPF | Mycocyclosin synthase | 1.14.21.9 | 1.000 | |
| 4iq7 | 1G9 | Mycocyclosin synthase | 1.14.21.9 | 0.605 | |
| 4ktl | 1CQ | Cytochrome P450 | / | 0.599 | |
| 4g48 | PZB | Mycocyclosin synthase | 1.14.21.9 | 0.591 | |
| 4ktf | 1TM | Cytochrome P450 | / | 0.589 | |
| 4ict | 1ED | Mycocyclosin synthase | 1.14.21.9 | 0.580 | |
| 4ktk | KTK | Cytochrome P450 | / | 0.578 | |
| 3g5h | YTT | Mycocyclosin synthase | 1.14.21.9 | 0.572 | |
| 4g2g | TDH | Mycocyclosin synthase | 1.14.21.9 | 0.567 | |
| 4g47 | TZF | Mycocyclosin synthase | 1.14.21.9 | 0.550 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.538 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.495 | |
| 1lsj | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.478 | |
| 2d29 | FAD | Acyl-CoA dehydrogenase | / | 0.477 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.475 | |
| 3ixp | 834 | Ecdysone receptor | / | 0.475 | |
| 1f17 | NAI | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.474 | |
| 3g4g | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.474 | |
| 3qpo | PFR | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.473 | |
| 2qd5 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.472 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.472 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.471 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.471 | |
| 1iid | NHM | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.470 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.470 | |
| 1f4g | TP4 | Thymidylate synthase | / | 0.469 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.468 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.466 | |
| 2pnj | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.465 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.464 | |
| 2w9s | TOP | Dihydrofolate reductase type 1 from Tn4003 | 1.5.1.3 | 0.464 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.463 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.463 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.463 | |
| 1f4f | TP3 | Thymidylate synthase | / | 0.462 | |
| 4ajm | 3A6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.462 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.462 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.461 | |
| 2aqk | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.460 | |
| 2ci0 | 1CM | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.460 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.460 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.459 | |
| 2ktd | PUC | Prostaglandin-H2 D-isomerase | 5.3.99.2 | 0.459 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.459 | |
| 3had | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.458 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.458 | |
| 5cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.458 | |
| 4dre | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.456 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.455 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.455 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.454 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.454 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.454 | |
| 4k9o | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.454 | |
| 4ku5 | DCC | 3-oxoacyl-[ACP] synthase III | / | 0.454 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.453 | |
| 1t87 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.453 | |
| 4d0l | 093 | Phosphatidylinositol 4-kinase beta | 2.7.1.67 | 0.453 | |
| 4klr | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.453 | |
| 4ure | 1PS | Cyclohexanol dehydrogenase | / | 0.453 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.452 | |
| 2hrc | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.452 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.452 | |
| 2xsz | ATP | RuvB-like 2 | 3.6.4.12 | 0.452 | |
| 4llk | MEW | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.452 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.451 | |
| 1tdr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.451 | |
| 4y1b | NAP | AntE | / | 0.451 | |
| 5cpb | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.451 | |
| 1dz8 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.450 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.450 | |
| 1t85 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 1xg5 | NAP | Dehydrogenase/reductase SDR family member 11 | / | 0.450 | |
| 3gob | HXX | DdmC | / | 0.450 | |
| 3is9 | AC7 | Gag-Pol polyprotein | 2.7.7.49 | 0.450 | |
| 3vvp | BNU | Uncharacterized protein | / | 0.450 | |
| 4rlh | 0WE | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.450 | |
| 4uym | VOR | 14-alpha sterol demethylase Cyp51B | / | 0.450 | |
| 1dhr | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.449 | |
| 2yxl | SFG | 450aa long hypothetical fmu protein | / | 0.449 | |
| 3fwg | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 3rr3 | FLR | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.449 | |
| 3t2y | FAD | Sulfide-quinone reductase | / | 0.449 | |
| 4g3r | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 5ccc | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 4z9g | 1Q5 | Corticotropin-releasing factor receptor 1 | / | 0.449 | |
| 1o0s | NAI | NAD-dependent malic enzyme, mitochondrial | 1.1.1.38 | 0.448 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.448 | |
| 3wrm | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.448 | |
| 1iwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 1yrc | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.447 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.447 | |
| 4l49 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 4oqy | NDP | (S)-imine reductase | / | 0.447 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.446 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.446 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.446 | |
| 3of2 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.446 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.446 | |
| 6cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 1fml | RTL | Retinol dehydratase | / | 0.445 | |
| 2a84 | ATP | Pantothenate synthetase | 6.3.2.1 | 0.445 | |
| 3atr | FDA | Conserved Archaeal protein | / | 0.445 | |
| 3bfa | 9OD | Odorant binding protein ASP1 | / | 0.445 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 3ids | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.445 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 4r20 | AER | Cytochrome P450 family 17 polypeptide 2 | / | 0.445 | |
| 1dz4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 1eup | ASD | 6-deoxyerythronolide B hydroxylase | / | 0.444 | |
| 1o5r | FR9 | Adenosine deaminase | 3.5.4.4 | 0.444 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 2ieb | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.444 | |
| 3czr | 3CZ | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.444 | |
| 3ns2 | PYV | Abscisic acid receptor PYL2 | / | 0.444 | |
| 3oez | STI | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.444 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.444 | |
| 3q2j | CKI | Aminoglycoside 3'-phosphotransferase | 2.7.1.95 | 0.444 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.444 | |
| 4gl4 | NAI | Alcohol dehydrogenase class-3 | / | 0.444 | |
| 1bvr | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.443 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.443 | |
| 3mdv | CL6 | Cholesterol 24-hydroxylase | / | 0.443 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.443 | |
| 4gmy | 0X5 | Tyrosine-protein kinase JAK2 | / | 0.443 | |
| 4ib4 | ERM | 5-hydroxytryptamine receptor 2B | / | 0.443 | |
| 5a3c | NAD | SIR2 family protein | / | 0.443 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 2brm | DFZ | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.442 | |
| 2yne | YNE | Glycylpeptide N-tetradecanoyltransferase | / | 0.442 | |
| 2zsb | ADP | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 3fwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.442 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.442 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.442 | |
| 4e0u | 0MV | Cyclic dipeptide N-prenyltransferase | / | 0.442 | |
| 4j53 | 1J4 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.442 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1pjc | NAD | Alanine dehydrogenase | / | 0.441 | |
| 2lfo | GCH | Fatty acid-binding protein, liver | / | 0.441 | |
| 3koo | 24D | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.441 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.441 | |
| 3t8x | T8X | T-cell surface glycoprotein CD1b | / | 0.441 | |
| 4b70 | WM9 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4bii | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 1yrd | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 2qbl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.440 | |
| 3wrh | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 4hnc | 0UT | Mandelate racemase | / | 0.440 | |
| 4jx1 | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 |