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 |
|---|---|---|---|
| 3ufy | NPX | Aldo-keto reductase family 1 member C3 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3ufy | NPX | Aldo-keto reductase family 1 member C3 | / | 1.000 | |
| 3r94 | FLR | Aldo-keto reductase family 1 member C3 | / | 0.795 | |
| 4h7c | 10H | Aldo-keto reductase family 1 member C3 | / | 0.685 | |
| 3r8h | ZOM | Aldo-keto reductase family 1 member C3 | / | 0.676 | |
| 3r7m | SUZ | Aldo-keto reductase family 1 member C3 | / | 0.673 | |
| 1zq5 | E04 | Aldo-keto reductase family 1 member C3 | / | 0.662 | |
| 3uwe | VJJ | Aldo-keto reductase family 1 member C3 | / | 0.662 | |
| 4hmn | 16J | Aldo-keto reductase family 1 member C3 | / | 0.660 | |
| 3r6i | JMS | Aldo-keto reductase family 1 member C3 | / | 0.659 | |
| 3r58 | NPS | Aldo-keto reductase family 1 member C3 | / | 0.633 | |
| 1s2c | FLF | Aldo-keto reductase family 1 member C3 | / | 0.620 | |
| 4fal | 0T0 | Aldo-keto reductase family 1 member C3 | / | 0.614 | |
| 4fa3 | 0SL | Aldo-keto reductase family 1 member C3 | / | 0.611 | |
| 3ug8 | IMN | Aldo-keto reductase family 1 member C3 | / | 0.607 | |
| 3r8g | IZP | Aldo-keto reductase family 1 member C3 | / | 0.602 | |
| 4dbw | 511 | Aldo-keto reductase family 1 member C3 | / | 0.602 | |
| 4fam | 0SZ | Aldo-keto reductase family 1 member C3 | / | 0.595 | |
| 1s1r | NAP | Aldo-keto reductase family 1 member C3 | / | 0.585 | |
| 3ugr | IMN | Aldo-keto reductase family 1 member C3 | / | 0.582 | |
| 4dbs | 0HV | Aldo-keto reductase family 1 member C3 | / | 0.578 | |
| 1ry0 | PG2 | Aldo-keto reductase family 1 member C3 | / | 0.573 | |
| 4dz5 | NAP | Aldo-keto reductase family 1 member C3 | / | 0.565 | |
| 1xf0 | ASD | Aldo-keto reductase family 1 member C3 | / | 0.560 | |
| 2f38 | 15M | Aldo-keto reductase family 1 member C3 | / | 0.540 | |
| 4dbu | BT9 | Aldo-keto reductase family 1 member C3 | / | 0.540 | |
| 1ry8 | RUT | Aldo-keto reductase family 1 member C3 | / | 0.523 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.493 | |
| 3r43 | ID8 | Aldo-keto reductase family 1 member C3 | / | 0.483 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.483 | |
| 3itu | IBM | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.476 | |
| 1s36 | CEI | Obelin | / | 0.473 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.473 | |
| 4ky4 | 04J | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.473 | |
| 1pq6 | 965 | Oxysterols receptor LXR-beta | / | 0.471 | |
| 2acl | L05 | Oxysterols receptor LXR-alpha | / | 0.471 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.470 | |
| 4fl0 | PLP | Aminotransferase ALD1, chloroplastic | 2.6.1 | 0.469 | |
| 2q15 | 3MR | Beta-secretase 1 | 3.4.23.46 | 0.467 | |
| 2vz0 | D64 | Pteridine reductase | / | 0.467 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.466 | |
| 2iq0 | NAP | Aldose reductase | 1.1.1.21 | 0.465 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.464 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.464 | |
| 1w6j | R71 | Lanosterol synthase | 5.4.99.7 | 0.464 | |
| 1z4i | UMP | 5'(3')-deoxyribonucleotidase, mitochondrial | 3.1.3 | 0.464 | |
| 1zp4 | C2F | 5,10-methylenetetrahydrofolate reductase | 1.5.1.20 | 0.464 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.464 | |
| 3f3y | 4OA | Bile salt sulfotransferase | 2.8.2.14 | 0.464 | |
| 4ddl | 0JQ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.464 | |
| 4fcd | 0T6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.464 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.464 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.463 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.463 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.463 | |
| 3dop | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.463 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.463 | |
| 3aiv | HBO | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase, chloroplastic | 3.2.1.182 | 0.462 | |
| 2aot | 2PM | Histamine N-methyltransferase | 2.1.1.8 | 0.461 | |
| 2gyu | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 2wu4 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 3g4g | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.461 | |
| 4jpg | 1OX | Pyruvate kinase PKM | 2.7.1.40 | 0.461 | |
| 1y2c | 3DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.460 | |
| 3aiq | HBO | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1b, chloroplastic | 3.2.1.182 | 0.460 | |
| 3fvu | IAC | Kynurenine--oxoglutarate transaminase 1 | 2.6.1.7 | 0.460 | |
| 4llk | MEW | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.460 | |
| 2xug | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.459 | |
| 3d3p | 20A | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.459 | |
| 3b9o | FMN | Alkane monoxygenase | / | 0.457 | |
| 4jq3 | NAP | Aldo-keto reductase family 1 member C2 | / | 0.457 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 1uhh | CZP | Aequorin-2 | / | 0.456 | |
| 2d06 | EST | Sulfotransferase 1A1 | 2.8.2.1 | 0.456 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.456 | |
| 1q83 | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 1y2k | 7DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.454 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.454 | |
| 3zg6 | APR | NAD-dependent protein deacetylase sirtuin-6 | 3.5.1 | 0.454 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.454 | |
| 4n4t | 2GV | Tankyrase-1 | 2.4.2.30 | 0.454 | |
| 2o8h | 227 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.453 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 3gnc | QQQ | Glutaryl-CoA dehydrogenase | / | 0.453 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.453 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 2pdl | TOL | Aldose reductase | 1.1.1.21 | 0.452 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 2wjo | QUD | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 2y0j | AXC | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.451 | |
| 3g1r | FIT | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.451 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 2y04 | 68H | Beta-1 adrenergic receptor | / | 0.451 | |
| 1ah4 | NAP | Aldose reductase | 1.1.1.21 | 0.450 | |
| 1ej3 | CZH | Aequorin-2 | / | 0.450 | |
| 1oyn | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.450 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.450 | |
| 4n1f | CZH | Obelin | / | 0.450 | |
| 2hdj | NDP | Aldo-keto reductase family 1 member C2 | / | 0.449 | |
| 3ipq | 965 | Oxysterols receptor LXR-alpha | / | 0.449 | |
| 3qpp | PFW | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.449 | |
| 4eil | FOL | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.449 | |
| 4u95 | MIY | Multidrug efflux pump subunit AcrB | / | 0.449 | |
| 1efy | BZC | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.448 | |
| 1gpn | HUB | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 1y2b | DEE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.448 | |
| 2c9z | QUE | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.448 | |
| 3d4b | DZD | NAD-dependent protein deacetylase | / | 0.448 | |
| 1mlz | PLP | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | 2.6.1.62 | 0.447 | |
| 3v94 | WYQ | Phosphodiesterase | / | 0.447 | |
| 4bjb | P34 | Tankyrase-2 | 2.4.2.30 | 0.447 | |
| 4li6 | 1XO | Tankyrase-1 | 2.4.2.30 | 0.447 | |
| 4bfy | ZVY | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 4fap | ARD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.446 | |
| 4fap | ARD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.446 | |
| 4kfj | 1R0 | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 4phl | PIL | Phosphodiesterase | / | 0.446 | |
| 4u14 | 0HK | Muscarinic acetylcholine receptor M3 | / | 0.446 | |
| 1y2d | 4DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.445 | |
| 2wd8 | VGF | Pteridine reductase | / | 0.445 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 3sn7 | 540 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.445 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.445 | |
| 4g5d | NDP | Prostaglandin F synthase | 1.1.1.188 | 0.445 | |
| 1ex7 | 5GP | Guanylate kinase | 2.7.4.8 | 0.444 | |
| 1y2e | 5DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 2h7j | H7J | Cathepsin S | 3.4.22.27 | 0.444 | |
| 2ovy | PFJ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.444 | |
| 3dr7 | GPD | GDP-perosamine synthase | / | 0.444 | |
| 3w5e | NVW | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.444 | |
| 4fcb | 0T7 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.444 | |
| 1rkw | PNT | HTH-type transcriptional regulator QacR | / | 0.443 | |
| 1u08 | PLP | Methionine aminotransferase | / | 0.443 | |
| 3p2v | DOY | Aldose reductase | 1.1.1.21 | 0.443 | |
| 3rvi | RVI | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 1fml | RTL | Retinol dehydratase | / | 0.442 | |
| 2c1z | U2F | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.442 | |
| 3o56 | ZG1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.442 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 4lng | JAN | CaaX farnesyltransferase beta subunit Ram1 | / | 0.442 | |
| 5cc9 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1v08 | NTZ | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1, chloroplastic | 3.2.1.182 | 0.441 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2g7y | MO9 | Cathepsin S | 3.4.22.27 | 0.441 | |
| 2our | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.441 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 3cgt | BCD | Cyclomaltodextrin glucanotransferase | 2.4.1.19 | 0.441 | |
| 3sfx | JAN | Uncharacterized protein | / | 0.441 | |
| 4bjc | RPB | Tankyrase-2 | 2.4.2.30 | 0.441 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.440 | |
| 4boe | CLR | Japanin | / | 0.440 | |
| 4muw | 2F4 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 |