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 |
|---|---|---|---|
| 3uzz | TES | 3-oxo-5-beta-steroid 4-dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3uzz | TES | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 1.000 | |
| 3uzx | AOM | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.625 | |
| 3cot | STR | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.622 | |
| 3g1r | FIT | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.614 | |
| 3uzz | ASD | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.609 | |
| 3uzx | AOX | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.589 | |
| 3cmf | PDN | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.563 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.512 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.510 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.503 | |
| 3uon | QNB | Muscarinic acetylcholine receptor M2 | / | 0.502 | |
| 4u14 | 0HK | Muscarinic acetylcholine receptor M3 | / | 0.501 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.500 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.498 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.497 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.496 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.493 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.492 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.490 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.487 | |
| 2jf0 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.486 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.486 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.485 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.484 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.484 | |
| 4u15 | 0HK | Muscarinic acetylcholine receptor M3 | / | 0.482 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.481 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.480 | |
| 3c1o | NAP | Eugenol synthase | / | 0.480 | |
| 5d5b | CAU | Beta-2 adrenergic receptor | / | 0.480 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.479 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.477 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.476 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.474 | |
| 3b8x | G4M | Putative pyridoxamine 5-phosphate-dependent dehydrase | / | 0.474 | |
| 3bur | TES | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.474 | |
| 4f0r | MTA | 5-methylthioadenosine/S-adenosylhomocysteine deaminase | / | 0.474 | |
| 1fds | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.473 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.473 | |
| 2xug | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.472 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.471 | |
| 1r5g | AO1 | Methionine aminopeptidase 2 | / | 0.470 | |
| 1yw8 | A75 | Methionine aminopeptidase 2 | / | 0.470 | |
| 2ckm | AA7 | Acetylcholinesterase | 3.1.1.7 | 0.470 | |
| 1nqv | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.469 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.469 | |
| 2xi4 | AFT | Acetylcholinesterase | 3.1.1.7 | 0.469 | |
| 4jtr | IZP | Aldo-keto reductase family 1 member C2 | / | 0.469 | |
| 2xuj | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.468 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.468 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.467 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.467 | |
| 4cax | 646 | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.467 | |
| 4l1x | NAP | Aldo-keto reductase family 1 member C2 | / | 0.467 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.466 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.466 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.465 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.465 | |
| 1ihi | IU5 | Aldo-keto reductase family 1 member C2 | / | 0.464 | |
| 1zgc | A2E | Acetylcholinesterase | 3.1.1.7 | 0.464 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.464 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.463 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.463 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.463 | |
| 4yp6 | NAP | Nicotinamide-nucleotide adenylyltransferase | 2.7.7.1 | 0.463 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.462 | |
| 4fl0 | PLP | Aminotransferase ALD1, chloroplastic | 2.6.1 | 0.462 | |
| 4mrm | 2BY | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.462 | |
| 1lke | DOG | Bilin-binding protein | / | 0.461 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.461 | |
| 3dop | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.461 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.461 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.461 | |
| 3qeo | LLT | Deoxycytidine kinase | 2.7.1.74 | 0.461 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.460 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.460 | |
| 1c7o | PPG | Hemolysin | / | 0.459 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.459 | |
| 1w6j | R71 | Lanosterol synthase | 5.4.99.7 | 0.459 | |
| 2fs4 | PZ1 | Renin | 3.4.23.15 | 0.458 | |
| 5d6l | CAU | Beta-2 adrenergic receptor | / | 0.458 | |
| 2cmf | F11 | Acetylcholinesterase | 3.1.1.7 | 0.457 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.457 | |
| 3fsj | D7K | Benzoylformate decarboxylase | 4.1.1.7 | 0.457 | |
| 2xnv | VU3 | Soluble acetylcholine receptor | / | 0.456 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.456 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 2aot | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.455 | |
| 2g5w | 8PG | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.455 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 3mjr | AC2 | Deoxycytidine kinase | 2.7.1.74 | 0.455 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.455 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.455 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.455 | |
| 3buv | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.453 | |
| 1e66 | HUX | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.452 | |
| 2xys | SY9 | Soluble acetylcholine receptor | / | 0.452 | |
| 4dbs | 0HV | Aldo-keto reductase family 1 member C3 | / | 0.452 | |
| 2gyw | OBI | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.451 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.451 | |
| 3e33 | ED7 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.451 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.451 | |
| 1vot | HUP | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 2xyt | TC9 | Soluble acetylcholine receptor | / | 0.450 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 4ms1 | 381 | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.450 | |
| 4gbr | CAU | Beta-2 adrenergic receptor | / | 0.450 | |
| 1gw2 | FER | Peroxidase C1A | 1.11.1.7 | 0.449 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.449 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.449 | |
| 4gdd | NAI | UDP-galactopyranose mutase | / | 0.449 | |
| 1qzy | TDE | Methionine aminopeptidase 2 | / | 0.448 | |
| 2g26 | 3LG | Renin | 3.4.23.15 | 0.448 | |
| 2vqq | TFG | Histone deacetylase 4 | 3.5.1.98 | 0.448 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.448 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.448 | |
| 4n9q | FMN | FMN-dependent NADH-azoreductase 1 | / | 0.448 | |
| 3ny8 | JRZ | Beta-2 adrenergic receptor | / | 0.448 | |
| 1gpn | HUB | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.447 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.447 | |
| 2e9a | B28 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.447 | |
| 2vut | NAD | Nitrogen metabolite repression protein nmrA | / | 0.447 | |
| 3bxo | UPP | dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose | / | 0.447 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.447 | |
| 4jq4 | IMN | Aldo-keto reductase family 1 member C2 | / | 0.447 | |
| 5d5a | CAU | Beta-2 adrenergic receptor | / | 0.447 | |
| 1t7o | 152 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.446 | |
| 2c9z | QUE | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.446 | |
| 2hrc | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.446 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.446 | |
| 4dz5 | NAP | Aldo-keto reductase family 1 member C3 | / | 0.446 | |
| 4pnm | NU1 | Tankyrase-2 | 2.4.2.30 | 0.446 | |
| 1icp | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.445 | |
| 2lba | CHO | Fatty acid binding protein 6 | / | 0.445 | |
| 3pke | Y10 | Methionine aminopeptidase 2 | / | 0.445 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.444 | |
| 1q83 | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 1qyx | ASD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 1xf0 | ASD | Aldo-keto reductase family 1 member C3 | / | 0.444 | |
| 2f38 | 15M | Aldo-keto reductase family 1 member C3 | / | 0.444 | |
| 2vq7 | NAP | Putative flavin-containing monooxygenase | / | 0.444 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 3zku | HCV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 5ero | 210 | Fusicoccadiene synthase | 2.5.1.29 | 0.444 | |
| 1rkw | PNT | HTH-type transcriptional regulator QacR | / | 0.443 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.443 | |
| 2aot | 2PM | Histamine N-methyltransferase | 2.1.1.8 | 0.443 | |
| 2evm | FC2 | Methionine aminopeptidase | / | 0.443 | |
| 2pnj | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.443 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.443 | |
| 2y01 | Y00 | Beta-1 adrenergic receptor | / | 0.443 | |
| 3cav | CI2 | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.443 | |
| 3qi4 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.442 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 5jqh | CAU | Beta-2 adrenergic receptor | / | 0.442 | |
| 1p0p | BCH | Cholinesterase | 3.1.1.8 | 0.441 | |
| 1y2b | DEE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.441 | |
| 1yw7 | A41 | Methionine aminopeptidase 2 | / | 0.441 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.441 | |
| 4jtq | FLP | Aldo-keto reductase family 1 member C2 | / | 0.441 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.441 | |
| 1mrq | STR | Aldo-keto reductase family 1 member C1 | / | 0.440 | |
| 1so2 | 666 | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.440 | |
| 2qd3 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.440 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.440 | |
| 3pzc | GAP | Amino acid--[acyl-carrier-protein] ligase 1 | 6.2.1.n2 | 0.440 | |
| 4a2z | VIQ | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 |