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 |
|---|---|---|---|
| 4knn | E1F | Carbonic anhydrase 13 | 4.2.1.1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4knn | E1F | Carbonic anhydrase 13 | 4.2.1.1 | 1.000 | |
| 4hu1 | V13 | Carbonic anhydrase 13 | 4.2.1.1 | 0.604 | |
| 1zsb | AZM | Carbonic anhydrase 2 | 4.2.1.1 | 0.537 | |
| 3kig | DA4 | Carbonic anhydrase 2 | 4.2.1.1 | 0.524 | |
| 3qyk | IE2 | Carbonic anhydrase 2 | 4.2.1.1 | 0.522 | |
| 1bn1 | AL5 | Carbonic anhydrase 2 | 4.2.1.1 | 0.521 | |
| 3nb5 | R21 | Carbonic anhydrase 2 | 4.2.1.1 | 0.519 | |
| 5flt | VJJ | Carbonic anhydrase 2 | 4.2.1.1 | 0.519 | |
| 2weh | FB1 | Carbonic anhydrase 2 | 4.2.1.1 | 0.515 | |
| 1if6 | FBU | Carbonic anhydrase 2 | 4.2.1.1 | 0.513 | |
| 1g54 | FFB | Carbonic anhydrase 2 | 4.2.1.1 | 0.510 | |
| 3oim | VZ5 | Carbonic anhydrase 2 | 4.2.1.1 | 0.507 | |
| 1i8z | INL | Carbonic anhydrase 2 | 4.2.1.1 | 0.506 | |
| 3bet | CTF | Carbonic anhydrase 2 | 4.2.1.1 | 0.505 | |
| 3t82 | SG4 | Carbonic anhydrase 2 | 4.2.1.1 | 0.504 | |
| 4knm | E1E | Carbonic anhydrase 13 | 4.2.1.1 | 0.504 | |
| 1a42 | BZU | Carbonic anhydrase 2 | 4.2.1.1 | 0.502 | |
| 1if4 | FBS | Carbonic anhydrase 2 | 4.2.1.1 | 0.501 | |
| 3dd8 | 2C7 | Carbonic anhydrase 2 | 4.2.1.1 | 0.497 | |
| 2wej | FB2 | Carbonic anhydrase 2 | 4.2.1.1 | 0.494 | |
| 3lxe | TOR | Carbonic anhydrase 1 | 4.2.1.1 | 0.493 | |
| 1bnn | AL1 | Carbonic anhydrase 2 | 4.2.1.1 | 0.492 | |
| 1ttm | 667 | Carbonic anhydrase 2 | 4.2.1.1 | 0.491 | |
| 4ilx | 1EZ | Carbonic anhydrase 2 | 4.2.1.1 | 0.491 | |
| 1kwr | SG2 | Carbonic anhydrase 2 | 4.2.1.1 | 0.489 | |
| 1if7 | SBR | Carbonic anhydrase 2 | 4.2.1.1 | 0.487 | |
| 3dd0 | EZL | Carbonic anhydrase 2 | 4.2.1.1 | 0.487 | |
| 3mdz | EZL | Carbonic anhydrase 7 | 4.2.1.1 | 0.487 | |
| 3s8x | E59 | Carbonic anhydrase 2 | 4.2.1.1 | 0.486 | |
| 3d9z | D9Z | Carbonic anhydrase 2 | 4.2.1.1 | 0.485 | |
| 3sbi | E90 | Carbonic anhydrase 2 | 4.2.1.1 | 0.485 | |
| 2x7u | WZA | Carbonic anhydrase 2 | 4.2.1.1 | 0.484 | |
| 1oq5 | CEL | Carbonic anhydrase 2 | 4.2.1.1 | 0.483 | |
| 1cny | EG3 | Carbonic anhydrase 2 | 4.2.1.1 | 0.482 | |
| 3daz | MZM | Carbonic anhydrase 2 | 4.2.1.1 | 0.481 | |
| 4l0q | NAD | Alcohol dehydrogenase class-3 | / | 0.481 | |
| 1i91 | INQ | Carbonic anhydrase 2 | 4.2.1.1 | 0.480 | |
| 3ffp | LC1 | Carbonic anhydrase 2 | 4.2.1.1 | 0.477 | |
| 2lba | CHO | Fatty acid binding protein 6 | / | 0.473 | |
| 1i9n | IOA | Carbonic anhydrase 2 | 4.2.1.1 | 0.470 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.470 | |
| 2h15 | B19 | Carbonic anhydrase 2 | 4.2.1.1 | 0.470 | |
| 3igp | DT7 | Carbonic anhydrase 2 | 4.2.1.1 | 0.469 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.468 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.467 | |
| 4itp | 1GD | Carbonic anhydrase 2 | 4.2.1.1 | 0.467 | |
| 3mho | J43 | Carbonic anhydrase 2 | 4.2.1.1 | 0.466 | |
| 4xbf | FAD | Lysine-specific histone demethylase 1A | 1 | 0.466 | |
| 3dc3 | AZM | Carbonic anhydrase 2 | 4.2.1.1 | 0.465 | |
| 3po6 | DT9 | Carbonic anhydrase 2 | 4.2.1.1 | 0.465 | |
| 1t87 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.464 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.464 | |
| 2a84 | ATP | Pantothenate synthetase | 6.3.2.1 | 0.464 | |
| 3dcs | MZM | Carbonic anhydrase 2 | 4.2.1.1 | 0.464 | |
| 3n4b | WWZ | Carbonic anhydrase 2 | 4.2.1.1 | 0.464 | |
| 2j9l | ATP | H(+)/Cl(-) exchange transporter 5 | / | 0.463 | |
| 2pam | TYD | TDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase | 5.3.2.3 | 0.462 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.462 | |
| 1kqw | RTL | Cellular retinol-binding protein type II | / | 0.461 | |
| 1bnm | AL8 | Carbonic anhydrase 2 | 4.2.1.1 | 0.460 | |
| 2weo | FBW | Carbonic anhydrase 2 | 4.2.1.1 | 0.460 | |
| 2xvv | 9DN | Serum albumin | / | 0.460 | |
| 2pow | I7C | Carbonic anhydrase 2 | 4.2.1.1 | 0.459 | |
| 3pm1 | ET | HTH-type transcriptional regulator QacR | / | 0.459 | |
| 4kni | E1E | Carbonic anhydrase 2 | 4.2.1.1 | 0.459 | |
| 3k2f | NKX | Carbonic anhydrase 2 | 4.2.1.1 | 0.458 | |
| 3sbh | E65 | Carbonic anhydrase 2 | 4.2.1.1 | 0.458 | |
| 4qzu | RTL | Retinol-binding protein 2 | / | 0.458 | |
| 1qkn | RAL | Estrogen receptor beta | / | 0.457 | |
| 3ixp | 834 | Ecdysone receptor | / | 0.457 | |
| 1kwq | SG1 | Carbonic anhydrase 2 | 4.2.1.1 | 0.456 | |
| 2onm | ADP | Aldehyde dehydrogenase, mitochondrial | 1.2.1.3 | 0.456 | |
| 3fwf | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.456 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.456 | |
| 3t84 | SG6 | Carbonic anhydrase 2 | 4.2.1.1 | 0.456 | |
| 1jpa | ANP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.455 | |
| 4kap | 1QV | Carbonic anhydrase 2 | 4.2.1.1 | 0.455 | |
| 1okl | MNS | Carbonic anhydrase 2 | 4.2.1.1 | 0.454 | |
| 2feu | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.454 | |
| 2eu3 | FF3 | Carbonic anhydrase 2 | 4.2.1.1 | 0.453 | |
| 2igy | A2T | Plasmepsin 2 | / | 0.453 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.453 | |
| 4ht2 | V50 | Carbonic anhydrase 12 | 4.2.1.1 | 0.453 | |
| 4ib4 | ERM | 5-hydroxytryptamine receptor 2B | / | 0.453 | |
| 2bxq | IMN | Serum albumin | / | 0.452 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.452 | |
| 3eek | 53S | Uncharacterized protein | / | 0.452 | |
| 3l63 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 3n0n | P9B | Carbonic anhydrase 2 | 4.2.1.1 | 0.452 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.452 | |
| 4a6n | FAD | TetX family tetracycline inactivation enzyme | / | 0.452 | |
| 4awo | 99B | Heat shock protein HSP 90-alpha | / | 0.452 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.451 | |
| 1gg5 | E09 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.451 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.451 | |
| 2fzi | DH3 | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.451 | |
| 2vd0 | D27 | Hematopoietic prostaglandin D synthase | / | 0.451 | |
| 3b9l | AZZ | Serum albumin | / | 0.451 | |
| 3mna | DWH | Carbonic anhydrase 2 | 4.2.1.1 | 0.451 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.451 | |
| 4bf1 | 9FK | Carbonic anhydrase 2 | 4.2.1.1 | 0.451 | |
| 4mzu | TYD | WxcM-like protein | / | 0.451 | |
| 1jd0 | AZM | Carbonic anhydrase 12 | 4.2.1.1 | 0.450 | |
| 1rx8 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.450 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.450 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.450 | |
| 1g4j | FFB | Carbonic anhydrase 2 | 4.2.1.1 | 0.449 | |
| 2bxm | IMN | Serum albumin | / | 0.449 | |
| 2xvw | 9NR | Serum albumin | / | 0.449 | |
| 3dg8 | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.449 | |
| 3oew | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.449 | |
| 3of2 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.449 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.449 | |
| 4u14 | 0HK | Muscarinic acetylcholine receptor M3 | / | 0.449 | |
| 1dhi | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.448 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.448 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 3wrj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.448 | |
| 1efa | NPF | Lactose operon repressor | / | 0.447 | |
| 1kt8 | ILP | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.447 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.447 | |
| 3dcw | EZL | Carbonic anhydrase 2 | 4.2.1.1 | 0.447 | |
| 3itu | IBM | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.447 | |
| 3t37 | FAD | Pyridoxine 4-oxidase | / | 0.447 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.447 | |
| 1f4f | TP3 | Thymidylate synthase | / | 0.446 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.446 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.446 | |
| 2z7g | EH9 | Adenosine deaminase | 3.5.4.4 | 0.446 | |
| 3c1o | NAP | Eugenol synthase | / | 0.446 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.446 | |
| 3oy0 | OY0 | Carbonic anhydrase 2 | 4.2.1.1 | 0.446 | |
| 3qg2 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.446 | |
| 3sf6 | FDA | Glutaryl-CoA dehydrogenase | / | 0.446 | |
| 3tk3 | CPZ | Cytochrome P450 2B4 | 1.14.14.1 | 0.446 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 4dz7 | D02 | Carbonic anhydrase 2 | 4.2.1.1 | 0.446 | |
| 4n16 | CHD | Carbonic anhydrase 2 | 4.2.1.1 | 0.446 | |
| 1e1k | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.445 | |
| 1lsj | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.445 | |
| 2ji9 | TPW | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.445 | |
| 3b7d | CNI | Glutamate receptor 2 | / | 0.445 | |
| 3ch6 | 311 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.445 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.445 | |
| 3uxy | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.445 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 3gdp | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.444 | |
| 3s3v | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 4e2b | FMN | Dehydrogenase | / | 0.444 | |
| 1i9m | INW | Carbonic anhydrase 2 | 4.2.1.1 | 0.443 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.443 | |
| 2w3v | TOP | Dihydrofolate reductase | / | 0.443 | |
| 2wey | EV1 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.443 | |
| 5ai5 | BSU | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.443 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.442 | |
| 1g52 | F2B | Carbonic anhydrase 2 | 4.2.1.1 | 0.442 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.442 | |
| 2w9h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3dxj | NE6 | DNA-directed RNA polymerase subunit beta | / | 0.442 | |
| 3dxj | NE6 | DNA-directed RNA polymerase subunit beta' | / | 0.442 | |
| 3own | 3OW | Renin | 3.4.23.15 | 0.442 | |
| 3qdd | 94M | Heat shock protein HSP 90-alpha | / | 0.442 | |
| 4ha6 | PXM | Pyridoxine 4-oxidase | / | 0.442 | |
| 1fdu | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.441 | |
| 1ykd | CMP | Adenylate cyclase | / | 0.441 | |
| 3bbp | GTP | Ras-related protein Rab-6A | / | 0.441 | |
| 3biy | 01K | Histone acetyltransferase p300 | / | 0.441 | |
| 3mhl | J71 | Carbonic anhydrase 2 | 4.2.1.1 | 0.441 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.441 | |
| 3oik | WZB | Carbonic anhydrase 2 | 4.2.1.1 | 0.441 | |
| 4elf | 35I | Dihydrofolate reductase | / | 0.441 | |
| 5hs1 | VOR | Lanosterol 14-alpha demethylase | / | 0.441 | |
| 6cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 1bnv | AL7 | Carbonic anhydrase 2 | 4.2.1.1 | 0.440 | |
| 1cnx | EG2 | Carbonic anhydrase 2 | 4.2.1.1 | 0.440 | |
| 1rek | B8L | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 2poq | ISD | Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase | 1.3.1.20 | 0.440 | |
| 2rl5 | 2RL | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.440 | |
| 4g1d | 0VK | Vitamin D3 receptor A | / | 0.440 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.440 |