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 |
|---|---|---|---|
| 3dc3 | AZM | Carbonic anhydrase 2 | 4.2.1.1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3dc3 | AZM | Carbonic anhydrase 2 | 4.2.1.1 | 1.000 | |
| 3dcs | MZM | Carbonic anhydrase 2 | 4.2.1.1 | 0.771 | |
| 4m2r | BZ1 | Carbonic anhydrase 2 | 4.2.1.1 | 0.749 | |
| 4kap | 1QV | Carbonic anhydrase 2 | 4.2.1.1 | 0.742 | |
| 2x7t | WZB | Carbonic anhydrase 2 | 4.2.1.1 | 0.706 | |
| 1i91 | INQ | Carbonic anhydrase 2 | 4.2.1.1 | 0.701 | |
| 3qyk | IE2 | Carbonic anhydrase 2 | 4.2.1.1 | 0.696 | |
| 2h15 | B19 | Carbonic anhydrase 2 | 4.2.1.1 | 0.688 | |
| 3d9z | D9Z | Carbonic anhydrase 2 | 4.2.1.1 | 0.674 | |
| 1bnn | AL1 | Carbonic anhydrase 2 | 4.2.1.1 | 0.672 | |
| 3daz | MZM | Carbonic anhydrase 2 | 4.2.1.1 | 0.672 | |
| 1bn1 | AL5 | Carbonic anhydrase 2 | 4.2.1.1 | 0.669 | |
| 1a42 | BZU | Carbonic anhydrase 2 | 4.2.1.1 | 0.667 | |
| 1bn4 | AL9 | Carbonic anhydrase 2 | 4.2.1.1 | 0.667 | |
| 3m5e | JDR | Carbonic anhydrase 2 | 4.2.1.1 | 0.666 | |
| 1bnq | AL4 | Carbonic anhydrase 2 | 4.2.1.1 | 0.663 | |
| 1bnw | TPD | Carbonic anhydrase 2 | 4.2.1.1 | 0.661 | |
| 3po6 | DT9 | Carbonic anhydrase 2 | 4.2.1.1 | 0.661 | |
| 4m2v | BZ1 | Carbonic anhydrase 2 | 4.2.1.1 | 0.652 | |
| 1kwr | SG2 | Carbonic anhydrase 2 | 4.2.1.1 | 0.650 | |
| 1bnt | AL2 | Carbonic anhydrase 2 | 4.2.1.1 | 0.649 | |
| 1g1d | FSB | Carbonic anhydrase 2 | 4.2.1.1 | 0.646 | |
| 3hku | TOR | Carbonic anhydrase 2 | 4.2.1.1 | 0.638 | |
| 3kig | DA4 | Carbonic anhydrase 2 | 4.2.1.1 | 0.638 | |
| 3mhl | J71 | Carbonic anhydrase 2 | 4.2.1.1 | 0.633 | |
| 2eu3 | FF3 | Carbonic anhydrase 2 | 4.2.1.1 | 0.632 | |
| 3eft | 3BS | Carbonic anhydrase 2 | 4.2.1.1 | 0.630 | |
| 1if5 | FBT | Carbonic anhydrase 2 | 4.2.1.1 | 0.629 | |
| 1zsb | AZM | Carbonic anhydrase 2 | 4.2.1.1 | 0.627 | |
| 1cil | ETS | Carbonic anhydrase 2 | 4.2.1.1 | 0.619 | |
| 2h4n | AZM | Carbonic anhydrase 2 | 4.2.1.1 | 0.619 | |
| 3dbu | D8W | Carbonic anhydrase 2 | 4.2.1.1 | 0.619 | |
| 1g4o | BSB | Carbonic anhydrase 2 | 4.2.1.1 | 0.618 | |
| 3t84 | SG6 | Carbonic anhydrase 2 | 4.2.1.1 | 0.615 | |
| 1bn3 | AL6 | Carbonic anhydrase 2 | 4.2.1.1 | 0.613 | |
| 3b4f | TUO | Carbonic anhydrase 2 | 4.2.1.1 | 0.613 | |
| 3k2f | NKX | Carbonic anhydrase 2 | 4.2.1.1 | 0.613 | |
| 1if7 | SBR | Carbonic anhydrase 2 | 4.2.1.1 | 0.610 | |
| 5flt | VJJ | Carbonic anhydrase 2 | 4.2.1.1 | 0.608 | |
| 3m67 | E36 | Carbonic anhydrase 2 | 4.2.1.1 | 0.606 | |
| 1g52 | F2B | Carbonic anhydrase 2 | 4.2.1.1 | 0.605 | |
| 1i9p | IOE | Carbonic anhydrase 2 | 4.2.1.1 | 0.605 | |
| 4bf6 | X0Q | Carbonic anhydrase 2 | 4.2.1.1 | 0.604 | |
| 4iwz | 1GO | Carbonic anhydrase 2 | 4.2.1.1 | 0.602 | |
| 1if4 | FBS | Carbonic anhydrase 2 | 4.2.1.1 | 0.601 | |
| 3f4x | KLT | Carbonic anhydrase 2 | 4.2.1.1 | 0.597 | |
| 3m2y | BE0 | Carbonic anhydrase 2 | 4.2.1.1 | 0.597 | |
| 1i9m | INW | Carbonic anhydrase 2 | 4.2.1.1 | 0.596 | |
| 4ito | MPX | Carbonic anhydrase 2 | 4.2.1.1 | 0.594 | |
| 1if6 | FBU | Carbonic anhydrase 2 | 4.2.1.1 | 0.593 | |
| 3n2p | AYX | Carbonic anhydrase 2 | 4.2.1.1 | 0.591 | |
| 1ttm | 667 | Carbonic anhydrase 2 | 4.2.1.1 | 0.588 | |
| 3igp | DT7 | Carbonic anhydrase 2 | 4.2.1.1 | 0.588 | |
| 1i90 | INM | Carbonic anhydrase 2 | 4.2.1.1 | 0.586 | |
| 1g54 | FFB | Carbonic anhydrase 2 | 4.2.1.1 | 0.583 | |
| 3n4b | WWZ | Carbonic anhydrase 2 | 4.2.1.1 | 0.582 | |
| 4kni | E1E | Carbonic anhydrase 2 | 4.2.1.1 | 0.580 | |
| 3m2n | J74 | Carbonic anhydrase 2 | 4.2.1.1 | 0.578 | |
| 3ni5 | C1H | Carbonic anhydrase 2 | 4.2.1.1 | 0.578 | |
| 4k13 | ETS | Carbonic anhydrase 2 | 4.2.1.1 | 0.578 | |
| 1kwq | SG1 | Carbonic anhydrase 2 | 4.2.1.1 | 0.577 | |
| 3t82 | SG4 | Carbonic anhydrase 2 | 4.2.1.1 | 0.576 | |
| 1i8z | INL | Carbonic anhydrase 2 | 4.2.1.1 | 0.575 | |
| 1xpz | 4TZ | Carbonic anhydrase 2 | 4.2.1.1 | 0.573 | |
| 4itp | 1GD | Carbonic anhydrase 2 | 4.2.1.1 | 0.573 | |
| 4n16 | CHD | Carbonic anhydrase 2 | 4.2.1.1 | 0.573 | |
| 3sax | E50 | Carbonic anhydrase 2 | 4.2.1.1 | 0.569 | |
| 1g45 | FSB | Carbonic anhydrase 2 | 4.2.1.1 | 0.567 | |
| 3nb5 | R21 | Carbonic anhydrase 2 | 4.2.1.1 | 0.566 | |
| 4ilx | 1EZ | Carbonic anhydrase 2 | 4.2.1.1 | 0.566 | |
| 3oik | WZB | Carbonic anhydrase 2 | 4.2.1.1 | 0.565 | |
| 3sbh | E65 | Carbonic anhydrase 2 | 4.2.1.1 | 0.565 | |
| 3mho | J43 | Carbonic anhydrase 2 | 4.2.1.1 | 0.563 | |
| 3dcc | D9Z | Carbonic anhydrase 2 | 4.2.1.1 | 0.562 | |
| 3bet | CTF | Carbonic anhydrase 2 | 4.2.1.1 | 0.561 | |
| 1bnm | AL8 | Carbonic anhydrase 2 | 4.2.1.1 | 0.560 | |
| 1g4j | FFB | Carbonic anhydrase 2 | 4.2.1.1 | 0.560 | |
| 2weh | FB1 | Carbonic anhydrase 2 | 4.2.1.1 | 0.560 | |
| 3mhc | ARZ | Carbonic anhydrase 2 | 4.2.1.1 | 0.557 | |
| 1okl | MNS | Carbonic anhydrase 2 | 4.2.1.1 | 0.556 | |
| 3sbi | E90 | Carbonic anhydrase 2 | 4.2.1.1 | 0.556 | |
| 3d8w | D8W | Carbonic anhydrase 2 | 4.2.1.1 | 0.555 | |
| 3mdz | EZL | Carbonic anhydrase 7 | 4.2.1.1 | 0.554 | |
| 1bnu | AL3 | Carbonic anhydrase 2 | 4.2.1.1 | 0.551 | |
| 1i9q | IOF | Carbonic anhydrase 2 | 4.2.1.1 | 0.550 | |
| 2wej | FB2 | Carbonic anhydrase 2 | 4.2.1.1 | 0.550 | |
| 2weo | FBW | Carbonic anhydrase 2 | 4.2.1.1 | 0.548 | |
| 1i9n | IOA | Carbonic anhydrase 2 | 4.2.1.1 | 0.547 | |
| 3m98 | E02 | Carbonic anhydrase 2 | 4.2.1.1 | 0.547 | |
| 2x7u | WZA | Carbonic anhydrase 2 | 4.2.1.1 | 0.546 | |
| 3dcw | EZL | Carbonic anhydrase 2 | 4.2.1.1 | 0.545 | |
| 3f7b | AG5 | Carbonic anhydrase 4 | 4.2.1.1 | 0.543 | |
| 3ffp | LC1 | Carbonic anhydrase 2 | 4.2.1.1 | 0.540 | |
| 3znc | BZ1 | Carbonic anhydrase 4 | 4.2.1.1 | 0.540 | |
| 4mo8 | 2VQ | Carbonic anhydrase 2 | 4.2.1.1 | 0.540 | |
| 2wd2 | MS5 | Carbonic anhydrase 2 | 4.2.1.1 | 0.538 | |
| 4k0t | D9Z | Carbonic anhydrase 2 | 4.2.1.1 | 0.538 | |
| 1bnv | AL7 | Carbonic anhydrase 2 | 4.2.1.1 | 0.535 | |
| 3m40 | J45 | Carbonic anhydrase 2 | 4.2.1.1 | 0.535 | |
| 3mzc | S6I | Carbonic anhydrase 2 | 4.2.1.1 | 0.532 | |
| 3oys | OYS | Carbonic anhydrase 2 | 4.2.1.1 | 0.532 | |
| 1xq0 | 4TR | Carbonic anhydrase 2 | 4.2.1.1 | 0.531 | |
| 3dd8 | 2C7 | Carbonic anhydrase 2 | 4.2.1.1 | 0.531 | |
| 3mna | DWH | Carbonic anhydrase 2 | 4.2.1.1 | 0.529 | |
| 1jd0 | AZM | Carbonic anhydrase 12 | 4.2.1.1 | 0.528 | |
| 3ml2 | SU0 | Carbonic anhydrase 2 | 4.2.1.1 | 0.526 | |
| 3l14 | I7B | Carbonic anhydrase 2 | 4.2.1.1 | 0.524 | |
| 4bf1 | 9FK | Carbonic anhydrase 2 | 4.2.1.1 | 0.523 | |
| 3n0n | P9B | Carbonic anhydrase 2 | 4.2.1.1 | 0.521 | |
| 3bl1 | BL1 | Carbonic anhydrase 2 | 4.2.1.1 | 0.519 | |
| 3s9t | E49 | Carbonic anhydrase 2 | 4.2.1.1 | 0.517 | |
| 3s8x | E59 | Carbonic anhydrase 2 | 4.2.1.1 | 0.516 | |
| 4pxx | CHD | Carbonic anhydrase 2 | 4.2.1.1 | 0.516 | |
| 3m96 | E38 | Carbonic anhydrase 2 | 4.2.1.1 | 0.512 | |
| 3p5l | IT5 | Carbonic anhydrase 2 | 4.2.1.1 | 0.512 | |
| 3myq | E27 | Carbonic anhydrase 2 | 4.2.1.1 | 0.509 | |
| 3t85 | SG7 | Carbonic anhydrase 2 | 4.2.1.1 | 0.509 | |
| 4kp8 | E1G | Carbonic anhydrase 12 | 4.2.1.1 | 0.509 | |
| 1if8 | SBS | Carbonic anhydrase 2 | 4.2.1.1 | 0.508 | |
| 3oyq | OYQ | Carbonic anhydrase 2 | 4.2.1.1 | 0.508 | |
| 4ht2 | V50 | Carbonic anhydrase 12 | 4.2.1.1 | 0.505 | |
| 4knj | E1F | Carbonic anhydrase 2 | 4.2.1.1 | 0.504 | |
| 1cnx | EG2 | Carbonic anhydrase 2 | 4.2.1.1 | 0.501 | |
| 4x5s | AZM | Carbonic anhydrase (Carbonate dehydratase) | / | 0.500 | |
| 1cny | EG3 | Carbonic anhydrase 2 | 4.2.1.1 | 0.499 | |
| 1eou | SMS | Carbonic anhydrase 2 | 4.2.1.1 | 0.499 | |
| 3oim | VZ5 | Carbonic anhydrase 2 | 4.2.1.1 | 0.498 | |
| 3fw3 | ETS | Carbonic anhydrase 4 | 4.2.1.1 | 0.497 | |
| 1oq5 | CEL | Carbonic anhydrase 2 | 4.2.1.1 | 0.496 | |
| 2weg | FBV | Carbonic anhydrase 2 | 4.2.1.1 | 0.496 | |
| 3oy0 | OY0 | Carbonic anhydrase 2 | 4.2.1.1 | 0.495 | |
| 3mmf | D9H | Carbonic anhydrase 2 | 4.2.1.1 | 0.493 | |
| 3f7u | AG4 | Carbonic anhydrase 4 | 4.2.1.1 | 0.492 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.492 | |
| 3mhi | J90 | Carbonic anhydrase 2 | 4.2.1.1 | 0.491 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.488 | |
| 4kp5 | E1F | Carbonic anhydrase 12 | 4.2.1.1 | 0.488 | |
| 3v2j | AZM | Carbonic anhydrase 2 | 4.2.1.1 | 0.487 | |
| 1yda | AZM | Carbonic anhydrase 2 | 4.2.1.1 | 0.485 | |
| 4uov | AZM | Carbonate dehydratase | / | 0.485 | |
| 3n3j | WWV | Carbonic anhydrase 2 | 4.2.1.1 | 0.479 | |
| 2pow | I7C | Carbonic anhydrase 2 | 4.2.1.1 | 0.477 | |
| 1okn | STB | Carbonic anhydrase 2 | 4.2.1.1 | 0.476 | |
| 3lxe | TOR | Carbonic anhydrase 1 | 4.2.1.1 | 0.476 | |
| 4hu1 | V13 | Carbonic anhydrase 13 | 4.2.1.1 | 0.476 | |
| 1cnw | EG1 | Carbonic anhydrase 2 | 4.2.1.1 | 0.475 | |
| 1okm | SAB | Carbonic anhydrase 2 | 4.2.1.1 | 0.474 | |
| 1rj6 | AZM | Carbonic anhydrase 14 | 4.2.1.1 | 0.474 | |
| 4lu3 | AZM | Carbonic anhydrase 14 | 4.2.1.1 | 0.472 | |
| 4xiw | AZM | Carbonic anhydrase, alpha type | / | 0.469 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.467 | |
| 1x1d | SAH | C-20 methyltransferase | / | 0.467 | |
| 3apw | DP0 | Alpha-1-acid glycoprotein 2 | / | 0.467 | |
| 4dz7 | D02 | Carbonic anhydrase 2 | 4.2.1.1 | 0.466 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.462 | |
| 4iae | 1DX | Alr2278 protein | / | 0.461 | |
| 2g20 | L1A | Renin | 3.4.23.15 | 0.460 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.460 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.458 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.457 | |
| 4iah | 1DX | Alr2278 protein | / | 0.457 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.456 | |
| 3dd0 | EZL | Carbonic anhydrase 2 | 4.2.1.1 | 0.456 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.456 | |
| 4a87 | NAR | Major pollen allergen Bet v 1-A | / | 0.456 | |
| 1wze | NAD | Malate dehydrogenase | / | 0.455 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.455 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.455 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.454 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 4knm | E1E | Carbonic anhydrase 13 | 4.2.1.1 | 0.453 | |
| 1h60 | STR | Pentaerythritol tetranitrate reductase | / | 0.452 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.452 | |
| 2v16 | C47 | Renin | 3.4.23.15 | 0.452 | |
| 4a86 | H35 | Major pollen allergen Bet v 1-A | / | 0.452 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.451 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 1a72 | PAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.449 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.449 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.449 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.448 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.448 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.447 | |
| 2y1t | DUD | SPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS | 3.6.1.23 | 0.447 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.447 | |
| 1tll | FMN | Nitric oxide synthase, brain | 1.14.13.39 | 0.446 | |
| 2a1h | GBN | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.446 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.445 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.445 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 1p0p | BCH | Cholinesterase | 3.1.1.8 | 0.444 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.444 | |
| 3rz8 | RZ8 | Carbonic anhydrase 2 | 4.2.1.1 | 0.444 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.443 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.443 | |
| 1rkw | PNT | HTH-type transcriptional regulator QacR | / | 0.443 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.443 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.443 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.443 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.443 | |
| 1vi2 | NAD | Quinate/shikimate dehydrogenase | / | 0.442 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.442 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 4a84 | DXC | Major pollen allergen Bet v 1-A | / | 0.442 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.441 | |
| 2npi | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.441 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.441 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.441 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.441 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.441 | |
| 3zbs | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.441 | |
| 2q1q | OSP | Carbonic anhydrase 2 | 4.2.1.1 | 0.440 | |
| 4a86 | 2AN | Major pollen allergen Bet v 1-A | / | 0.440 |