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 |
|---|---|---|---|
| 1ttm | 667 | Carbonic anhydrase 2 | 4.2.1.1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1ttm | 667 | Carbonic anhydrase 2 | 4.2.1.1 | 1.000 | |
| 1xpz | 4TZ | Carbonic anhydrase 2 | 4.2.1.1 | 0.691 | |
| 1bnn | AL1 | Carbonic anhydrase 2 | 4.2.1.1 | 0.649 | |
| 2h15 | B19 | Carbonic anhydrase 2 | 4.2.1.1 | 0.644 | |
| 3k2f | NKX | Carbonic anhydrase 2 | 4.2.1.1 | 0.644 | |
| 1i91 | INQ | Carbonic anhydrase 2 | 4.2.1.1 | 0.635 | |
| 1a42 | BZU | Carbonic anhydrase 2 | 4.2.1.1 | 0.632 | |
| 1bn1 | AL5 | Carbonic anhydrase 2 | 4.2.1.1 | 0.624 | |
| 3daz | MZM | Carbonic anhydrase 2 | 4.2.1.1 | 0.621 | |
| 1bn4 | AL9 | Carbonic anhydrase 2 | 4.2.1.1 | 0.620 | |
| 1xq0 | 4TR | Carbonic anhydrase 2 | 4.2.1.1 | 0.618 | |
| 3d9z | D9Z | Carbonic anhydrase 2 | 4.2.1.1 | 0.612 | |
| 3eft | 3BS | Carbonic anhydrase 2 | 4.2.1.1 | 0.611 | |
| 1bn3 | AL6 | Carbonic anhydrase 2 | 4.2.1.1 | 0.610 | |
| 1if6 | FBU | Carbonic anhydrase 2 | 4.2.1.1 | 0.610 | |
| 2eu3 | FF3 | Carbonic anhydrase 2 | 4.2.1.1 | 0.609 | |
| 3dcs | MZM | Carbonic anhydrase 2 | 4.2.1.1 | 0.608 | |
| 4kni | E1E | Carbonic anhydrase 2 | 4.2.1.1 | 0.608 | |
| 1kwr | SG2 | Carbonic anhydrase 2 | 4.2.1.1 | 0.607 | |
| 3m5e | JDR | Carbonic anhydrase 2 | 4.2.1.1 | 0.607 | |
| 1if4 | FBS | Carbonic anhydrase 2 | 4.2.1.1 | 0.606 | |
| 1g1d | FSB | Carbonic anhydrase 2 | 4.2.1.1 | 0.605 | |
| 4n16 | CHD | Carbonic anhydrase 2 | 4.2.1.1 | 0.605 | |
| 1i8z | INL | Carbonic anhydrase 2 | 4.2.1.1 | 0.603 | |
| 1zsb | AZM | Carbonic anhydrase 2 | 4.2.1.1 | 0.603 | |
| 1g52 | F2B | Carbonic anhydrase 2 | 4.2.1.1 | 0.600 | |
| 1i90 | INM | Carbonic anhydrase 2 | 4.2.1.1 | 0.598 | |
| 3dc3 | AZM | Carbonic anhydrase 2 | 4.2.1.1 | 0.598 | |
| 3sbh | E65 | Carbonic anhydrase 2 | 4.2.1.1 | 0.597 | |
| 1i9n | IOA | Carbonic anhydrase 2 | 4.2.1.1 | 0.595 | |
| 3ffp | LC1 | Carbonic anhydrase 2 | 4.2.1.1 | 0.593 | |
| 1bnw | TPD | Carbonic anhydrase 2 | 4.2.1.1 | 0.592 | |
| 1bnv | AL7 | Carbonic anhydrase 2 | 4.2.1.1 | 0.591 | |
| 3dd8 | 2C7 | Carbonic anhydrase 2 | 4.2.1.1 | 0.590 | |
| 3b4f | TUO | Carbonic anhydrase 2 | 4.2.1.1 | 0.587 | |
| 1bnt | AL2 | Carbonic anhydrase 2 | 4.2.1.1 | 0.585 | |
| 4itp | 1GD | Carbonic anhydrase 2 | 4.2.1.1 | 0.585 | |
| 1g4j | FFB | Carbonic anhydrase 2 | 4.2.1.1 | 0.581 | |
| 1i9m | INW | Carbonic anhydrase 2 | 4.2.1.1 | 0.580 | |
| 3hku | TOR | Carbonic anhydrase 2 | 4.2.1.1 | 0.580 | |
| 1if5 | FBT | Carbonic anhydrase 2 | 4.2.1.1 | 0.576 | |
| 3qyk | IE2 | Carbonic anhydrase 2 | 4.2.1.1 | 0.576 | |
| 3mho | J43 | Carbonic anhydrase 2 | 4.2.1.1 | 0.575 | |
| 2weh | FB1 | Carbonic anhydrase 2 | 4.2.1.1 | 0.572 | |
| 3po6 | DT9 | Carbonic anhydrase 2 | 4.2.1.1 | 0.572 | |
| 5flt | VJJ | Carbonic anhydrase 2 | 4.2.1.1 | 0.572 | |
| 1g4o | BSB | Carbonic anhydrase 2 | 4.2.1.1 | 0.571 | |
| 1okl | MNS | Carbonic anhydrase 2 | 4.2.1.1 | 0.567 | |
| 1g45 | FSB | Carbonic anhydrase 2 | 4.2.1.1 | 0.566 | |
| 1i9q | IOF | Carbonic anhydrase 2 | 4.2.1.1 | 0.566 | |
| 3oys | OYS | Carbonic anhydrase 2 | 4.2.1.1 | 0.566 | |
| 4pxx | CHD | Carbonic anhydrase 2 | 4.2.1.1 | 0.566 | |
| 3kig | DA4 | Carbonic anhydrase 2 | 4.2.1.1 | 0.565 | |
| 3mhl | J71 | Carbonic anhydrase 2 | 4.2.1.1 | 0.565 | |
| 3m2y | BE0 | Carbonic anhydrase 2 | 4.2.1.1 | 0.564 | |
| 4ht2 | V50 | Carbonic anhydrase 12 | 4.2.1.1 | 0.564 | |
| 4kap | 1QV | Carbonic anhydrase 2 | 4.2.1.1 | 0.564 | |
| 2x7t | WZB | Carbonic anhydrase 2 | 4.2.1.1 | 0.563 | |
| 3mdz | EZL | Carbonic anhydrase 7 | 4.2.1.1 | 0.562 | |
| 3ni5 | C1H | Carbonic anhydrase 2 | 4.2.1.1 | 0.562 | |
| 4ito | MPX | Carbonic anhydrase 2 | 4.2.1.1 | 0.562 | |
| 3igp | DT7 | Carbonic anhydrase 2 | 4.2.1.1 | 0.561 | |
| 1bnm | AL8 | Carbonic anhydrase 2 | 4.2.1.1 | 0.560 | |
| 1kwq | SG1 | Carbonic anhydrase 2 | 4.2.1.1 | 0.560 | |
| 2wd2 | MS5 | Carbonic anhydrase 2 | 4.2.1.1 | 0.560 | |
| 2weo | FBW | Carbonic anhydrase 2 | 4.2.1.1 | 0.559 | |
| 3mzc | S6I | Carbonic anhydrase 2 | 4.2.1.1 | 0.558 | |
| 3n0n | P9B | Carbonic anhydrase 2 | 4.2.1.1 | 0.558 | |
| 3m96 | E38 | Carbonic anhydrase 2 | 4.2.1.1 | 0.557 | |
| 3oik | WZB | Carbonic anhydrase 2 | 4.2.1.1 | 0.557 | |
| 3v2j | AZM | Carbonic anhydrase 2 | 4.2.1.1 | 0.557 | |
| 3nb5 | R21 | Carbonic anhydrase 2 | 4.2.1.1 | 0.556 | |
| 1bnu | AL3 | Carbonic anhydrase 2 | 4.2.1.1 | 0.555 | |
| 1if7 | SBR | Carbonic anhydrase 2 | 4.2.1.1 | 0.555 | |
| 3f7u | AG4 | Carbonic anhydrase 4 | 4.2.1.1 | 0.554 | |
| 3sax | E50 | Carbonic anhydrase 2 | 4.2.1.1 | 0.554 | |
| 3m2n | J74 | Carbonic anhydrase 2 | 4.2.1.1 | 0.553 | |
| 3s8x | E59 | Carbonic anhydrase 2 | 4.2.1.1 | 0.553 | |
| 3sbi | E90 | Carbonic anhydrase 2 | 4.2.1.1 | 0.553 | |
| 3t82 | SG4 | Carbonic anhydrase 2 | 4.2.1.1 | 0.552 | |
| 3mna | DWH | Carbonic anhydrase 2 | 4.2.1.1 | 0.551 | |
| 1cil | ETS | Carbonic anhydrase 2 | 4.2.1.1 | 0.550 | |
| 1jd0 | AZM | Carbonic anhydrase 12 | 4.2.1.1 | 0.548 | |
| 3dcc | D9Z | Carbonic anhydrase 2 | 4.2.1.1 | 0.548 | |
| 3m98 | E02 | Carbonic anhydrase 2 | 4.2.1.1 | 0.548 | |
| 3oim | VZ5 | Carbonic anhydrase 2 | 4.2.1.1 | 0.548 | |
| 4iwz | 1GO | Carbonic anhydrase 2 | 4.2.1.1 | 0.547 | |
| 4knj | E1F | Carbonic anhydrase 2 | 4.2.1.1 | 0.547 | |
| 3n2p | AYX | Carbonic anhydrase 2 | 4.2.1.1 | 0.546 | |
| 1bnq | AL4 | Carbonic anhydrase 2 | 4.2.1.1 | 0.545 | |
| 1cnw | EG1 | Carbonic anhydrase 2 | 4.2.1.1 | 0.545 | |
| 3d8w | D8W | Carbonic anhydrase 2 | 4.2.1.1 | 0.545 | |
| 4m2r | BZ1 | Carbonic anhydrase 2 | 4.2.1.1 | 0.545 | |
| 4ilx | 1EZ | Carbonic anhydrase 2 | 4.2.1.1 | 0.544 | |
| 4bf6 | X0Q | Carbonic anhydrase 2 | 4.2.1.1 | 0.541 | |
| 2wej | FB2 | Carbonic anhydrase 2 | 4.2.1.1 | 0.540 | |
| 2x7u | WZA | Carbonic anhydrase 2 | 4.2.1.1 | 0.539 | |
| 4kp8 | E1G | Carbonic anhydrase 12 | 4.2.1.1 | 0.539 | |
| 1if8 | SBS | Carbonic anhydrase 2 | 4.2.1.1 | 0.536 | |
| 3bet | CTF | Carbonic anhydrase 2 | 4.2.1.1 | 0.536 | |
| 3m67 | E36 | Carbonic anhydrase 2 | 4.2.1.1 | 0.536 | |
| 3s9t | E49 | Carbonic anhydrase 2 | 4.2.1.1 | 0.536 | |
| 1g54 | FFB | Carbonic anhydrase 2 | 4.2.1.1 | 0.535 | |
| 2weg | FBV | Carbonic anhydrase 2 | 4.2.1.1 | 0.534 | |
| 3ml2 | SU0 | Carbonic anhydrase 2 | 4.2.1.1 | 0.533 | |
| 3mmf | D9H | Carbonic anhydrase 2 | 4.2.1.1 | 0.533 | |
| 1eou | SMS | Carbonic anhydrase 2 | 4.2.1.1 | 0.532 | |
| 3t84 | SG6 | Carbonic anhydrase 2 | 4.2.1.1 | 0.531 | |
| 4kp5 | E1F | Carbonic anhydrase 12 | 4.2.1.1 | 0.530 | |
| 3fw3 | ETS | Carbonic anhydrase 4 | 4.2.1.1 | 0.529 | |
| 1okn | STB | Carbonic anhydrase 2 | 4.2.1.1 | 0.528 | |
| 4k13 | ETS | Carbonic anhydrase 2 | 4.2.1.1 | 0.528 | |
| 2h4n | AZM | Carbonic anhydrase 2 | 4.2.1.1 | 0.527 | |
| 3znc | BZ1 | Carbonic anhydrase 4 | 4.2.1.1 | 0.525 | |
| 3f4x | KLT | Carbonic anhydrase 2 | 4.2.1.1 | 0.523 | |
| 3n3j | WWV | Carbonic anhydrase 2 | 4.2.1.1 | 0.523 | |
| 2pow | I7C | Carbonic anhydrase 2 | 4.2.1.1 | 0.521 | |
| 3oy0 | OY0 | Carbonic anhydrase 2 | 4.2.1.1 | 0.521 | |
| 1cny | EG3 | Carbonic anhydrase 2 | 4.2.1.1 | 0.520 | |
| 1i9p | IOE | Carbonic anhydrase 2 | 4.2.1.1 | 0.520 | |
| 1oq5 | CEL | Carbonic anhydrase 2 | 4.2.1.1 | 0.519 | |
| 1yda | AZM | Carbonic anhydrase 2 | 4.2.1.1 | 0.518 | |
| 4m2v | BZ1 | Carbonic anhydrase 2 | 4.2.1.1 | 0.518 | |
| 1okm | SAB | Carbonic anhydrase 2 | 4.2.1.1 | 0.517 | |
| 3bl1 | BL1 | Carbonic anhydrase 2 | 4.2.1.1 | 0.517 | |
| 4mo8 | 2VQ | Carbonic anhydrase 2 | 4.2.1.1 | 0.516 | |
| 3n4b | WWZ | Carbonic anhydrase 2 | 4.2.1.1 | 0.515 | |
| 4knm | E1E | Carbonic anhydrase 13 | 4.2.1.1 | 0.515 | |
| 3dbu | D8W | Carbonic anhydrase 2 | 4.2.1.1 | 0.514 | |
| 3m40 | J45 | Carbonic anhydrase 2 | 4.2.1.1 | 0.511 | |
| 4bf1 | 9FK | Carbonic anhydrase 2 | 4.2.1.1 | 0.511 | |
| 3f7b | AG5 | Carbonic anhydrase 4 | 4.2.1.1 | 0.510 | |
| 4k0t | D9Z | Carbonic anhydrase 2 | 4.2.1.1 | 0.510 | |
| 4k0z | MZM | Carbonic anhydrase 2 | 4.2.1.1 | 0.510 | |
| 3dd0 | EZL | Carbonic anhydrase 2 | 4.2.1.1 | 0.507 | |
| 3dcw | EZL | Carbonic anhydrase 2 | 4.2.1.1 | 0.505 | |
| 3oyq | OYQ | Carbonic anhydrase 2 | 4.2.1.1 | 0.505 | |
| 3mhc | ARZ | Carbonic anhydrase 2 | 4.2.1.1 | 0.503 | |
| 4uov | AZM | Carbonate dehydratase | / | 0.498 | |
| 1cnx | EG2 | Carbonic anhydrase 2 | 4.2.1.1 | 0.496 | |
| 4x5s | AZM | Carbonic anhydrase (Carbonate dehydratase) | / | 0.496 | |
| 3t85 | SG7 | Carbonic anhydrase 2 | 4.2.1.1 | 0.495 | |
| 4lu3 | AZM | Carbonic anhydrase 14 | 4.2.1.1 | 0.494 | |
| 3p5l | IT5 | Carbonic anhydrase 2 | 4.2.1.1 | 0.488 | |
| 3mhi | J90 | Carbonic anhydrase 2 | 4.2.1.1 | 0.485 | |
| 5fl4 | 9FK | Carbonic anhydrase 9 | 4.2.1.1 | 0.485 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.484 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.483 | |
| 3myq | E27 | Carbonic anhydrase 2 | 4.2.1.1 | 0.480 | |
| 2q1q | OSP | Carbonic anhydrase 2 | 4.2.1.1 | 0.478 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.472 | |
| 7std | CRP | Scytalone dehydratase | 4.2.1.94 | 0.472 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.471 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.470 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.469 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.468 | |
| 2vte | IK4 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.468 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.468 | |
| 4dz7 | D02 | Carbonic anhydrase 2 | 4.2.1.1 | 0.467 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.465 | |
| 3apw | DP0 | Alpha-1-acid glycoprotein 2 | / | 0.465 | |
| 1rj6 | AZM | Carbonic anhydrase 14 | 4.2.1.1 | 0.464 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.463 | |
| 2q7o | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.463 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.462 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.461 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.459 | |
| 3jyo | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.459 | |
| 3l14 | I7B | Carbonic anhydrase 2 | 4.2.1.1 | 0.458 | |
| 3lxe | TOR | Carbonic anhydrase 1 | 4.2.1.1 | 0.458 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.458 | |
| 4dbc | 3QP | Aspartate aminotransferase | 2.6.1.1 | 0.457 | |
| 4rls | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.456 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.455 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.455 | |
| 1jf2 | CZH | Obelin | / | 0.454 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.454 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.454 | |
| 4boe | CLR | Japanin | / | 0.454 | |
| 1gpd | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.453 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.453 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.453 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.453 | |
| 5d5b | CAU | Beta-2 adrenergic receptor | / | 0.453 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.452 | |
| 4knn | E1F | Carbonic anhydrase 13 | 4.2.1.1 | 0.452 | |
| 2pbw | DOQ | Glutamate receptor ionotropic, kainate 1 | / | 0.451 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.451 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.451 | |
| 4hu1 | V13 | Carbonic anhydrase 13 | 4.2.1.1 | 0.450 | |
| 4j8t | DOG | Uncharacterized PhzA/B-like protein PA3332 | / | 0.450 | |
| 1vi2 | NAD | Quinate/shikimate dehydrogenase | / | 0.449 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.449 | |
| 3aos | JH2 | Hemolymph juvenile hormone binding protein | / | 0.449 | |
| 4xsv | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.449 | |
| 1akb | PPD | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.448 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.448 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.447 | |
| 3i0p | NAD | Malate dehydrogenase, putative | / | 0.447 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.447 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.446 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.445 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.445 | |
| 6std | MS2 | Scytalone dehydratase | 4.2.1.94 | 0.445 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.444 | |
| 2idk | C2F | Glycine N-methyltransferase | 2.1.1.20 | 0.444 | |
| 3faz | NOS | Purine nucleoside phosphorylase | / | 0.444 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.444 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.443 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.443 | |
| 2vtd | LKM | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.443 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.443 | |
| 3img | BZ3 | Pantothenate synthetase | 6.3.2.1 | 0.443 | |
| 5e5h | 0T1 | Succinyl-CoA:acetate CoA-transferase | / | 0.443 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.442 | |
| 3p82 | FMN | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.441 | |
| 2hs6 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.441 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.440 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.440 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.440 | |
| 2ga2 | A19 | Methionine aminopeptidase 2 | / | 0.440 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.440 | |
| 2zvc | SAH | Precorrin-3 C17-methyltransferase | / | 0.440 | |
| 3jyq | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.440 | |
| 4eb5 | PLP | Cysteine desulfurase IscS 2 | / | 0.440 |