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 |
|---|---|---|---|
| 3v2j | AZM | Carbonic anhydrase 2 | 4.2.1.1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3v2j | AZM | Carbonic anhydrase 2 | 4.2.1.1 | 1.000 | |
| 1a42 | BZU | Carbonic anhydrase 2 | 4.2.1.1 | 0.753 | |
| 3dcc | D9Z | Carbonic anhydrase 2 | 4.2.1.1 | 0.746 | |
| 3d8w | D8W | Carbonic anhydrase 2 | 4.2.1.1 | 0.741 | |
| 3daz | MZM | Carbonic anhydrase 2 | 4.2.1.1 | 0.726 | |
| 2h15 | B19 | Carbonic anhydrase 2 | 4.2.1.1 | 0.714 | |
| 1cnw | EG1 | Carbonic anhydrase 2 | 4.2.1.1 | 0.713 | |
| 3dcw | EZL | Carbonic anhydrase 2 | 4.2.1.1 | 0.703 | |
| 3p5l | IT5 | Carbonic anhydrase 2 | 4.2.1.1 | 0.703 | |
| 3k2f | NKX | Carbonic anhydrase 2 | 4.2.1.1 | 0.692 | |
| 1bnw | TPD | Carbonic anhydrase 2 | 4.2.1.1 | 0.678 | |
| 4bf1 | 9FK | Carbonic anhydrase 2 | 4.2.1.1 | 0.675 | |
| 3m5e | JDR | Carbonic anhydrase 2 | 4.2.1.1 | 0.674 | |
| 2eu3 | FF3 | Carbonic anhydrase 2 | 4.2.1.1 | 0.672 | |
| 1g52 | F2B | Carbonic anhydrase 2 | 4.2.1.1 | 0.670 | |
| 3b4f | TUO | Carbonic anhydrase 2 | 4.2.1.1 | 0.667 | |
| 3oik | WZB | Carbonic anhydrase 2 | 4.2.1.1 | 0.667 | |
| 1cnx | EG2 | Carbonic anhydrase 2 | 4.2.1.1 | 0.663 | |
| 1bnn | AL1 | Carbonic anhydrase 2 | 4.2.1.1 | 0.660 | |
| 3eft | 3BS | Carbonic anhydrase 2 | 4.2.1.1 | 0.659 | |
| 3d9z | D9Z | Carbonic anhydrase 2 | 4.2.1.1 | 0.653 | |
| 1kwr | SG2 | Carbonic anhydrase 2 | 4.2.1.1 | 0.649 | |
| 1bn4 | AL9 | Carbonic anhydrase 2 | 4.2.1.1 | 0.648 | |
| 3dbu | D8W | Carbonic anhydrase 2 | 4.2.1.1 | 0.648 | |
| 1okn | STB | Carbonic anhydrase 2 | 4.2.1.1 | 0.642 | |
| 2q1q | OSP | Carbonic anhydrase 2 | 4.2.1.1 | 0.641 | |
| 1g1d | FSB | Carbonic anhydrase 2 | 4.2.1.1 | 0.640 | |
| 1bnu | AL3 | Carbonic anhydrase 2 | 4.2.1.1 | 0.639 | |
| 2wej | FB2 | Carbonic anhydrase 2 | 4.2.1.1 | 0.638 | |
| 1i9n | IOA | Carbonic anhydrase 2 | 4.2.1.1 | 0.636 | |
| 1bn1 | AL5 | Carbonic anhydrase 2 | 4.2.1.1 | 0.635 | |
| 1if6 | FBU | Carbonic anhydrase 2 | 4.2.1.1 | 0.634 | |
| 3mhc | ARZ | Carbonic anhydrase 2 | 4.2.1.1 | 0.631 | |
| 3bl1 | BL1 | Carbonic anhydrase 2 | 4.2.1.1 | 0.629 | |
| 4ito | MPX | Carbonic anhydrase 2 | 4.2.1.1 | 0.629 | |
| 1xpz | 4TZ | Carbonic anhydrase 2 | 4.2.1.1 | 0.628 | |
| 3sbh | E65 | Carbonic anhydrase 2 | 4.2.1.1 | 0.627 | |
| 4mo8 | 2VQ | Carbonic anhydrase 2 | 4.2.1.1 | 0.625 | |
| 1if7 | SBR | Carbonic anhydrase 2 | 4.2.1.1 | 0.624 | |
| 3ml2 | SU0 | Carbonic anhydrase 2 | 4.2.1.1 | 0.621 | |
| 3oy0 | OY0 | Carbonic anhydrase 2 | 4.2.1.1 | 0.621 | |
| 2weh | FB1 | Carbonic anhydrase 2 | 4.2.1.1 | 0.620 | |
| 3dd8 | 2C7 | Carbonic anhydrase 2 | 4.2.1.1 | 0.619 | |
| 3rz8 | RZ8 | Carbonic anhydrase 2 | 4.2.1.1 | 0.618 | |
| 1bnv | AL7 | Carbonic anhydrase 2 | 4.2.1.1 | 0.617 | |
| 1zsb | AZM | Carbonic anhydrase 2 | 4.2.1.1 | 0.617 | |
| 2h4n | AZM | Carbonic anhydrase 2 | 4.2.1.1 | 0.616 | |
| 3oyq | OYQ | Carbonic anhydrase 2 | 4.2.1.1 | 0.616 | |
| 1kwq | SG1 | Carbonic anhydrase 2 | 4.2.1.1 | 0.615 | |
| 3bet | CTF | Carbonic anhydrase 2 | 4.2.1.1 | 0.615 | |
| 4ilx | 1EZ | Carbonic anhydrase 2 | 4.2.1.1 | 0.615 | |
| 3m2n | J74 | Carbonic anhydrase 2 | 4.2.1.1 | 0.611 | |
| 1g4o | BSB | Carbonic anhydrase 2 | 4.2.1.1 | 0.609 | |
| 1ttm | 667 | Carbonic anhydrase 2 | 4.2.1.1 | 0.608 | |
| 3mho | J43 | Carbonic anhydrase 2 | 4.2.1.1 | 0.608 | |
| 4dz7 | D02 | Carbonic anhydrase 2 | 4.2.1.1 | 0.608 | |
| 1i9m | INW | Carbonic anhydrase 2 | 4.2.1.1 | 0.607 | |
| 2weo | FBW | Carbonic anhydrase 2 | 4.2.1.1 | 0.606 | |
| 1cil | ETS | Carbonic anhydrase 2 | 4.2.1.1 | 0.602 | |
| 1bnq | AL4 | Carbonic anhydrase 2 | 4.2.1.1 | 0.600 | |
| 3qyk | IE2 | Carbonic anhydrase 2 | 4.2.1.1 | 0.596 | |
| 1bnt | AL2 | Carbonic anhydrase 2 | 4.2.1.1 | 0.594 | |
| 1i90 | INM | Carbonic anhydrase 2 | 4.2.1.1 | 0.592 | |
| 4kap | 1QV | Carbonic anhydrase 2 | 4.2.1.1 | 0.588 | |
| 4iwz | 1GO | Carbonic anhydrase 2 | 4.2.1.1 | 0.585 | |
| 1if4 | FBS | Carbonic anhydrase 2 | 4.2.1.1 | 0.584 | |
| 4bf6 | X0Q | Carbonic anhydrase 2 | 4.2.1.1 | 0.584 | |
| 3n4b | WWZ | Carbonic anhydrase 2 | 4.2.1.1 | 0.583 | |
| 4kni | E1E | Carbonic anhydrase 2 | 4.2.1.1 | 0.582 | |
| 3dc3 | AZM | Carbonic anhydrase 2 | 4.2.1.1 | 0.580 | |
| 1cny | EG3 | Carbonic anhydrase 2 | 4.2.1.1 | 0.579 | |
| 1bn3 | AL6 | Carbonic anhydrase 2 | 4.2.1.1 | 0.578 | |
| 1i91 | INQ | Carbonic anhydrase 2 | 4.2.1.1 | 0.578 | |
| 1okm | SAB | Carbonic anhydrase 2 | 4.2.1.1 | 0.578 | |
| 3n3j | WWV | Carbonic anhydrase 2 | 4.2.1.1 | 0.578 | |
| 1eou | SMS | Carbonic anhydrase 2 | 4.2.1.1 | 0.577 | |
| 1if5 | FBT | Carbonic anhydrase 2 | 4.2.1.1 | 0.577 | |
| 1okl | MNS | Carbonic anhydrase 2 | 4.2.1.1 | 0.577 | |
| 4n16 | CHD | Carbonic anhydrase 2 | 4.2.1.1 | 0.577 | |
| 3m2y | BE0 | Carbonic anhydrase 2 | 4.2.1.1 | 0.576 | |
| 3l14 | I7B | Carbonic anhydrase 2 | 4.2.1.1 | 0.574 | |
| 3n2p | AYX | Carbonic anhydrase 2 | 4.2.1.1 | 0.572 | |
| 3mna | DWH | Carbonic anhydrase 2 | 4.2.1.1 | 0.571 | |
| 3mzc | S6I | Carbonic anhydrase 2 | 4.2.1.1 | 0.570 | |
| 3ffp | LC1 | Carbonic anhydrase 2 | 4.2.1.1 | 0.568 | |
| 3oim | VZ5 | Carbonic anhydrase 2 | 4.2.1.1 | 0.567 | |
| 1bnm | AL8 | Carbonic anhydrase 2 | 4.2.1.1 | 0.566 | |
| 3m98 | E02 | Carbonic anhydrase 2 | 4.2.1.1 | 0.566 | |
| 3po6 | DT9 | Carbonic anhydrase 2 | 4.2.1.1 | 0.566 | |
| 3oys | OYS | Carbonic anhydrase 2 | 4.2.1.1 | 0.563 | |
| 4k0t | D9Z | Carbonic anhydrase 2 | 4.2.1.1 | 0.561 | |
| 3m67 | E36 | Carbonic anhydrase 2 | 4.2.1.1 | 0.560 | |
| 3mhl | J71 | Carbonic anhydrase 2 | 4.2.1.1 | 0.560 | |
| 3igp | DT7 | Carbonic anhydrase 2 | 4.2.1.1 | 0.557 | |
| 3dcs | MZM | Carbonic anhydrase 2 | 4.2.1.1 | 0.556 | |
| 1g4j | FFB | Carbonic anhydrase 2 | 4.2.1.1 | 0.554 | |
| 3n0n | P9B | Carbonic anhydrase 2 | 4.2.1.1 | 0.552 | |
| 2weg | FBV | Carbonic anhydrase 2 | 4.2.1.1 | 0.549 | |
| 3f4x | KLT | Carbonic anhydrase 2 | 4.2.1.1 | 0.549 | |
| 1i8z | INL | Carbonic anhydrase 2 | 4.2.1.1 | 0.546 | |
| 3mmf | D9H | Carbonic anhydrase 2 | 4.2.1.1 | 0.544 | |
| 3myq | E27 | Carbonic anhydrase 2 | 4.2.1.1 | 0.544 | |
| 3kig | DA4 | Carbonic anhydrase 2 | 4.2.1.1 | 0.543 | |
| 3mhi | J90 | Carbonic anhydrase 2 | 4.2.1.1 | 0.542 | |
| 1g45 | FSB | Carbonic anhydrase 2 | 4.2.1.1 | 0.541 | |
| 2wd2 | MS5 | Carbonic anhydrase 2 | 4.2.1.1 | 0.539 | |
| 4itp | 1GD | Carbonic anhydrase 2 | 4.2.1.1 | 0.537 | |
| 4k0z | MZM | Carbonic anhydrase 2 | 4.2.1.1 | 0.535 | |
| 3hku | TOR | Carbonic anhydrase 2 | 4.2.1.1 | 0.534 | |
| 1if8 | SBS | Carbonic anhydrase 2 | 4.2.1.1 | 0.533 | |
| 3m40 | J45 | Carbonic anhydrase 2 | 4.2.1.1 | 0.530 | |
| 3s8x | E59 | Carbonic anhydrase 2 | 4.2.1.1 | 0.528 | |
| 3sax | E50 | Carbonic anhydrase 2 | 4.2.1.1 | 0.526 | |
| 3mdz | EZL | Carbonic anhydrase 7 | 4.2.1.1 | 0.524 | |
| 4pxx | CHD | Carbonic anhydrase 2 | 4.2.1.1 | 0.522 | |
| 1xq0 | 4TR | Carbonic anhydrase 2 | 4.2.1.1 | 0.520 | |
| 2pow | I7C | Carbonic anhydrase 2 | 4.2.1.1 | 0.520 | |
| 4m2r | BZ1 | Carbonic anhydrase 2 | 4.2.1.1 | 0.520 | |
| 3dd0 | EZL | Carbonic anhydrase 2 | 4.2.1.1 | 0.516 | |
| 1yda | AZM | Carbonic anhydrase 2 | 4.2.1.1 | 0.515 | |
| 3t84 | SG6 | Carbonic anhydrase 2 | 4.2.1.1 | 0.510 | |
| 5fl4 | 9FK | Carbonic anhydrase 9 | 4.2.1.1 | 0.509 | |
| 3sbi | E90 | Carbonic anhydrase 2 | 4.2.1.1 | 0.507 | |
| 3t82 | SG4 | Carbonic anhydrase 2 | 4.2.1.1 | 0.503 | |
| 3ni5 | C1H | Carbonic anhydrase 2 | 4.2.1.1 | 0.501 | |
| 2x7u | WZA | Carbonic anhydrase 2 | 4.2.1.1 | 0.500 | |
| 5flt | VJJ | Carbonic anhydrase 2 | 4.2.1.1 | 0.500 | |
| 1oq5 | CEL | Carbonic anhydrase 2 | 4.2.1.1 | 0.498 | |
| 2x7t | WZB | Carbonic anhydrase 2 | 4.2.1.1 | 0.494 | |
| 3nb5 | R21 | Carbonic anhydrase 2 | 4.2.1.1 | 0.494 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.492 | |
| 4knm | E1E | Carbonic anhydrase 13 | 4.2.1.1 | 0.489 | |
| 3s9t | E49 | Carbonic anhydrase 2 | 4.2.1.1 | 0.488 | |
| 4knj | E1F | Carbonic anhydrase 2 | 4.2.1.1 | 0.487 | |
| 1jd0 | AZM | Carbonic anhydrase 12 | 4.2.1.1 | 0.486 | |
| 4k13 | ETS | Carbonic anhydrase 2 | 4.2.1.1 | 0.484 | |
| 4ht2 | V50 | Carbonic anhydrase 12 | 4.2.1.1 | 0.481 | |
| 3f7u | AG4 | Carbonic anhydrase 4 | 4.2.1.1 | 0.480 | |
| 4m2v | BZ1 | Carbonic anhydrase 2 | 4.2.1.1 | 0.476 | |
| 4kp8 | E1G | Carbonic anhydrase 12 | 4.2.1.1 | 0.475 | |
| 3f7b | AG5 | Carbonic anhydrase 4 | 4.2.1.1 | 0.474 | |
| 2xje | U5P | Cytosolic purine 5'-nucleotidase | 3.1.3.5 | 0.472 | |
| 3t85 | SG7 | Carbonic anhydrase 2 | 4.2.1.1 | 0.472 | |
| 1a5b | IGP | Tryptophan synthase alpha chain | / | 0.470 | |
| 1g54 | FFB | Carbonic anhydrase 2 | 4.2.1.1 | 0.470 | |
| 4kp5 | E1F | Carbonic anhydrase 12 | 4.2.1.1 | 0.470 | |
| 1i9p | IOE | Carbonic anhydrase 2 | 4.2.1.1 | 0.469 | |
| 3fw3 | ETS | Carbonic anhydrase 4 | 4.2.1.1 | 0.469 | |
| 1i9q | IOF | Carbonic anhydrase 2 | 4.2.1.1 | 0.468 | |
| 3znc | BZ1 | Carbonic anhydrase 4 | 4.2.1.1 | 0.467 | |
| 3m96 | E38 | Carbonic anhydrase 2 | 4.2.1.1 | 0.465 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.464 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.464 | |
| 1h85 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.463 | |
| 1k4m | NAD | Nicotinate-nucleotide adenylyltransferase | 2.7.7.18 | 0.462 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.462 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.460 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.458 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.455 | |
| 4bqz | GNP | Ectonucleoside triphosphate diphosphohydrolase 2 | / | 0.455 | |
| 2yq9 | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.454 | |
| 3tqx | PLP | 2-amino-3-ketobutyrate coenzyme A ligase | / | 0.454 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.454 | |
| 1foa | UD1 | Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase | 2.4.1.101 | 0.452 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.452 | |
| 3aw9 | GDU | NAD-dependent epimerase/dehydratase | / | 0.452 | |
| 3tyd | XHP | Dihydropteroate synthase | / | 0.452 | |
| 4lu3 | AZM | Carbonic anhydrase 14 | 4.2.1.1 | 0.452 | |
| 4mrm | 2BY | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.452 | |
| 2q7o | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.451 | |
| 4xiw | AZM | Carbonic anhydrase, alpha type | / | 0.451 | |
| 1b5e | DCM | Deoxycytidylate 5-hydroxymethyltransferase | 2.1.2.8 | 0.449 | |
| 1qh0 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.449 | |
| 3otb | DGT | Probable tRNA(His) guanylyltransferase | 2.7.7.79 | 0.449 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.449 | |
| 3af1 | GDP | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.448 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 5c3r | HMU | Thymine dioxygenase | / | 0.447 | |
| 4xnw | 2ID | P2Y purinoceptor 1 | / | 0.447 | |
| 1ivs | VAA | Valine--tRNA ligase | 6.1.1.9 | 0.446 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.446 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 4jic | FMN | GTN Reductase | / | 0.446 | |
| 4xrb | NDP | Possible bifunctional enzyme riboflavin biosynthesis protein RibD: diaminohydroxyphosphoribosylaminopyrimidine deaminase (Riboflavin-specific deaminase) + 5-amino-6-(5-phosphoribosylamino)uracil reduc | / | 0.446 | |
| 1mmk | H4B | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.445 | |
| 1qgy | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.445 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.445 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.445 | |
| 4dbc | 3QP | Aspartate aminotransferase | 2.6.1.1 | 0.445 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.444 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.444 | |
| 1f8g | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.443 | |
| 3c35 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.443 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3lxe | TOR | Carbonic anhydrase 1 | 4.2.1.1 | 0.443 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.442 | |
| 5ah5 | LSS | Leucine--tRNA ligase | / | 0.442 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.441 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.440 |