sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 3dcs | MZM | Carbonic anhydrase 2 | 4.2.1.1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3dcs | MZM | Carbonic anhydrase 2 | 4.2.1.1 | 1.000 | |
| 3dc3 | AZM | Carbonic anhydrase 2 | 4.2.1.1 | 0.741 | |
| 3hku | TOR | Carbonic anhydrase 2 | 4.2.1.1 | 0.718 | |
| 4kap | 1QV | Carbonic anhydrase 2 | 4.2.1.1 | 0.708 | |
| 1if5 | FBT | Carbonic anhydrase 2 | 4.2.1.1 | 0.705 | |
| 1if6 | FBU | Carbonic anhydrase 2 | 4.2.1.1 | 0.690 | |
| 4m2r | BZ1 | Carbonic anhydrase 2 | 4.2.1.1 | 0.686 | |
| 3qyk | IE2 | Carbonic anhydrase 2 | 4.2.1.1 | 0.674 | |
| 1if7 | SBR | Carbonic anhydrase 2 | 4.2.1.1 | 0.662 | |
| 2h15 | B19 | Carbonic anhydrase 2 | 4.2.1.1 | 0.652 | |
| 3m5e | JDR | Carbonic anhydrase 2 | 4.2.1.1 | 0.650 | |
| 1bnn | AL1 | Carbonic anhydrase 2 | 4.2.1.1 | 0.647 | |
| 1bn3 | AL6 | Carbonic anhydrase 2 | 4.2.1.1 | 0.644 | |
| 1i91 | INQ | Carbonic anhydrase 2 | 4.2.1.1 | 0.644 | |
| 3d9z | D9Z | Carbonic anhydrase 2 | 4.2.1.1 | 0.644 | |
| 4kni | E1E | Carbonic anhydrase 2 | 4.2.1.1 | 0.643 | |
| 4m2v | BZ1 | Carbonic anhydrase 2 | 4.2.1.1 | 0.643 | |
| 1bn1 | AL5 | Carbonic anhydrase 2 | 4.2.1.1 | 0.642 | |
| 2x7t | WZB | Carbonic anhydrase 2 | 4.2.1.1 | 0.641 | |
| 1a42 | BZU | Carbonic anhydrase 2 | 4.2.1.1 | 0.636 | |
| 1g52 | F2B | Carbonic anhydrase 2 | 4.2.1.1 | 0.636 | |
| 1kwr | SG2 | Carbonic anhydrase 2 | 4.2.1.1 | 0.635 | |
| 3sbi | E90 | Carbonic anhydrase 2 | 4.2.1.1 | 0.635 | |
| 1i9q | IOF | Carbonic anhydrase 2 | 4.2.1.1 | 0.633 | |
| 3t82 | SG4 | Carbonic anhydrase 2 | 4.2.1.1 | 0.630 | |
| 1bn4 | AL9 | Carbonic anhydrase 2 | 4.2.1.1 | 0.627 | |
| 1g45 | FSB | Carbonic anhydrase 2 | 4.2.1.1 | 0.625 | |
| 3daz | MZM | Carbonic anhydrase 2 | 4.2.1.1 | 0.625 | |
| 1cil | ETS | Carbonic anhydrase 2 | 4.2.1.1 | 0.622 | |
| 3eft | 3BS | Carbonic anhydrase 2 | 4.2.1.1 | 0.622 | |
| 3k2f | NKX | Carbonic anhydrase 2 | 4.2.1.1 | 0.622 | |
| 1ttm | 667 | Carbonic anhydrase 2 | 4.2.1.1 | 0.621 | |
| 3dbu | D8W | Carbonic anhydrase 2 | 4.2.1.1 | 0.615 | |
| 3mhl | J71 | Carbonic anhydrase 2 | 4.2.1.1 | 0.610 | |
| 1if4 | FBS | Carbonic anhydrase 2 | 4.2.1.1 | 0.607 | |
| 3ffp | LC1 | Carbonic anhydrase 2 | 4.2.1.1 | 0.607 | |
| 1g1d | FSB | Carbonic anhydrase 2 | 4.2.1.1 | 0.606 | |
| 1zsb | AZM | Carbonic anhydrase 2 | 4.2.1.1 | 0.606 | |
| 3n0n | P9B | Carbonic anhydrase 2 | 4.2.1.1 | 0.606 | |
| 1bnw | TPD | Carbonic anhydrase 2 | 4.2.1.1 | 0.603 | |
| 1kwq | SG1 | Carbonic anhydrase 2 | 4.2.1.1 | 0.603 | |
| 1xpz | 4TZ | Carbonic anhydrase 2 | 4.2.1.1 | 0.602 | |
| 3po6 | DT9 | Carbonic anhydrase 2 | 4.2.1.1 | 0.601 | |
| 1bnt | AL2 | Carbonic anhydrase 2 | 4.2.1.1 | 0.598 | |
| 2weo | FBW | Carbonic anhydrase 2 | 4.2.1.1 | 0.595 | |
| 3t84 | SG6 | Carbonic anhydrase 2 | 4.2.1.1 | 0.592 | |
| 4bf6 | X0Q | Carbonic anhydrase 2 | 4.2.1.1 | 0.592 | |
| 1g54 | FFB | Carbonic anhydrase 2 | 4.2.1.1 | 0.591 | |
| 1if8 | SBS | Carbonic anhydrase 2 | 4.2.1.1 | 0.591 | |
| 1g4j | FFB | Carbonic anhydrase 2 | 4.2.1.1 | 0.590 | |
| 3nb5 | R21 | Carbonic anhydrase 2 | 4.2.1.1 | 0.589 | |
| 3kig | DA4 | Carbonic anhydrase 2 | 4.2.1.1 | 0.587 | |
| 4itp | 1GD | Carbonic anhydrase 2 | 4.2.1.1 | 0.584 | |
| 3mna | DWH | Carbonic anhydrase 2 | 4.2.1.1 | 0.583 | |
| 1bnq | AL4 | Carbonic anhydrase 2 | 4.2.1.1 | 0.582 | |
| 3t85 | SG7 | Carbonic anhydrase 2 | 4.2.1.1 | 0.582 | |
| 2eu3 | FF3 | Carbonic anhydrase 2 | 4.2.1.1 | 0.581 | |
| 3m2n | J74 | Carbonic anhydrase 2 | 4.2.1.1 | 0.580 | |
| 1cnw | EG1 | Carbonic anhydrase 2 | 4.2.1.1 | 0.579 | |
| 3mdz | EZL | Carbonic anhydrase 7 | 4.2.1.1 | 0.575 | |
| 4ilx | 1EZ | Carbonic anhydrase 2 | 4.2.1.1 | 0.575 | |
| 3f4x | KLT | Carbonic anhydrase 2 | 4.2.1.1 | 0.574 | |
| 3dcc | D9Z | Carbonic anhydrase 2 | 4.2.1.1 | 0.573 | |
| 1oq5 | CEL | Carbonic anhydrase 2 | 4.2.1.1 | 0.571 | |
| 2x7u | WZA | Carbonic anhydrase 2 | 4.2.1.1 | 0.571 | |
| 5flt | VJJ | Carbonic anhydrase 2 | 4.2.1.1 | 0.569 | |
| 2wej | FB2 | Carbonic anhydrase 2 | 4.2.1.1 | 0.568 | |
| 3b4f | TUO | Carbonic anhydrase 2 | 4.2.1.1 | 0.568 | |
| 4ito | MPX | Carbonic anhydrase 2 | 4.2.1.1 | 0.566 | |
| 1xq0 | 4TR | Carbonic anhydrase 2 | 4.2.1.1 | 0.565 | |
| 2weh | FB1 | Carbonic anhydrase 2 | 4.2.1.1 | 0.565 | |
| 3oys | OYS | Carbonic anhydrase 2 | 4.2.1.1 | 0.564 | |
| 4iwz | 1GO | Carbonic anhydrase 2 | 4.2.1.1 | 0.564 | |
| 1i9n | IOA | Carbonic anhydrase 2 | 4.2.1.1 | 0.563 | |
| 3m98 | E02 | Carbonic anhydrase 2 | 4.2.1.1 | 0.563 | |
| 1bnu | AL3 | Carbonic anhydrase 2 | 4.2.1.1 | 0.562 | |
| 2h4n | AZM | Carbonic anhydrase 2 | 4.2.1.1 | 0.562 | |
| 2pow | I7C | Carbonic anhydrase 2 | 4.2.1.1 | 0.562 | |
| 3bet | CTF | Carbonic anhydrase 2 | 4.2.1.1 | 0.560 | |
| 4n16 | CHD | Carbonic anhydrase 2 | 4.2.1.1 | 0.560 | |
| 1i90 | INM | Carbonic anhydrase 2 | 4.2.1.1 | 0.559 | |
| 3m67 | E36 | Carbonic anhydrase 2 | 4.2.1.1 | 0.559 | |
| 3dd8 | 2C7 | Carbonic anhydrase 2 | 4.2.1.1 | 0.557 | |
| 3s9t | E49 | Carbonic anhydrase 2 | 4.2.1.1 | 0.557 | |
| 3ml2 | SU0 | Carbonic anhydrase 2 | 4.2.1.1 | 0.554 | |
| 3mzc | S6I | Carbonic anhydrase 2 | 4.2.1.1 | 0.554 | |
| 3n4b | WWZ | Carbonic anhydrase 2 | 4.2.1.1 | 0.554 | |
| 3ni5 | C1H | Carbonic anhydrase 2 | 4.2.1.1 | 0.554 | |
| 4k0t | D9Z | Carbonic anhydrase 2 | 4.2.1.1 | 0.552 | |
| 3d8w | D8W | Carbonic anhydrase 2 | 4.2.1.1 | 0.551 | |
| 3oik | WZB | Carbonic anhydrase 2 | 4.2.1.1 | 0.551 | |
| 3mhc | ARZ | Carbonic anhydrase 2 | 4.2.1.1 | 0.550 | |
| 4k13 | ETS | Carbonic anhydrase 2 | 4.2.1.1 | 0.550 | |
| 1g4o | BSB | Carbonic anhydrase 2 | 4.2.1.1 | 0.549 | |
| 3mho | J43 | Carbonic anhydrase 2 | 4.2.1.1 | 0.549 | |
| 1bnm | AL8 | Carbonic anhydrase 2 | 4.2.1.1 | 0.543 | |
| 3p5l | IT5 | Carbonic anhydrase 2 | 4.2.1.1 | 0.543 | |
| 3znc | BZ1 | Carbonic anhydrase 4 | 4.2.1.1 | 0.543 | |
| 3igp | DT7 | Carbonic anhydrase 2 | 4.2.1.1 | 0.542 | |
| 4kp8 | E1G | Carbonic anhydrase 12 | 4.2.1.1 | 0.541 | |
| 4pxx | CHD | Carbonic anhydrase 2 | 4.2.1.1 | 0.541 | |
| 3f7u | AG4 | Carbonic anhydrase 4 | 4.2.1.1 | 0.540 | |
| 3sbh | E65 | Carbonic anhydrase 2 | 4.2.1.1 | 0.539 | |
| 2wd2 | MS5 | Carbonic anhydrase 2 | 4.2.1.1 | 0.538 | |
| 3n3j | WWV | Carbonic anhydrase 2 | 4.2.1.1 | 0.533 | |
| 1jd0 | AZM | Carbonic anhydrase 12 | 4.2.1.1 | 0.532 | |
| 3bl1 | BL1 | Carbonic anhydrase 2 | 4.2.1.1 | 0.532 | |
| 3m2y | BE0 | Carbonic anhydrase 2 | 4.2.1.1 | 0.532 | |
| 1bnv | AL7 | Carbonic anhydrase 2 | 4.2.1.1 | 0.531 | |
| 1yda | AZM | Carbonic anhydrase 2 | 4.2.1.1 | 0.530 | |
| 3s8x | E59 | Carbonic anhydrase 2 | 4.2.1.1 | 0.529 | |
| 1i9p | IOE | Carbonic anhydrase 2 | 4.2.1.1 | 0.526 | |
| 1okl | MNS | Carbonic anhydrase 2 | 4.2.1.1 | 0.526 | |
| 3v2j | AZM | Carbonic anhydrase 2 | 4.2.1.1 | 0.525 | |
| 4bf1 | 9FK | Carbonic anhydrase 2 | 4.2.1.1 | 0.525 | |
| 4ht2 | V50 | Carbonic anhydrase 12 | 4.2.1.1 | 0.525 | |
| 1cnx | EG2 | Carbonic anhydrase 2 | 4.2.1.1 | 0.524 | |
| 3oim | VZ5 | Carbonic anhydrase 2 | 4.2.1.1 | 0.524 | |
| 4kp5 | E1F | Carbonic anhydrase 12 | 4.2.1.1 | 0.524 | |
| 3fw3 | ETS | Carbonic anhydrase 4 | 4.2.1.1 | 0.523 | |
| 3sax | E50 | Carbonic anhydrase 2 | 4.2.1.1 | 0.523 | |
| 3dd0 | EZL | Carbonic anhydrase 2 | 4.2.1.1 | 0.522 | |
| 3mmf | D9H | Carbonic anhydrase 2 | 4.2.1.1 | 0.522 | |
| 4knj | E1F | Carbonic anhydrase 2 | 4.2.1.1 | 0.522 | |
| 3l14 | I7B | Carbonic anhydrase 2 | 4.2.1.1 | 0.521 | |
| 3f7b | AG5 | Carbonic anhydrase 4 | 4.2.1.1 | 0.520 | |
| 3dcw | EZL | Carbonic anhydrase 2 | 4.2.1.1 | 0.518 | |
| 4mo8 | 2VQ | Carbonic anhydrase 2 | 4.2.1.1 | 0.518 | |
| 1i8z | INL | Carbonic anhydrase 2 | 4.2.1.1 | 0.514 | |
| 2weg | FBV | Carbonic anhydrase 2 | 4.2.1.1 | 0.514 | |
| 4x5s | AZM | Carbonic anhydrase (Carbonate dehydratase) | / | 0.514 | |
| 3n2p | AYX | Carbonic anhydrase 2 | 4.2.1.1 | 0.513 | |
| 4xiw | AZM | Carbonic anhydrase, alpha type | / | 0.509 | |
| 1rj6 | AZM | Carbonic anhydrase 14 | 4.2.1.1 | 0.508 | |
| 1cny | EG3 | Carbonic anhydrase 2 | 4.2.1.1 | 0.505 | |
| 3mhi | J90 | Carbonic anhydrase 2 | 4.2.1.1 | 0.504 | |
| 3m40 | J45 | Carbonic anhydrase 2 | 4.2.1.1 | 0.502 | |
| 1okm | SAB | Carbonic anhydrase 2 | 4.2.1.1 | 0.501 | |
| 3m96 | E38 | Carbonic anhydrase 2 | 4.2.1.1 | 0.499 | |
| 4uov | AZM | Carbonate dehydratase | / | 0.498 | |
| 4lu3 | AZM | Carbonic anhydrase 14 | 4.2.1.1 | 0.495 | |
| 1eou | SMS | Carbonic anhydrase 2 | 4.2.1.1 | 0.488 | |
| 3lxe | TOR | Carbonic anhydrase 1 | 4.2.1.1 | 0.488 | |
| 3oy0 | OY0 | Carbonic anhydrase 2 | 4.2.1.1 | 0.484 | |
| 1okn | STB | Carbonic anhydrase 2 | 4.2.1.1 | 0.480 | |
| 7std | CRP | Scytalone dehydratase | 4.2.1.94 | 0.479 | |
| 3oyq | OYQ | Carbonic anhydrase 2 | 4.2.1.1 | 0.477 | |
| 4knm | E1E | Carbonic anhydrase 13 | 4.2.1.1 | 0.476 | |
| 1q45 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.474 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.474 | |
| 4k0z | MZM | Carbonic anhydrase 2 | 4.2.1.1 | 0.474 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.473 | |
| 3zbs | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.473 | |
| 3myq | E27 | Carbonic anhydrase 2 | 4.2.1.1 | 0.472 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.471 | |
| 4iae | 1DX | Alr2278 protein | / | 0.471 | |
| 4dz7 | D02 | Carbonic anhydrase 2 | 4.2.1.1 | 0.468 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.467 | |
| 2q1q | OSP | Carbonic anhydrase 2 | 4.2.1.1 | 0.466 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.465 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.465 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.464 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.463 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.462 | |
| 1tow | CRZ | Fatty acid-binding protein, adipocyte | / | 0.460 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.460 | |
| 2d3a | ADP | Glutamine synthetase root isozyme 3 | 6.3.1.2 | 0.459 | |
| 1zxm | ANP | DNA topoisomerase 2-alpha | 5.99.1.3 | 0.458 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.457 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.457 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.455 | |
| 2vn1 | FK5 | Peptidylprolyl isomerase | / | 0.455 | |
| 3otb | DGT | Probable tRNA(His) guanylyltransferase | 2.7.7.79 | 0.454 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.453 | |
| 2hs8 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.453 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.453 | |
| 2lfo | GCH | Fatty acid-binding protein, liver | / | 0.452 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.452 | |
| 1dmy | AZM | Carbonic anhydrase 5A, mitochondrial | 4.2.1.1 | 0.451 | |
| 1fml | RTL | Retinol dehydratase | / | 0.450 | |
| 2wqp | WQP | Polysialic acid capsule biosynthesis protein SiaC | / | 0.450 | |
| 1icp | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.449 | |
| 2xve | FAD | Putative flavin-containing monooxygenase | / | 0.448 | |
| 1ygj | RMC | Pyridoxal kinase | 2.7.1.35 | 0.447 | |
| 2a9y | 26A | Adenosine kinase | 2.7.1.20 | 0.447 | |
| 2q7o | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.447 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.447 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.447 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.446 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.446 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.445 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.445 | |
| 3fr4 | F8A | Fatty acid-binding protein, adipocyte | / | 0.445 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.445 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.445 | |
| 4jic | FMN | GTN Reductase | / | 0.445 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.444 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.444 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.444 | |
| 4hu1 | V13 | Carbonic anhydrase 13 | 4.2.1.1 | 0.444 | |
| 5fd8 | A5A | Putative carboxypeptidase yocD | / | 0.444 | |
| 1bvr | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.443 | |
| 2r0c | FAD | Putative FAD-monooxygenase | / | 0.443 | |
| 4j8t | DOG | Uncharacterized PhzA/B-like protein PA3332 | / | 0.443 | |
| 4knn | E1F | Carbonic anhydrase 13 | 4.2.1.1 | 0.443 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 1p0p | BCH | Cholinesterase | 3.1.1.8 | 0.442 | |
| 3bj8 | COA | Diamine acetyltransferase 1 | / | 0.442 | |
| 3g1r | FIT | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.442 | |
| 3p82 | FMN | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 4r1f | ADP | DNA topoisomerase 2-alpha | 5.99.1.3 | 0.442 | |
| 4xsv | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.442 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.441 | |
| 3cmf | PDN | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.441 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3elb | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.441 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.441 | |
| 3rud | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.441 | |
| 3zht | TD9 | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.441 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.440 | |
| 3akz | GSU | Glutamate--tRNA ligase 2 | / | 0.440 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.440 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.440 | |
| 3l6j | Z90 | Alr2278 protein | / | 0.440 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 4zzi | 1NS | NAD-dependent protein deacetylase sirtuin-1 | 3.5.1 | 0.440 | |
| 6std | MS2 | Scytalone dehydratase | 4.2.1.94 | 0.440 |