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 |
|---|---|---|---|
| 2bu8 | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | 2.7.11.2 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2bu8 | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | 2.7.11.2 | 1.000 | |
| 3crl | ANP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | 2.7.11.2 | 0.597 | |
| 2bu2 | ATP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | 2.7.11.2 | 0.588 | |
| 2iwu | NP5 | ATP-dependent molecular chaperone HSP82 | / | 0.541 | |
| 4jql | VJ6 | Heat shock protein HSP 90-alpha | / | 0.539 | |
| 1byq | ADP | Heat shock protein HSP 90-alpha | / | 0.535 | |
| 2e0a | ANP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.533 | |
| 3t10 | ACP | Heat shock protein HSP 90-alpha | / | 0.532 | |
| 3d2r | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.529 | |
| 3t2s | AGS | Heat shock protein HSP 90-alpha | / | 0.525 | |
| 4bqj | XKL | Heat shock protein HSP 90-alpha | / | 0.524 | |
| 3hhu | 819 | Heat shock protein HSP 90-alpha | / | 0.521 | |
| 2xk2 | ADP | Heat shock protein HSP 90-alpha | / | 0.515 | |
| 2fyp | RDE | Endoplasmin | / | 0.510 | |
| 2yef | ANP | Heat shock protein HSP 90-alpha | / | 0.510 | |
| 4xcj | ADP | Heat shock cognate 90 kDa protein | / | 0.510 | |
| 1qy8 | RDI | Endoplasmin | / | 0.508 | |
| 2q8i | RDC | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 3, mitochondrial | 2.7.11.2 | 0.507 | |
| 2yeg | XQG | Heat shock protein HSP 90-alpha | / | 0.507 | |
| 4xcl | AGS | Heat shock cognate 90 kDa protein | / | 0.507 | |
| 2byh | 2D7 | Heat shock protein HSP 90-alpha | / | 0.506 | |
| 2xx2 | 13C | ATP-dependent molecular chaperone HSP82 | / | 0.506 | |
| 3qdd | 94M | Heat shock protein HSP 90-alpha | / | 0.506 | |
| 1i59 | ANP | Chemotaxis protein CheA | 2.7.13.3 | 0.504 | |
| 3peh | IBD | Endoplasmin homolog, putative | / | 0.504 | |
| 3c11 | GDM | ATP-dependent molecular chaperone HSP82 | / | 0.502 | |
| 1bgq | RDC | ATP-dependent molecular chaperone HSP82 | / | 0.500 | |
| 2zkj | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.500 | |
| 1uy7 | PU4 | Heat shock protein HSP 90-alpha | / | 0.499 | |
| 2gfd | RDA | Endoplasmin | / | 0.499 | |
| 3eko | PYU | Heat shock protein HSP 90-alpha | / | 0.498 | |
| 1uym | PU3 | Heat shock protein HSP 90-beta | / | 0.497 | |
| 1qy5 | NEC | Endoplasmin | / | 0.496 | |
| 3ekr | PY9 | Heat shock protein HSP 90-alpha | / | 0.496 | |
| 4as9 | 4QS | ATP-dependent molecular chaperone HSP82 | / | 0.496 | |
| 4gqt | ADP | Heat shock protein 90 | / | 0.496 | |
| 3ics | ADP | Coenzyme A disulfide reductase | / | 0.495 | |
| 4eft | EFT | Heat shock protein HSP 90-alpha | / | 0.495 | |
| 2yee | 2EC | Heat shock protein HSP 90-alpha | / | 0.491 | |
| 1nhh | ANP | DNA mismatch repair protein MutL | / | 0.490 | |
| 2vwc | BC2 | ATP-dependent molecular chaperone HSP82 | / | 0.489 | |
| 1i58 | ADP | Chemotaxis protein CheA | 2.7.13.3 | 0.488 | |
| 1ysz | NEC | Endoplasmin | / | 0.487 | |
| 3q5l | KX2 | Heat shock protein 83-1 | / | 0.486 | |
| 1yet | GDM | Heat shock protein HSP 90-alpha | / | 0.485 | |
| 2hch | N5A | Endoplasmin | / | 0.485 | |
| 2xht | C0Y | Heat shock protein HSP 90-alpha | / | 0.485 | |
| 1amw | ADP | ATP-dependent molecular chaperone HSP82 | / | 0.484 | |
| 2byi | 2DD | Heat shock protein HSP 90-alpha | / | 0.484 | |
| 3hyz | 42C | Heat shock protein HSP 90-alpha | / | 0.484 | |
| 2xd6 | XD6 | ATP-dependent molecular chaperone HSP82 | / | 0.483 | |
| 3hz1 | 42C | Heat shock protein HSP 90-alpha | / | 0.483 | |
| 3k97 | 4CD | Heat shock protein HSP 90-alpha | / | 0.483 | |
| 2wep | ADP | ATP-dependent molecular chaperone HSP82 | / | 0.482 | |
| 4zoh | FAD | Putative oxidoreductase FAD-binding subunit | / | 0.482 | |
| 2wer | RDC | ATP-dependent molecular chaperone HSP82 | / | 0.481 | |
| 4asg | 814 | ATP-dependent molecular chaperone HSP82 | / | 0.481 | |
| 2wi7 | 2KL | Heat shock protein HSP 90-alpha | / | 0.480 | |
| 3hz1 | 37D | Heat shock protein HSP 90-alpha | / | 0.479 | |
| 3r4p | FU7 | Heat shock protein HSP 90-alpha | / | 0.479 | |
| 4bqg | 50Q | Heat shock protein HSP 90-alpha | / | 0.479 | |
| 2fxs | RDA | ATP-dependent molecular chaperone HSP82 | / | 0.478 | |
| 1yc3 | 4BC | Heat shock protein HSP 90-alpha | / | 0.477 | |
| 3t0z | ATP | Heat shock protein HSP 90-alpha | / | 0.477 | |
| 1i58 | ACP | Chemotaxis protein CheA | 2.7.13.3 | 0.476 | |
| 5f5r | ANP | Heat shock protein 75 kDa, mitochondrial | / | 0.476 | |
| 1uyi | PUZ | Heat shock protein HSP 90-alpha | / | 0.475 | |
| 2qg2 | A91 | Heat shock protein HSP 90-alpha | / | 0.474 | |
| 3rlq | 3RQ | Heat shock protein HSP 90-alpha | / | 0.474 | |
| 2zdx | P4A | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.473 | |
| 3r4o | FU3 | Heat shock protein HSP 90-alpha | / | 0.473 | |
| 3t1k | ANP | Heat shock protein HSP 90-alpha | / | 0.473 | |
| 2fwz | H71 | Heat shock protein HSP 90-alpha | / | 0.472 | |
| 2xcm | ADP | Cytosolic heat shock protein 90 | / | 0.472 | |
| 1uye | PU9 | Heat shock protein HSP 90-alpha | / | 0.471 | |
| 4egi | B2J | Heat shock protein HSP 90-alpha | / | 0.471 | |
| 2gqp | PA7 | Endoplasmin | / | 0.470 | |
| 3opd | HIE | Heat shock protein 83 | / | 0.470 | |
| 4xc0 | ACP | Heat shock cognate 90 kDa protein | / | 0.470 | |
| 1u0z | RDC | Endoplasmin | / | 0.469 | |
| 1uy6 | PU3 | Heat shock protein HSP 90-alpha | / | 0.469 | |
| 3ict | ADP | Coenzyme A disulfide reductase | / | 0.469 | |
| 4mp7 | PFT | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | 2.7.11.2 | 0.469 | |
| 2bz5 | AB4 | Heat shock protein HSP 90-alpha | / | 0.468 | |
| 2yjx | YJX | Heat shock protein HSP 90-alpha | / | 0.467 | |
| 3inx | JZC | Heat shock protein HSP 90-alpha | / | 0.467 | |
| 2brc | CT5 | ATP-dependent molecular chaperone HSP82 | / | 0.466 | |
| 4ce2 | BO5 | ATP-dependent molecular chaperone HSP82 | / | 0.466 | |
| 1am1 | ADP | ATP-dependent molecular chaperone HSP82 | / | 0.465 | |
| 2h55 | DZ8 | Heat shock protein HSP 90-alpha | / | 0.464 | |
| 2iws | NP4 | ATP-dependent molecular chaperone HSP82 | / | 0.464 | |
| 2yke | YKE | Heat shock protein HSP 90-alpha | / | 0.464 | |
| 4fcr | 0TM | Heat shock protein HSP 90-alpha | / | 0.464 | |
| 4asf | 62U | ATP-dependent molecular chaperone HSP82 | / | 0.463 | |
| 2o1u | ANP | Endoplasmin | / | 0.462 | |
| 2xab | VHD | Heat shock protein HSP 90-alpha | / | 0.462 | |
| 3b28 | B2X | Heat shock protein HSP 90-alpha | / | 0.462 | |
| 3cuk | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.462 | |
| 3pju | C2E | Diguanylate cyclase/phosphodiesterase | / | 0.462 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.461 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.461 | |
| 2bre | KJ2 | ATP-dependent molecular chaperone HSP82 | / | 0.461 | |
| 3o0i | P54 | Heat shock protein HSP 90-alpha | / | 0.461 | |
| 1uy9 | PU6 | Heat shock protein HSP 90-alpha | / | 0.460 | |
| 1uyh | PU0 | Heat shock protein HSP 90-alpha | / | 0.459 | |
| 3rlr | 3RR | Heat shock protein HSP 90-alpha | / | 0.459 | |
| 3cgc | COA | Coenzyme A disulfide reductase | / | 0.458 | |
| 3hz5 | Z64 | Heat shock protein HSP 90-alpha | / | 0.458 | |
| 1mdu | ATP | Actin, alpha skeletal muscle | / | 0.457 | |
| 2esa | GDM | Endoplasmin | / | 0.457 | |
| 2yk2 | YJW | Heat shock protein HSP 90-alpha | / | 0.457 | |
| 4riy | ADP | Epidermal growth factor receptor | 2.7.10.1 | 0.457 | |
| 1uyk | PUX | Heat shock protein HSP 90-alpha | / | 0.456 | |
| 3cge | COA | Coenzyme A disulfide reductase | / | 0.456 | |
| 3k99 | PFT | Heat shock protein HSP 90-alpha | / | 0.456 | |
| 1u2o | NEC | Endoplasmin | / | 0.455 | |
| 2vcj | 2EQ | Heat shock protein HSP 90-alpha | / | 0.455 | |
| 3wha | WHA | Heat shock protein HSP 90-alpha | / | 0.455 | |
| 2ch6 | ADP | N-acetyl-D-glucosamine kinase | 2.7.1.59 | 0.454 | |
| 3tm5 | SFG | Uncharacterized protein | / | 0.454 | |
| 2yei | XQI | Heat shock protein HSP 90-alpha | / | 0.453 | |
| 3nta | COA | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.453 | |
| 2xhr | C0P | Heat shock protein HSP 90-alpha | / | 0.452 | |
| 4ce3 | L4V | ATP-dependent molecular chaperone HSP82 | / | 0.452 | |
| 1y4s | ADP | Chaperone protein HtpG | / | 0.451 | |
| 2hg1 | N5O | Endoplasmin | / | 0.451 | |
| 2yk2 | YJX | Heat shock protein HSP 90-alpha | / | 0.451 | |
| 2wi4 | ZZ4 | Heat shock protein HSP 90-alpha | / | 0.450 | |
| 2xx4 | 13I | ATP-dependent molecular chaperone HSP82 | / | 0.450 | |
| 4egh | 0OY | Heat shock protein HSP 90-alpha | / | 0.449 | |
| 4wud | ANP | DNA gyrase subunit B | / | 0.449 | |
| 1g9a | BAB | Botulinum neurotoxin type B | 3.4.24.69 | 0.448 | |
| 1lrj | UD1 | UDP-glucose 4-epimerase | 5.1.3.2 | 0.448 | |
| 2bt0 | CT5 | Heat shock protein HSP 90-alpha | / | 0.448 | |
| 3s79 | ASD | Aromatase | 1.14.14.14 | 0.448 | |
| 2exl | GDM | Endoplasmin | / | 0.447 | |
| 3ied | AN2 | HSP90 | / | 0.447 | |
| 1uyf | PU1 | Heat shock protein HSP 90-alpha | / | 0.446 | |
| 2fwy | H64 | Heat shock protein HSP 90-alpha | / | 0.446 | |
| 3u9n | 09H | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.446 | |
| 3vs3 | VSE | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.446 | |
| 4ce1 | 7FK | ATP-dependent molecular chaperone HSP82 | / | 0.446 | |
| 3ge1 | ADP | Glycerol kinase | / | 0.445 | |
| 4wo5 | 324 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.445 | |
| 1yt0 | ADP | Endoplasmin | / | 0.444 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.444 | |
| 3zew | STU | Ephrin type-B receptor 4 | 2.7.10.1 | 0.444 | |
| 4jlc | SU6 | Serine/threonine-protein kinase TBK1 | 2.7.11.1 | 0.444 | |
| 1v9a | SAH | Uncharacterized protein | / | 0.443 | |
| 1z59 | ADP | Type 2 DNA topoisomerase 6 subunit B | / | 0.443 | |
| 1zrz | BI1 | Protein kinase C iota type | 2.7.11.13 | 0.443 | |
| 2pmd | GNP | Translation initiation factor 2 subunit gamma | / | 0.443 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.443 | |
| 1kvs | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.442 | |
| 1qrr | UPG | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.442 | |
| 2y1t | DUD | SPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS | 3.6.1.23 | 0.442 | |
| 4ejh | 0QA | Cytochrome P450 2A13 | 1.14.14.1 | 0.441 | |
| 4pl9 | ADP | Ethylene receptor 1 | / | 0.441 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.440 | |
| 1i5b | ANP | Chemotaxis protein CheA | 2.7.13.3 | 0.440 | |
| 1kvt | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.440 | |
| 1uyc | PU7 | Heat shock protein HSP 90-alpha | / | 0.440 | |
| 2x60 | GTP | Mannose-1-phosphate guanylyltransferase | / | 0.440 | |
| 3r4n | FU5 | Heat shock protein HSP 90-alpha | / | 0.440 | |
| 3upy | FOM | Oxidoreductase, putative | / | 0.440 | |
| 4be7 | ATP | Type I restriction enzyme EcoR124II R protein | 3.1.21.3 | 0.440 |