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 |
|---|---|---|---|
| 1yt0 | ADP | Endoplasmin |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1yt0 | ADP | Endoplasmin | / | 1.000 | |
| 2xx2 | 13C | ATP-dependent molecular chaperone HSP82 | / | 0.554 | |
| 2gqp | PA7 | Endoplasmin | / | 0.540 | |
| 3t0z | ATP | Heat shock protein HSP 90-alpha | / | 0.536 | |
| 2fxs | RDA | ATP-dependent molecular chaperone HSP82 | / | 0.525 | |
| 4gqt | ADP | Heat shock protein 90 | / | 0.518 | |
| 1u0z | RDC | Endoplasmin | / | 0.517 | |
| 1osf | KOS | Heat shock protein HSP 90-alpha | / | 0.516 | |
| 2yef | ANP | Heat shock protein HSP 90-alpha | / | 0.516 | |
| 3t2s | AGS | Heat shock protein HSP 90-alpha | / | 0.516 | |
| 3rlq | 3RQ | Heat shock protein HSP 90-alpha | / | 0.515 | |
| 1bgq | RDC | ATP-dependent molecular chaperone HSP82 | / | 0.514 | |
| 1byq | ADP | Heat shock protein HSP 90-alpha | / | 0.513 | |
| 2xk2 | ADP | Heat shock protein HSP 90-alpha | / | 0.513 | |
| 1u2o | NEC | Endoplasmin | / | 0.511 | |
| 3t1k | ANP | Heat shock protein HSP 90-alpha | / | 0.511 | |
| 2gfd | RDA | Endoplasmin | / | 0.509 | |
| 2hch | N5A | Endoplasmin | / | 0.509 | |
| 1yc3 | 4BC | Heat shock protein HSP 90-alpha | / | 0.508 | |
| 3ekr | PY9 | Heat shock protein HSP 90-alpha | / | 0.508 | |
| 2o1u | ANP | Endoplasmin | / | 0.506 | |
| 3t10 | ACP | Heat shock protein HSP 90-alpha | / | 0.506 | |
| 2fyp | RDE | Endoplasmin | / | 0.501 | |
| 4jql | VJ6 | Heat shock protein HSP 90-alpha | / | 0.499 | |
| 2yeg | XQG | Heat shock protein HSP 90-alpha | / | 0.497 | |
| 4xcj | ADP | Heat shock cognate 90 kDa protein | / | 0.493 | |
| 2byh | 2D7 | Heat shock protein HSP 90-alpha | / | 0.487 | |
| 2exl | GDM | Endoplasmin | / | 0.487 | |
| 2hg1 | N5O | Endoplasmin | / | 0.487 | |
| 2xht | C0Y | Heat shock protein HSP 90-alpha | / | 0.487 | |
| 4bqj | XKL | Heat shock protein HSP 90-alpha | / | 0.486 | |
| 3ied | AN2 | HSP90 | / | 0.484 | |
| 3k99 | PFT | Heat shock protein HSP 90-alpha | / | 0.484 | |
| 1amw | ADP | ATP-dependent molecular chaperone HSP82 | / | 0.482 | |
| 1qy5 | NEC | Endoplasmin | / | 0.482 | |
| 2xab | VHD | Heat shock protein HSP 90-alpha | / | 0.482 | |
| 3hyz | 42C | Heat shock protein HSP 90-alpha | / | 0.482 | |
| 2bre | KJ2 | ATP-dependent molecular chaperone HSP82 | / | 0.481 | |
| 2iwu | NP5 | ATP-dependent molecular chaperone HSP82 | / | 0.481 | |
| 5f5r | ANP | Heat shock protein 75 kDa, mitochondrial | / | 0.481 | |
| 4xc0 | ACP | Heat shock cognate 90 kDa protein | / | 0.480 | |
| 1y4s | ADP | Chaperone protein HtpG | / | 0.479 | |
| 2byi | 2DD | Heat shock protein HSP 90-alpha | / | 0.477 | |
| 2o1v | ADP | Endoplasmin | / | 0.477 | |
| 3d2r | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.477 | |
| 1qy8 | RDI | Endoplasmin | / | 0.476 | |
| 2qg0 | A94 | Heat shock protein HSP 90-alpha | / | 0.474 | |
| 3r4p | FU7 | Heat shock protein HSP 90-alpha | / | 0.473 | |
| 3c11 | GDM | ATP-dependent molecular chaperone HSP82 | / | 0.471 | |
| 1yc1 | 4BC | Heat shock protein HSP 90-alpha | / | 0.470 | |
| 4ce1 | 7FK | ATP-dependent molecular chaperone HSP82 | / | 0.469 | |
| 4egi | B2J | Heat shock protein HSP 90-alpha | / | 0.469 | |
| 1z59 | ADP | Type 2 DNA topoisomerase 6 subunit B | / | 0.468 | |
| 2iws | NP4 | ATP-dependent molecular chaperone HSP82 | / | 0.468 | |
| 1yet | GDM | Heat shock protein HSP 90-alpha | / | 0.467 | |
| 3hhu | 819 | Heat shock protein HSP 90-alpha | / | 0.467 | |
| 3r4n | FU5 | Heat shock protein HSP 90-alpha | / | 0.467 | |
| 5ej9 | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.467 | |
| 3ngu | ADP | Nucleoside diphosphate kinase | / | 0.466 | |
| 2xcm | ADP | Cytosolic heat shock protein 90 | / | 0.465 | |
| 2ylz | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.465 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.464 | |
| 3vha | VHA | Heat shock protein HSP 90-alpha | / | 0.464 | |
| 4fcr | 0TM | Heat shock protein HSP 90-alpha | / | 0.464 | |
| 4fc0 | 0T2 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.463 | |
| 2bt0 | CT5 | Heat shock protein HSP 90-alpha | / | 0.462 | |
| 2wer | RDC | ATP-dependent molecular chaperone HSP82 | / | 0.462 | |
| 3cly | ACP | Fibroblast growth factor receptor 2 | / | 0.462 | |
| 3img | BZ3 | Pantothenate synthetase | 6.3.2.1 | 0.462 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.462 | |
| 1am1 | ADP | ATP-dependent molecular chaperone HSP82 | / | 0.459 | |
| 2esa | GDM | Endoplasmin | / | 0.459 | |
| 3iod | A6D | Pantothenate synthetase | 6.3.2.1 | 0.459 | |
| 3r4o | FU3 | Heat shock protein HSP 90-alpha | / | 0.459 | |
| 3vid | 4TT | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.459 | |
| 1u0y | PA7 | Endoplasmin | / | 0.458 | |
| 2wep | ADP | ATP-dependent molecular chaperone HSP82 | / | 0.458 | |
| 4s26 | SAH | Phosphomethylpyrimidine synthase, chloroplastic | 4.1.99.17 | 0.458 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.457 | |
| 2yi5 | YI5 | Heat shock protein HSP 90-alpha | / | 0.457 | |
| 4dti | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.457 | |
| 3eko | PYU | Heat shock protein HSP 90-alpha | / | 0.456 | |
| 4xcl | AGS | Heat shock cognate 90 kDa protein | / | 0.456 | |
| 2jlc | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.455 | |
| 2qfo | A13 | Heat shock protein HSP 90-alpha | / | 0.455 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.455 | |
| 1krh | FAD | Benzoate 1,2-dioxygenase electron transfer component | 1.18.1.3 | 0.454 | |
| 1p0h | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.454 | |
| 5c93 | ACP | Two-component system histidine protein kinase | / | 0.454 | |
| 4as9 | 4QS | ATP-dependent molecular chaperone HSP82 | / | 0.453 | |
| 4eft | EFT | Heat shock protein HSP 90-alpha | / | 0.453 | |
| 4egk | RDC | Heat shock protein HSP 90-alpha | / | 0.453 | |
| 5ej8 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.453 | |
| 3img | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.452 | |
| 4do3 | 0LA | Fatty-acid amide hydrolase 1 | 3.5.1.99 | 0.452 | |
| 4l4a | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 2zkj | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.451 | |
| 3iw1 | ASD | Steroid C26-monooxygenase | 1.14.13.141 | 0.451 | |
| 3k4n | FAD | Pyranose 2-oxidase | / | 0.451 | |
| 3wrm | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.451 | |
| 4bf2 | STU | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.451 | |
| 4ce2 | BO5 | ATP-dependent molecular chaperone HSP82 | / | 0.451 | |
| 5eja | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.451 | |
| 1i5a | ACP | Chemotaxis protein CheA | 2.7.13.3 | 0.450 | |
| 1rrm | APR | Lactaldehyde reductase | 1.1.1.77 | 0.450 | |
| 3c50 | ADP | Rhodopsin kinase | / | 0.450 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.449 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.449 | |
| 2cgf | P2N | ATP-dependent molecular chaperone HSP82 | / | 0.448 | |
| 4nh9 | 2LC | Endoplasmin | / | 0.448 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.447 | |
| 3hek | BD0 | Heat shock protein HSP 90-alpha | / | 0.447 | |
| 3iph | G11 | Mitogen-activated protein kinase 14 | / | 0.447 | |
| 1ysz | NEC | Endoplasmin | / | 0.446 | |
| 2qfo | A51 | Heat shock protein HSP 90-alpha | / | 0.446 | |
| 2xx4 | 13I | ATP-dependent molecular chaperone HSP82 | / | 0.446 | |
| 6cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 1a27 | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.445 | |
| 2bu8 | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | 2.7.11.2 | 0.445 | |
| 3flz | FLZ | Mitogen-activated protein kinase 14 | / | 0.445 | |
| 3zbs | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.445 | |
| 4asg | 814 | ATP-dependent molecular chaperone HSP82 | / | 0.444 | |
| 1uy7 | PU4 | Heat shock protein HSP 90-alpha | / | 0.443 | |
| 2brc | CT5 | ATP-dependent molecular chaperone HSP82 | / | 0.443 | |
| 2bu2 | ATP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | 2.7.11.2 | 0.443 | |
| 3rlr | 3RR | Heat shock protein HSP 90-alpha | / | 0.443 | |
| 3wha | WHA | Heat shock protein HSP 90-alpha | / | 0.443 | |
| 1oir | HDY | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.442 | |
| 3tk3 | CPZ | Cytochrome P450 2B4 | 1.14.14.1 | 0.442 | |
| 4gb9 | 0WR | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.442 | |
| 1i5b | ANP | Chemotaxis protein CheA | 2.7.13.3 | 0.441 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.441 | |
| 2bri | ANP | Uridylate kinase | 2.7.4.22 | 0.441 | |
| 2e0a | ANP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.441 | |
| 2ivp | ATP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.441 | |
| 3clb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.441 | |
| 3iqh | TYR_ASP_ILE | Cysteine synthase | 2.5.1.47 | 0.441 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.441 | |
| 4gkv | NAD | Alcohol dehydrogenase, propanol-preferring | 1.1.1.1 | 0.441 | |
| 4l4x | NDP | AmphI | / | 0.441 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.441 | |
| 1mei | XMP | Inosine-5'-monophosphate dehydrogenase | / | 0.440 | |
| 1zth | ADP | RIO-type serine/threonine-protein kinase Rio1 | 2.7.11.1 | 0.440 | |
| 2c3q | GTX | Glutathione S-transferase theta-1 | 2.5.1.18 | 0.440 | |
| 2iwx | M1S | ATP-dependent molecular chaperone HSP82 | / | 0.440 | |
| 3f7b | AG5 | Carbonic anhydrase 4 | 4.2.1.1 | 0.440 | |
| 3k97 | 4CD | Heat shock protein HSP 90-alpha | / | 0.440 | |
| 4bcr | WY1 | Peroxisome proliferator-activated receptor alpha | / | 0.440 | |
| 4egn | TWO | Cytochrome P450 | / | 0.440 | |
| 4jd3 | COA | Alpha-pyrone synthesis polyketide synthase-like Pks11 | 2.3.1 | 0.440 | |
| 5ej6 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.440 | |
| 5fm7 | ADP | RuvB-like helicase | / | 0.440 |