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 |
|---|---|---|---|
| 2bu8 | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | 2.7.11.2 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site 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 | 0.599 | |
| 2bu2 | ATP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | 2.7.11.2 | 0.593 | |
| 2zdy | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.566 | |
| 2iwu | NP5 | ATP-dependent molecular chaperone HSP82 | / | 0.549 | |
| 4jql | VJ6 | Heat shock protein HSP 90-alpha | / | 0.537 | |
| 1byq | ADP | Heat shock protein HSP 90-alpha | / | 0.535 | |
| 2e0a | ANP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.535 | |
| 3t10 | ACP | Heat shock protein HSP 90-alpha | / | 0.532 | |
| 3d2r | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.528 | |
| 3t2s | AGS | Heat shock protein HSP 90-alpha | / | 0.528 | |
| 1gjv | AGS | [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial | 2.7.11.4 | 0.525 | |
| 3hhu | 819 | Heat shock protein HSP 90-alpha | / | 0.520 | |
| 4bqj | XKL | Heat shock protein HSP 90-alpha | / | 0.520 | |
| 2xk2 | ADP | Heat shock protein HSP 90-alpha | / | 0.516 | |
| 4xcj | ADP | Heat shock cognate 90 kDa protein | / | 0.514 | |
| 1qy8 | RDI | Endoplasmin | / | 0.513 | |
| 2yef | ANP | Heat shock protein HSP 90-alpha | / | 0.512 | |
| 4xcl | AGS | Heat shock cognate 90 kDa protein | / | 0.508 | |
| 2byh | 2D7 | Heat shock protein HSP 90-alpha | / | 0.507 | |
| 1i59 | ANP | Chemotaxis protein CheA | 2.7.13.3 | 0.506 | |
| 2qg0 | A94 | Heat shock protein HSP 90-alpha | / | 0.506 | |
| 2q8i | RDC | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 3, mitochondrial | 2.7.11.2 | 0.505 | |
| 2zkj | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.505 | |
| 3peh | IBD | Endoplasmin homolog, putative | / | 0.505 | |
| 2xx2 | 13C | ATP-dependent molecular chaperone HSP82 | / | 0.504 | |
| 3c11 | GDM | ATP-dependent molecular chaperone HSP82 | / | 0.504 | |
| 3ft8 | MOJ | Heat shock protein HSP 90-alpha | / | 0.504 | |
| 3q5l | KX2 | Heat shock protein 83-1 | / | 0.504 | |
| 4b7p | 9UN | Heat shock protein HSP 90-alpha | / | 0.503 | |
| 1uym | PU3 | Heat shock protein HSP 90-beta | / | 0.501 | |
| 1bgq | RDC | ATP-dependent molecular chaperone HSP82 | / | 0.500 | |
| 2gfd | RDA | Endoplasmin | / | 0.500 | |
| 1uy7 | PU4 | Heat shock protein HSP 90-alpha | / | 0.499 | |
| 2yee | 2EC | Heat shock protein HSP 90-alpha | / | 0.499 | |
| 4gqt | ADP | Heat shock protein 90 | / | 0.499 | |
| 3ekr | PY9 | Heat shock protein HSP 90-alpha | / | 0.498 | |
| 4as9 | 4QS | ATP-dependent molecular chaperone HSP82 | / | 0.498 | |
| 1qy5 | NEC | Endoplasmin | / | 0.497 | |
| 3qdd | 94M | Heat shock protein HSP 90-alpha | / | 0.497 | |
| 1uy8 | PU5 | Heat shock protein HSP 90-alpha | / | 0.494 | |
| 2hch | N5A | Endoplasmin | / | 0.493 | |
| 3vha | VHA | Heat shock protein HSP 90-alpha | / | 0.491 | |
| 1nhh | ANP | DNA mismatch repair protein MutL | / | 0.490 | |
| 1ysz | NEC | Endoplasmin | / | 0.490 | |
| 2vwc | BC2 | ATP-dependent molecular chaperone HSP82 | / | 0.490 | |
| 2yeg | XQG | Heat shock protein HSP 90-alpha | / | 0.490 | |
| 4efu | EFU | Heat shock protein HSP 90-alpha | / | 0.490 | |
| 2byi | 2DD | Heat shock protein HSP 90-alpha | / | 0.487 | |
| 1amw | ADP | ATP-dependent molecular chaperone HSP82 | / | 0.486 | |
| 1yet | GDM | Heat shock protein HSP 90-alpha | / | 0.486 | |
| 1i58 | ADP | Chemotaxis protein CheA | 2.7.13.3 | 0.485 | |
| 2wep | ADP | ATP-dependent molecular chaperone HSP82 | / | 0.485 | |
| 2fyp | RDE | Endoplasmin | / | 0.484 | |
| 3k97 | 4CD | Heat shock protein HSP 90-alpha | / | 0.484 | |
| 4zoh | FAD | Putative oxidoreductase FAD-binding subunit | / | 0.484 | |
| 1uyi | PUZ | Heat shock protein HSP 90-alpha | / | 0.483 | |
| 3rlq | 3RQ | Heat shock protein HSP 90-alpha | / | 0.483 | |
| 4asg | 814 | ATP-dependent molecular chaperone HSP82 | / | 0.483 | |
| 1uye | PU9 | Heat shock protein HSP 90-alpha | / | 0.481 | |
| 2fxs | RDA | ATP-dependent molecular chaperone HSP82 | / | 0.481 | |
| 2vw5 | BC6 | ATP-dependent molecular chaperone HSP82 | / | 0.481 | |
| 2xd6 | XD6 | ATP-dependent molecular chaperone HSP82 | / | 0.481 | |
| 3r4p | FU7 | Heat shock protein HSP 90-alpha | / | 0.481 | |
| 3t0z | ATP | Heat shock protein HSP 90-alpha | / | 0.481 | |
| 1yc3 | 4BC | Heat shock protein HSP 90-alpha | / | 0.480 | |
| 2fwz | H71 | Heat shock protein HSP 90-alpha | / | 0.480 | |
| 4ivg | ANP | TNF receptor-associated protein 1 | / | 0.480 | |
| 3hz1 | 42C | Heat shock protein HSP 90-alpha | / | 0.477 | |
| 3r4o | FU3 | Heat shock protein HSP 90-alpha | / | 0.477 | |
| 5f5r | ANP | Heat shock protein 75 kDa, mitochondrial | / | 0.477 | |
| 3h4l | ANP | DNA mismatch repair protein PMS1 | / | 0.476 | |
| 2zdx | P4A | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.475 | |
| 2gqp | PA7 | Endoplasmin | / | 0.474 | |
| 2xcm | ADP | Cytosolic heat shock protein 90 | / | 0.474 | |
| 3hyz | 42C | Heat shock protein HSP 90-alpha | / | 0.473 | |
| 1i58 | ACP | Chemotaxis protein CheA | 2.7.13.3 | 0.472 | |
| 1uy6 | PU3 | Heat shock protein HSP 90-alpha | / | 0.472 | |
| 3cuk | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.472 | |
| 4xc0 | ACP | Heat shock cognate 90 kDa protein | / | 0.472 | |
| 2h55 | DZ8 | Heat shock protein HSP 90-alpha | / | 0.471 | |
| 3t1k | ANP | Heat shock protein HSP 90-alpha | / | 0.471 | |
| 4egi | B2J | Heat shock protein HSP 90-alpha | / | 0.471 | |
| 4mp7 | PFT | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | 2.7.11.2 | 0.470 | |
| 2bz5 | AB4 | Heat shock protein HSP 90-alpha | / | 0.469 | |
| 1am1 | ADP | ATP-dependent molecular chaperone HSP82 | / | 0.468 | |
| 3inx | JZC | Heat shock protein HSP 90-alpha | / | 0.468 | |
| 4ce2 | BO5 | ATP-dependent molecular chaperone HSP82 | / | 0.467 | |
| 2brc | CT5 | ATP-dependent molecular chaperone HSP82 | / | 0.466 | |
| 3hz5 | Z64 | Heat shock protein HSP 90-alpha | / | 0.466 | |
| 1uy9 | PU6 | Heat shock protein HSP 90-alpha | / | 0.465 | |
| 1yc1 | 4BC | Heat shock protein HSP 90-alpha | / | 0.465 | |
| 2o1u | ANP | Endoplasmin | / | 0.465 | |
| 2yke | YKE | Heat shock protein HSP 90-alpha | / | 0.465 | |
| 4asf | 62U | ATP-dependent molecular chaperone HSP82 | / | 0.465 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.464 | |
| 3pju | C2E | Diguanylate cyclase/phosphodiesterase | / | 0.464 | |
| 4fcr | 0TM | Heat shock protein HSP 90-alpha | / | 0.464 | |
| 1uyk | PUX | Heat shock protein HSP 90-alpha | / | 0.463 | |
| 2iws | NP4 | ATP-dependent molecular chaperone HSP82 | / | 0.463 | |
| 3o0i | P54 | Heat shock protein HSP 90-alpha | / | 0.463 | |
| 2wer | RDC | ATP-dependent molecular chaperone HSP82 | / | 0.462 | |
| 4bqg | 50Q | Heat shock protein HSP 90-alpha | / | 0.462 | |
| 2bre | KJ2 | ATP-dependent molecular chaperone HSP82 | / | 0.461 | |
| 2yei | XQI | Heat shock protein HSP 90-alpha | / | 0.461 | |
| 1u2o | NEC | Endoplasmin | / | 0.459 | |
| 2esa | GDM | Endoplasmin | / | 0.459 | |
| 3b28 | B2X | Heat shock protein HSP 90-alpha | / | 0.459 | |
| 4riy | ADP | Epidermal growth factor receptor | 2.7.10.1 | 0.459 | |
| 3rlr | 3RR | Heat shock protein HSP 90-alpha | / | 0.458 | |
| 1psd | NAD | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.457 | |
| 1u0z | RDC | Endoplasmin | / | 0.457 | |
| 1uyd | PU8 | Heat shock protein HSP 90-alpha | / | 0.457 | |
| 2xhr | C0P | Heat shock protein HSP 90-alpha | / | 0.456 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.456 | |
| 1i5b | ANP | Chemotaxis protein CheA | 2.7.13.3 | 0.455 | |
| 1jm6 | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | 2.7.11.2 | 0.455 | |
| 2vcj | 2EQ | Heat shock protein HSP 90-alpha | / | 0.455 | |
| 2hg1 | N5O | Endoplasmin | / | 0.454 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.453 | |
| 3wha | WHA | Heat shock protein HSP 90-alpha | / | 0.453 | |
| 1qrr | UPG | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.452 | |
| 2xx4 | 13I | ATP-dependent molecular chaperone HSP82 | / | 0.452 | |
| 1y4s | ADP | Chaperone protein HtpG | / | 0.451 | |
| 4zas | TYD | CalS13 | / | 0.451 | |
| 1uyf | PU1 | Heat shock protein HSP 90-alpha | / | 0.450 | |
| 2fwy | H64 | Heat shock protein HSP 90-alpha | / | 0.450 | |
| 3tm5 | SFG | Uncharacterized protein | / | 0.450 | |
| 4ce3 | L4V | ATP-dependent molecular chaperone HSP82 | / | 0.450 | |
| 2exl | GDM | Endoplasmin | / | 0.449 | |
| 3zew | STU | Ephrin type-B receptor 4 | 2.7.10.1 | 0.448 | |
| 1uyc | PU7 | Heat shock protein HSP 90-alpha | / | 0.447 | |
| 1v9a | SAH | Uncharacterized protein | / | 0.447 | |
| 1yt0 | ADP | Endoplasmin | / | 0.447 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 2ch6 | ADP | N-acetyl-D-glucosamine kinase | 2.7.1.59 | 0.447 | |
| 3ied | AN2 | HSP90 | / | 0.447 | |
| 3q5k | D1U | Heat shock protein 83-1 | / | 0.447 | |
| 1zrz | BI1 | Protein kinase C iota type | 2.7.11.13 | 0.446 | |
| 2bt0 | CT5 | Heat shock protein HSP 90-alpha | / | 0.446 | |
| 2h8h | H8H | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.446 | |
| 3ge1 | ADP | Glycerol kinase | / | 0.446 | |
| 4anw | O92 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.446 | |
| 1e5q | NDP | Saccharopine dehydrogenase [NADP(+), L-glutamate-forming] | 1.5.1.10 | 0.445 | |
| 3u9n | 09H | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.445 | |
| 4f9m | FCM | Peroxisome proliferator-activated receptor gamma | / | 0.445 | |
| 2gn9 | UPG | UDP-N-acetylglucosamine 4,6-dehydratase (inverting) | 4.2.1.115 | 0.444 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.444 | |
| 2xab | VHD | Heat shock protein HSP 90-alpha | / | 0.444 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.444 | |
| 3r4n | FU5 | Heat shock protein HSP 90-alpha | / | 0.444 | |
| 4ce1 | 7FK | ATP-dependent molecular chaperone HSP82 | / | 0.444 | |
| 4pl9 | ADP | Ethylene receptor 1 | / | 0.444 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.443 | |
| 3frq | ERY | Erythromycin resistance repressor protein | / | 0.443 | |
| 3o6o | 94M | Heat shock protein 83 | / | 0.443 | |
| 3vs2 | VSB | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.443 | |
| 3vs3 | VSE | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.443 | |
| 1i5c | ADP | Chemotaxis protein CheA | 2.7.13.3 | 0.442 | |
| 2pmd | GNP | Translation initiation factor 2 subunit gamma | / | 0.442 | |
| 3tqh | NDP | Quinone oxidoreductase | / | 0.442 | |
| 5awm | ANP | Stress-activated protein kinase JNK | 2.7.11.24 | 0.442 | |
| 5eox | ADP | Type 4 fimbrial biogenesis protein PilM | / | 0.442 | |
| 1qvr | ANP | Chaperone protein ClpB | / | 0.441 | |
| 1z59 | ADP | Type 2 DNA topoisomerase 6 subunit B | / | 0.441 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.441 | |
| 3pej | BC2 | Endoplasmin homolog, putative | / | 0.441 | |
| 3te4 | ACO | Dopamine N-acetyltransferase | / | 0.441 | |
| 4nh8 | 2LC | Heat shock protein HSP 90-alpha | / | 0.441 | |
| 2ykj | YKJ | Heat shock protein HSP 90-alpha | / | 0.440 |