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 |
|---|---|---|---|
| 1yt0 | ADP | Endoplasmin |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1yt0 | ADP | Endoplasmin | / | 1.000 | |
| 2xx2 | 13C | ATP-dependent molecular chaperone HSP82 | / | 0.554 | |
| 3t0z | ATP | Heat shock protein HSP 90-alpha | / | 0.550 | |
| 2fxs | RDA | ATP-dependent molecular chaperone HSP82 | / | 0.538 | |
| 2gqp | PA7 | Endoplasmin | / | 0.538 | |
| 4gqt | ADP | Heat shock protein 90 | / | 0.531 | |
| 1osf | KOS | Heat shock protein HSP 90-alpha | / | 0.529 | |
| 2yef | ANP | Heat shock protein HSP 90-alpha | / | 0.529 | |
| 3t2s | AGS | Heat shock protein HSP 90-alpha | / | 0.529 | |
| 1bgq | RDC | ATP-dependent molecular chaperone HSP82 | / | 0.528 | |
| 1byq | ADP | Heat shock protein HSP 90-alpha | / | 0.526 | |
| 2xk2 | ADP | Heat shock protein HSP 90-alpha | / | 0.526 | |
| 3t1k | ANP | Heat shock protein HSP 90-alpha | / | 0.524 | |
| 1u2o | NEC | Endoplasmin | / | 0.521 | |
| 2hch | N5A | Endoplasmin | / | 0.519 | |
| 2o1u | ANP | Endoplasmin | / | 0.519 | |
| 3t10 | ACP | Heat shock protein HSP 90-alpha | / | 0.519 | |
| 3ekr | PY9 | Heat shock protein HSP 90-alpha | / | 0.518 | |
| 2gfd | RDA | Endoplasmin | / | 0.517 | |
| 4ivg | ANP | TNF receptor-associated protein 1 | / | 0.515 | |
| 4jql | VJ6 | Heat shock protein HSP 90-alpha | / | 0.511 | |
| 2yeg | XQG | Heat shock protein HSP 90-alpha | / | 0.509 | |
| 4ipe | ANP | TNF receptor-associated protein 1 | / | 0.509 | |
| 1u0z | RDC | Endoplasmin | / | 0.508 | |
| 3rlq | 3RQ | Heat shock protein HSP 90-alpha | / | 0.507 | |
| 4xcj | ADP | Heat shock cognate 90 kDa protein | / | 0.506 | |
| 2vw5 | BC6 | ATP-dependent molecular chaperone HSP82 | / | 0.502 | |
| 1yc3 | 4BC | Heat shock protein HSP 90-alpha | / | 0.500 | |
| 2byh | 2D7 | Heat shock protein HSP 90-alpha | / | 0.499 | |
| 2hg1 | N5O | Endoplasmin | / | 0.499 | |
| 4xc0 | ACP | Heat shock cognate 90 kDa protein | / | 0.499 | |
| 4bqj | XKL | Heat shock protein HSP 90-alpha | / | 0.498 | |
| 3hyz | 42C | Heat shock protein HSP 90-alpha | / | 0.496 | |
| 3ied | AN2 | HSP90 | / | 0.496 | |
| 1amw | ADP | ATP-dependent molecular chaperone HSP82 | / | 0.494 | |
| 1qy5 | NEC | Endoplasmin | / | 0.494 | |
| 2o1v | ADP | Endoplasmin | / | 0.493 | |
| 5f5r | ANP | Heat shock protein 75 kDa, mitochondrial | / | 0.493 | |
| 1y4s | ADP | Chaperone protein HtpG | / | 0.490 | |
| 2byi | 2DD | Heat shock protein HSP 90-alpha | / | 0.489 | |
| 2bre | KJ2 | ATP-dependent molecular chaperone HSP82 | / | 0.488 | |
| 2xab | VHD | Heat shock protein HSP 90-alpha | / | 0.488 | |
| 1qy8 | RDI | Endoplasmin | / | 0.487 | |
| 2fyp | RDE | Endoplasmin | / | 0.487 | |
| 2qg0 | A94 | Heat shock protein HSP 90-alpha | / | 0.487 | |
| 2xht | C0Y | Heat shock protein HSP 90-alpha | / | 0.486 | |
| 3d2r | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.486 | |
| 1yc1 | 4BC | Heat shock protein HSP 90-alpha | / | 0.485 | |
| 3r4n | FU5 | Heat shock protein HSP 90-alpha | / | 0.484 | |
| 2exl | GDM | Endoplasmin | / | 0.483 | |
| 3c11 | GDM | ATP-dependent molecular chaperone HSP82 | / | 0.483 | |
| 1i5b | ANP | Chemotaxis protein CheA | 2.7.13.3 | 0.481 | |
| 2wer | RDC | ATP-dependent molecular chaperone HSP82 | / | 0.481 | |
| 2xcm | ADP | Cytosolic heat shock protein 90 | / | 0.481 | |
| 4ce1 | 7FK | ATP-dependent molecular chaperone HSP82 | / | 0.481 | |
| 1z59 | ADP | Type 2 DNA topoisomerase 6 subunit B | / | 0.480 | |
| 1yet | GDM | Heat shock protein HSP 90-alpha | / | 0.479 | |
| 3hhu | 819 | Heat shock protein HSP 90-alpha | / | 0.479 | |
| 4fcr | 0TM | Heat shock protein HSP 90-alpha | / | 0.479 | |
| 3h4l | ANP | DNA mismatch repair protein PMS1 | / | 0.477 | |
| 3vha | VHA | Heat shock protein HSP 90-alpha | / | 0.477 | |
| 1krh | FAD | Benzoate 1,2-dioxygenase electron transfer component | 1.18.1.3 | 0.475 | |
| 2bt0 | CT5 | Heat shock protein HSP 90-alpha | / | 0.474 | |
| 1am1 | ADP | ATP-dependent molecular chaperone HSP82 | / | 0.472 | |
| 2iws | NP4 | ATP-dependent molecular chaperone HSP82 | / | 0.472 | |
| 3r4o | FU3 | Heat shock protein HSP 90-alpha | / | 0.472 | |
| 4eft | EFT | Heat shock protein HSP 90-alpha | / | 0.472 | |
| 2esa | GDM | Endoplasmin | / | 0.471 | |
| 2wep | ADP | ATP-dependent molecular chaperone HSP82 | / | 0.471 | |
| 2ylz | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.471 | |
| 1u0y | PA7 | Endoplasmin | / | 0.470 | |
| 2qfo | A13 | Heat shock protein HSP 90-alpha | / | 0.470 | |
| 4egi | B2J | Heat shock protein HSP 90-alpha | / | 0.469 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.466 | |
| 3iod | A6D | Pantothenate synthetase | 6.3.2.1 | 0.466 | |
| 4egk | RDC | Heat shock protein HSP 90-alpha | / | 0.466 | |
| 4fc0 | 0T2 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.465 | |
| 1uyk | PUX | Heat shock protein HSP 90-alpha | / | 0.464 | |
| 4as9 | 4QS | ATP-dependent molecular chaperone HSP82 | / | 0.464 | |
| 2iwu | NP5 | ATP-dependent molecular chaperone HSP82 | / | 0.463 | |
| 4bqg | 50Q | Heat shock protein HSP 90-alpha | / | 0.463 | |
| 4ce2 | BO5 | ATP-dependent molecular chaperone HSP82 | / | 0.463 | |
| 4xcl | AGS | Heat shock cognate 90 kDa protein | / | 0.463 | |
| 3r4p | FU7 | Heat shock protein HSP 90-alpha | / | 0.462 | |
| 4xdm | GDM | Heat shock cognate 90 kDa protein | / | 0.462 | |
| 1fnn | ADP | ORC1-type DNA replication protein | / | 0.461 | |
| 1i5a | ACP | Chemotaxis protein CheA | 2.7.13.3 | 0.461 | |
| 2ivp | ATP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.461 | |
| 3c0g | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.460 | |
| 5c93 | ACP | Two-component system histidine protein kinase | / | 0.460 | |
| 1ysz | NEC | Endoplasmin | / | 0.459 | |
| 4s26 | SAH | Phosphomethylpyrimidine synthase, chloroplastic | 4.1.99.17 | 0.459 | |
| 1p0h | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.458 | |
| 2xx4 | 13I | ATP-dependent molecular chaperone HSP82 | / | 0.458 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.457 | |
| 2bu8 | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | 2.7.11.2 | 0.456 | |
| 3d4p | NAD | L-lactate dehydrogenase 1 | 1.1.1.27 | 0.456 | |
| 3rlr | 3RR | Heat shock protein HSP 90-alpha | / | 0.456 | |
| 4asg | 814 | ATP-dependent molecular chaperone HSP82 | / | 0.456 | |
| 1uy7 | PU4 | Heat shock protein HSP 90-alpha | / | 0.455 | |
| 2brc | CT5 | ATP-dependent molecular chaperone HSP82 | / | 0.455 | |
| 2c3q | GTX | Glutathione S-transferase theta-1 | 2.5.1.18 | 0.455 | |
| 2ior | ADP | Chaperone protein HtpG | / | 0.455 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.455 | |
| 3crl | ANP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | 2.7.11.2 | 0.455 | |
| 3k97 | 4CD | Heat shock protein HSP 90-alpha | / | 0.455 | |
| 2bu2 | ATP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | 2.7.11.2 | 0.454 | |
| 2zkj | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.454 | |
| 3wha | WHA | Heat shock protein HSP 90-alpha | / | 0.454 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.454 | |
| 3iph | G11 | Mitogen-activated protein kinase 14 | / | 0.453 | |
| 3ngu | ADP | Nucleoside diphosphate kinase | / | 0.453 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.453 | |
| 2cgf | P2N | ATP-dependent molecular chaperone HSP82 | / | 0.452 | |
| 2xd6 | XD6 | ATP-dependent molecular chaperone HSP82 | / | 0.452 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.452 | |
| 2vnh | FAD | NADPH:ferredoxin reductase | / | 0.451 | |
| 3hek | BD0 | Heat shock protein HSP 90-alpha | / | 0.451 | |
| 3hz5 | Z64 | Heat shock protein HSP 90-alpha | / | 0.451 | |
| 3o0i | P54 | Heat shock protein HSP 90-alpha | / | 0.451 | |
| 1xq6 | NAP | Uncharacterized protein At5g02240 | / | 0.450 | |
| 2e0a | ANP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.450 | |
| 2fwy | H64 | Heat shock protein HSP 90-alpha | / | 0.450 | |
| 3kq7 | KQ7 | Mitogen-activated protein kinase 14 | / | 0.450 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.450 | |
| 4y93 | 746 | Tyrosine-protein kinase | / | 0.450 | |
| 3coy | 53H | Pantothenate synthetase | 6.3.2.1 | 0.449 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.449 | |
| 4nmj | NAP | Aldehyde dehydrogenase | / | 0.449 | |
| 1uye | PU9 | Heat shock protein HSP 90-alpha | / | 0.448 | |
| 2bz5 | AB4 | Heat shock protein HSP 90-alpha | / | 0.448 | |
| 3peh | IBD | Endoplasmin homolog, putative | / | 0.448 | |
| 4do3 | 0LA | Fatty-acid amide hydrolase 1 | 3.5.1.99 | 0.448 | |
| 4xj3 | GTP | Cyclic GMP-AMP synthase | / | 0.448 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.447 | |
| 3ft8 | MOJ | Heat shock protein HSP 90-alpha | / | 0.447 | |
| 1rrm | APR | Lactaldehyde reductase | 1.1.1.77 | 0.446 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.446 | |
| 2wi6 | ZZ6 | Heat shock protein HSP 90-alpha | / | 0.446 | |
| 3frq | ERY | Erythromycin resistance repressor protein | / | 0.446 | |
| 3pgq | GY3 | Acetyl-CoA carboxylase | / | 0.446 | |
| 1uym | PU3 | Heat shock protein HSP 90-beta | / | 0.445 | |
| 2w3b | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 3crz | FAD | Ferredoxin--NADP+ reductase | / | 0.445 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.445 | |
| 4ge7 | 0K5 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.445 | |
| 4gkv | NAD | Alcohol dehydrogenase, propanol-preferring | 1.1.1.1 | 0.445 | |
| 1ot7 | IU5 | Bile acid receptor | / | 0.444 | |
| 2q59 | 240 | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 2yxu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.444 | |
| 3b28 | B2X | Heat shock protein HSP 90-alpha | / | 0.444 | |
| 3m6i | NAD | L-arabinitol 4-dehydrogenase | 1.1.1.12 | 0.444 | |
| 3zbs | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.444 | |
| 4g2r | H1L | Probable propionyl-CoA carboxylase beta chain 6 | 6.4.1.3 | 0.444 | |
| 4jin | 1L7 | RIO-type serine/threonine-protein kinase Rio1 | 2.7.11.1 | 0.444 | |
| 4nh9 | 2LC | Endoplasmin | / | 0.444 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.444 | |
| 1esv | LAR | Actin, alpha skeletal muscle | / | 0.443 | |
| 1i59 | ANP | Chemotaxis protein CheA | 2.7.13.3 | 0.443 | |
| 2wi5 | ZZ5 | Heat shock protein HSP 90-alpha | / | 0.443 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.443 | |
| 3hz1 | 42C | Heat shock protein HSP 90-alpha | / | 0.443 | |
| 3kpk | FAD | Sulfide-quinone reductase | / | 0.443 | |
| 4dja | FAD | (6-4) photolyase | / | 0.443 | |
| 4z34 | ON7 | Lysophosphatidic acid receptor 1 | / | 0.443 | |
| 1rby | KEU | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.442 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.442 | |
| 2i4j | DRJ | Peroxisome proliferator-activated receptor gamma | / | 0.442 | |
| 2jam | J60 | Calcium/calmodulin-dependent protein kinase type 1G | 2.7.11.17 | 0.442 | |
| 4a9m | P9M | Bromodomain-containing protein 2 | / | 0.442 | |
| 1jio | DEB | 6-deoxyerythronolide B hydroxylase | / | 0.441 | |
| 1k7f | IAV | Tryptophan synthase alpha chain | / | 0.441 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.441 | |
| 1xaj | NAD | 3-dehydroquinate synthase | / | 0.441 | |
| 1ydr | IQP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.441 | |
| 2bxo | OPB | Serum albumin | / | 0.441 | |
| 3bbt | FMM | Receptor tyrosine-protein kinase erbB-4 | 2.7.10.1 | 0.441 | |
| 4fcw | ADP | Chaperone protein ClpB | / | 0.441 | |
| 4wdg | A2P | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.441 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.440 | |
| 2ovh | AS0 | Progesterone receptor | / | 0.440 | |
| 2vwc | BC2 | ATP-dependent molecular chaperone HSP82 | / | 0.440 | |
| 2vwq | NAP | Glucose 1-dehydrogenase | / | 0.440 | |
| 3d0b | SNX | Heat shock protein HSP 90-alpha | / | 0.440 | |
| 3eko | PYU | Heat shock protein HSP 90-alpha | / | 0.440 | |
| 4asf | 62U | ATP-dependent molecular chaperone HSP82 | / | 0.440 | |
| 4bcr | WY1 | Peroxisome proliferator-activated receptor alpha | / | 0.440 | |
| 4y95 | 746 | Tyrosine-protein kinase | / | 0.440 |