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 |
|---|---|---|---|
| 3d5f | L41 | Peroxisome proliferator-activated receptor delta |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3d5f | L41 | Peroxisome proliferator-activated receptor delta | / | 1.000 | |
| 1knu | YPA | Peroxisome proliferator-activated receptor gamma | / | 0.566 | |
| 1rdt | 570 | Peroxisome proliferator-activated receptor gamma | / | 0.556 | |
| 2hwr | DRD | Peroxisome proliferator-activated receptor gamma | / | 0.556 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.553 | |
| 2j14 | GNI | Peroxisome proliferator-activated receptor delta | / | 0.552 | |
| 3vjh | J35 | Peroxisome proliferator-activated receptor gamma | / | 0.548 | |
| 1zeo | C01 | Peroxisome proliferator-activated receptor gamma | / | 0.547 | |
| 2rew | REW | Peroxisome proliferator-activated receptor alpha | / | 0.539 | |
| 3vsp | EK8 | Peroxisome proliferator-activated receptor gamma | / | 0.539 | |
| 2i4j | DRJ | Peroxisome proliferator-activated receptor gamma | / | 0.532 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.527 | |
| 3gbk | 2PQ | Peroxisome proliferator-activated receptor gamma | / | 0.522 | |
| 1fm9 | 570 | Peroxisome proliferator-activated receptor gamma | / | 0.520 | |
| 2om9 | AJA | Peroxisome proliferator-activated receptor gamma | / | 0.520 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.517 | |
| 2pob | GW4 | Peroxisome proliferator-activated receptor gamma | / | 0.515 | |
| 2q8s | L92 | Peroxisome proliferator-activated receptor gamma | / | 0.515 | |
| 1nyx | DRF | Peroxisome proliferator-activated receptor gamma | / | 0.512 | |
| 3vn2 | TLS | Peroxisome proliferator-activated receptor gamma | / | 0.512 | |
| 4f9m | FCM | Peroxisome proliferator-activated receptor gamma | / | 0.512 | |
| 2i4z | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.511 | |
| 2zno | S44 | Peroxisome proliferator-activated receptor gamma | / | 0.511 | |
| 2i4p | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.509 | |
| 2npa | MMB | Peroxisome proliferator-activated receptor alpha | / | 0.508 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.507 | |
| 1db1 | VDX | Vitamin D3 receptor | / | 0.500 | |
| 3ua5 | 06X | Cytochrome P450 2B6 | 1.14.13 | 0.500 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.496 | |
| 1i7i | AZ2 | Peroxisome proliferator-activated receptor gamma | / | 0.493 | |
| 3sp6 | IL2 | Peroxisome proliferator-activated receptor alpha | / | 0.493 | |
| 1fm6 | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.491 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.490 | |
| 2has | C3O | Vitamin D3 receptor | / | 0.489 | |
| 3v9y | 24L | Peroxisome proliferator-activated receptor gamma | / | 0.489 | |
| 1zgy | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.488 | |
| 2hfp | NSI | Peroxisome proliferator-activated receptor gamma | / | 0.488 | |
| 3vso | EK1 | Peroxisome proliferator-activated receptor gamma | / | 0.487 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.487 | |
| 3bej | MUF | Bile acid receptor | / | 0.481 | |
| 4hee | 14R | Peroxisome proliferator-activated receptor gamma | / | 0.481 | |
| 1iwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.480 | |
| 1og5 | SWF | Cytochrome P450 2C9 | / | 0.480 | |
| 3a0i | AJI | Glucokinase | 2.7.1.2 | 0.480 | |
| 2o4r | VD5 | Vitamin D3 receptor | / | 0.478 | |
| 1s19 | MC9 | Vitamin D3 receptor | / | 0.477 | |
| 4fhi | 0S4 | Vitamin D3 receptor A | / | 0.477 | |
| 3vt3 | VDX | Vitamin D3 receptor | / | 0.476 | |
| 1k74 | 544 | Peroxisome proliferator-activated receptor gamma | / | 0.475 | |
| 2q61 | SF1 | Peroxisome proliferator-activated receptor gamma | / | 0.475 | |
| 3vrv | YSD | Vitamin D3 receptor | / | 0.475 | |
| 1rkg | VD1 | Vitamin D3 receptor | / | 0.474 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.473 | |
| 3cpp | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.473 | |
| 3fwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.473 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.472 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.472 | |
| 3h1v | TK1 | Glucokinase | 2.7.1.2 | 0.472 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.472 | |
| 4fhh | 0U3 | Vitamin D3 receptor A | / | 0.472 | |
| 2hb7 | O1C | Vitamin D3 receptor | / | 0.471 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.471 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.471 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.470 | |
| 1iwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.470 | |
| 2p4y | C03 | Peroxisome proliferator-activated receptor gamma | / | 0.470 | |
| 3vru | YS3 | Vitamin D3 receptor | / | 0.469 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.469 | |
| 3tnl | NAD | Shikimate dehydrogenase (NADP(+)) | / | 0.468 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.468 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.468 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.467 | |
| 1rjk | VDZ | Vitamin D3 receptor | / | 0.467 | |
| 2har | OCC | Vitamin D3 receptor | / | 0.466 | |
| 2o4j | VD4 | Vitamin D3 receptor | / | 0.466 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.466 | |
| 4l4a | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.466 | |
| 4o8f | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.466 | |
| 2c3q | GTX | Glutathione S-transferase theta-1 | 2.5.1.18 | 0.465 | |
| 3tmz | 06X | Cytochrome P450 2B4 | 1.14.14.1 | 0.465 | |
| 4y8w | STR | Steroid 21-hydroxylase | / | 0.465 | |
| 1w2x | RCP | Acetyl-CoA carboxylase | / | 0.464 | |
| 3ruk | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.464 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.464 | |
| 2zlc | VDX | Vitamin D3 receptor | / | 0.463 | |
| 4l49 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.463 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.462 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.462 | |
| 2q5p | 241 | Peroxisome proliferator-activated receptor gamma | / | 0.462 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.462 | |
| 4iui | 1GQ | Estrogen receptor | / | 0.462 | |
| 3klj | FAD | NADH-rubredoxin oxidoreductase | 1.18.1.1 | 0.461 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.461 | |
| 4jbt | ASD | Cytochrome P450 monooxygenase | / | 0.461 | |
| 4l4b | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.461 | |
| 4nky | 3QZ | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.461 | |
| 1rk3 | VDX | Vitamin D3 receptor | / | 0.460 | |
| 1s0z | EB1 | Vitamin D3 receptor | / | 0.460 | |
| 2qo4 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.460 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 4awq | 592 | Heat shock protein HSP 90-alpha | / | 0.460 | |
| 6cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.460 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.459 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.459 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.459 | |
| 1ie9 | VDX | Vitamin D3 receptor | / | 0.458 | |
| 2vzm | NRB | Cytochrome P450 monooxygenase PikC | / | 0.458 | |
| 3h0a | 9RA | Retinoic acid receptor RXR-alpha | / | 0.458 | |
| 3vt4 | 5YI | Vitamin D3 receptor | / | 0.458 | |
| 4h3c | 0YZ | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.458 | |
| 4i8v | BHF | Cytochrome P450 1A1 | 1.14.14.1 | 0.458 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.458 | |
| 4q0a | 4OA | Vitamin D3 receptor A | / | 0.458 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 2go4 | TUX | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.457 | |
| 3stv | 3HO | Methylketone synthase I | / | 0.457 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.457 | |
| 5hs1 | VOR | Lanosterol 14-alpha demethylase | / | 0.457 | |
| 2aqk | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.456 | |
| 2hb8 | MVD | Vitamin D3 receptor | / | 0.456 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.456 | |
| 3m7r | VDX | Vitamin D3 receptor | / | 0.456 | |
| 4wa9 | AXI | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.456 | |
| 2z97 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.455 | |
| 3vtc | TK3 | Vitamin D3 receptor | / | 0.455 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 1w06 | W05 | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 2ieb | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.454 | |
| 3cyz | 9OD | Pheromone-binding protein ASP1 | / | 0.454 | |
| 3w0i | O11 | Vitamin D3 receptor | / | 0.454 | |
| 4g3r | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.454 | |
| 4v12 | POG | MaoC like domain protein | / | 0.454 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 2rhg | IGP | Tryptophan synthase alpha chain | / | 0.453 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.453 | |
| 3tk3 | CPZ | Cytochrome P450 2B4 | 1.14.14.1 | 0.453 | |
| 4gyz | D5M | Tyrosyl-DNA phosphodiesterase 2 | 3.1.4 | 0.453 | |
| 4j6b | PLO | Cytochrome P450 monooxygenase | / | 0.453 | |
| 4lb2 | DM5 | Serum albumin | / | 0.453 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.453 | |
| 4ryv | ZEA | Protein LlR18A | / | 0.453 | |
| 4xuh | SFI | Peroxisome proliferator-activated receptor gamma | / | 0.453 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 2uxi | G50 | HTH-type transcriptional regulator TtgR | / | 0.452 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.452 | |
| 2zl9 | VDA | Vitamin D3 receptor | / | 0.452 | |
| 3a9w | NAD | NDP-sugar epimerase | / | 0.452 | |
| 4xld | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.452 | |
| 3vtb | TKA | Vitamin D3 receptor | / | 0.451 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 4a4v | YFD | Peroxisome proliferator-activated receptor gamma | / | 0.451 | |
| 1t88 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.450 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 4ejg | NCT | Cytochrome P450 2A13 | 1.14.14.1 | 0.450 | |
| 4qe6 | JN3 | Bile acid receptor | / | 0.450 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 2pg0 | FAD | Acyl-CoA dehydrogenase | / | 0.449 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 3v9v | 21L | Peroxisome proliferator-activated receptor gamma | / | 0.449 | |
| 4dhy | S41 | Glucokinase | 2.7.1.2 | 0.449 | |
| 4l4c | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 1dr3 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.448 | |
| 1r9o | FLP | Cytochrome P450 2C9 | / | 0.448 | |
| 2ca0 | PXI | Cytochrome P450 monooxygenase PikC | / | 0.448 | |
| 2zla | VDB | Vitamin D3 receptor | / | 0.448 | |
| 3abi | NAD | Uncharacterized protein | / | 0.448 | |
| 3mdv | CL6 | Cholesterol 24-hydroxylase | / | 0.448 | |
| 3vev | 0H4 | Glucokinase | 2.7.1.2 | 0.448 | |
| 3w0c | 6DS | Vitamin D3 receptor | / | 0.448 | |
| 4g20 | 484 | Vitamin D3 receptor A | / | 0.448 | |
| 4l4d | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.448 | |
| 4rup | H97 | Vitamin D3 receptor A | / | 0.448 | |
| 4ubs | DIF | Pentalenic acid synthase | 1.14.15.11 | 0.448 | |
| 1dz4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 1xuo | LA1 | Integrin alpha-L | / | 0.447 | |
| 2c7x | NRB | Cytochrome P450 monooxygenase PikC | / | 0.447 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.447 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 2ykc | YKC | Heat shock protein HSP 90-alpha | / | 0.447 | |
| 3stx | BKA | Methylketone synthase I | / | 0.447 | |
| 3sz0 | FAD | Sulfide-quinone reductase | / | 0.447 | |
| 4ema | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.447 | |
| 5cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.446 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 1v59 | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.445 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.445 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.445 | |
| 3gob | HXX | DdmC | / | 0.445 | |
| 3inw | JZB | Heat shock protein HSP 90-alpha | / | 0.445 | |
| 3kjm | 245 | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.445 | |
| 3vt6 | 5YI | Vitamin D3 receptor | / | 0.445 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.445 | |
| 4l8u | 9AZ | Serum albumin | / | 0.445 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 1soz | VAL_TYR_GLN_PHE | Serine endoprotease DegS | 3.4.21.107 | 0.444 | |
| 2acw | UPG | Glycosyltransferase | / | 0.444 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 2ykj | YKJ | Heat shock protein HSP 90-alpha | / | 0.444 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.444 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.444 | |
| 3eon | 341 | Glutaryl-CoA dehydrogenase | / | 0.444 | |
| 3id8 | MRK | Glucokinase | 2.7.1.2 | 0.444 | |
| 3vrt | YS2 | Vitamin D3 receptor | / | 0.444 | |
| 3w0g | W07 | Vitamin D3 receptor | / | 0.444 | |
| 3w0j | T08 | Vitamin D3 receptor | / | 0.444 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.443 | |
| 1suo | CPZ | Cytochrome P450 2B4 | 1.14.14.1 | 0.443 | |
| 1xdi | FAD | NAD(P)H dehydrogenase (quinone) | / | 0.443 | |
| 2hk9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.443 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.443 | |
| 3bfa | 9OD | Odorant binding protein ASP1 | / | 0.443 | |
| 3r3b | 4CO | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.443 | |
| 3w0h | W12 | Vitamin D3 receptor | / | 0.443 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.443 | |
| 1jip | KTN | 6-deoxyerythronolide B hydroxylase | / | 0.442 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.442 | |
| 4jvb | 1M0 | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.442 | |
| 1iyz | NDP | Probable quinone oxidoreductase | / | 0.441 | |
| 1phe | PIY | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 2hbh | XE4 | Vitamin D3 receptor A | / | 0.441 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.441 | |
| 3qi4 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.441 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.441 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.441 | |
| 4ge4 | 0KE | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.441 | |
| 4iae | 1DX | Alr2278 protein | / | 0.441 | |
| 4nkv | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.441 | |
| 1kfb | IGP | Tryptophan synthase alpha chain | / | 0.440 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 2a1m | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 2y30 | SM8 | Putative repressor SimReg2 | / | 0.440 | |
| 3ce3 | 1FN | Hepatocyte growth factor receptor | 2.7.10.1 | 0.440 | |
| 3p9t | TCL | Repressor | / | 0.440 | |
| 3s79 | ASD | Aromatase | 1.14.14.14 | 0.440 | |
| 3t3r | 9PL | Cytochrome P450 2A6 | 1.14.13 | 0.440 | |
| 3w5r | LOA | Vitamin D3 receptor | / | 0.440 | |
| 4g1y | 0VO | Vitamin D3 receptor A | / | 0.440 | |
| 4g2h | 0VQ | Vitamin D3 receptor A | / | 0.440 | |
| 4kla | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.440 | |
| 4z63 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.440 |