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 |
|---|---|---|---|
| 3d5f | L41 | Peroxisome proliferator-activated receptor delta |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3d5f | L41 | Peroxisome proliferator-activated receptor delta | / | 1.000 | |
| 2znp | K55 | Peroxisome proliferator-activated receptor delta | / | 0.588 | |
| 1knu | YPA | Peroxisome proliferator-activated receptor gamma | / | 0.580 | |
| 3kdu | NKS | Peroxisome proliferator-activated receptor alpha | / | 0.573 | |
| 2hwr | DRD | Peroxisome proliferator-activated receptor gamma | / | 0.572 | |
| 1rdt | 570 | Peroxisome proliferator-activated receptor gamma | / | 0.568 | |
| 2j14 | GNI | Peroxisome proliferator-activated receptor delta | / | 0.566 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.566 | |
| 2ath | 3EA | Peroxisome proliferator-activated receptor gamma | / | 0.558 | |
| 3vjh | J35 | Peroxisome proliferator-activated receptor gamma | / | 0.556 | |
| 1k74 | 544 | Peroxisome proliferator-activated receptor gamma | / | 0.553 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.553 | |
| 3vsp | EK8 | Peroxisome proliferator-activated receptor gamma | / | 0.550 | |
| 3sp9 | IL2 | Peroxisome proliferator-activated receptor delta | / | 0.547 | |
| 1fm9 | 570 | Peroxisome proliferator-activated receptor gamma | / | 0.544 | |
| 2rew | REW | Peroxisome proliferator-activated receptor alpha | / | 0.539 | |
| 1k7l | 544 | Peroxisome proliferator-activated receptor alpha | / | 0.537 | |
| 2gtk | 208 | Peroxisome proliferator-activated receptor gamma | / | 0.536 | |
| 3gbk | 2PQ | Peroxisome proliferator-activated receptor gamma | / | 0.535 | |
| 2pob | GW4 | Peroxisome proliferator-activated receptor gamma | / | 0.534 | |
| 2npa | MMB | Peroxisome proliferator-activated receptor alpha | / | 0.529 | |
| 2zno | S44 | Peroxisome proliferator-activated receptor gamma | / | 0.529 | |
| 2q8s | L92 | Peroxisome proliferator-activated receptor gamma | / | 0.525 | |
| 2i4j | DRJ | Peroxisome proliferator-activated receptor gamma | / | 0.521 | |
| 1i7g | AZ2 | Peroxisome proliferator-activated receptor alpha | / | 0.520 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.518 | |
| 1zgy | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.516 | |
| 4f9m | FCM | Peroxisome proliferator-activated receptor gamma | / | 0.508 | |
| 1i7i | AZ2 | Peroxisome proliferator-activated receptor gamma | / | 0.504 | |
| 1db1 | VDX | Vitamin D3 receptor | / | 0.500 | |
| 3vso | EK1 | Peroxisome proliferator-activated receptor gamma | / | 0.500 | |
| 4xld | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.500 | |
| 1fm6 | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.499 | |
| 3sp6 | IL2 | Peroxisome proliferator-activated receptor alpha | / | 0.499 | |
| 3v9y | 24L | Peroxisome proliferator-activated receptor gamma | / | 0.496 | |
| 2i4p | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.493 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.490 | |
| 2has | C3O | Vitamin D3 receptor | / | 0.489 | |
| 4hee | 14R | Peroxisome proliferator-activated receptor gamma | / | 0.486 | |
| 3a0i | AJI | Glucokinase | 2.7.1.2 | 0.483 | |
| 3bej | MUF | Bile acid receptor | / | 0.483 | |
| 4o8f | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.482 | |
| 1s19 | MC9 | Vitamin D3 receptor | / | 0.479 | |
| 2o4r | VD5 | Vitamin D3 receptor | / | 0.478 | |
| 3vrv | YSD | Vitamin D3 receptor | / | 0.478 | |
| 3vt3 | VDX | Vitamin D3 receptor | / | 0.477 | |
| 4fhi | 0S4 | Vitamin D3 receptor A | / | 0.477 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.476 | |
| 2go4 | TUX | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.474 | |
| 3h1v | TK1 | Glucokinase | 2.7.1.2 | 0.473 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.472 | |
| 2p4y | C03 | Peroxisome proliferator-activated receptor gamma | / | 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 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.470 | |
| 3th8 | TH9 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.470 | |
| 1ppj | ANY | Cytochrome b | / | 0.469 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.469 | |
| 2qo4 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.469 | |
| 3vru | YS3 | Vitamin D3 receptor | / | 0.469 | |
| 4xuh | SFI | Peroxisome proliferator-activated receptor gamma | / | 0.468 | |
| 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 | |
| 1w2x | RCP | Acetyl-CoA carboxylase | / | 0.465 | |
| 3sz0 | FAD | Sulfide-quinone reductase | / | 0.465 | |
| 2zlc | VDX | Vitamin D3 receptor | / | 0.464 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.464 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.464 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.464 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.463 | |
| 5hs1 | VOR | Lanosterol 14-alpha demethylase | / | 0.463 | |
| 3tda | PN0 | Cytochrome P450 2D6 | / | 0.461 | |
| 1rk3 | VDX | Vitamin D3 receptor | / | 0.460 | |
| 1s0z | EB1 | Vitamin D3 receptor | / | 0.460 | |
| 3vt4 | 5YI | Vitamin D3 receptor | / | 0.460 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.460 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.459 | |
| 2pr2 | DG1 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.459 | |
| 2q5p | 241 | Peroxisome proliferator-activated receptor gamma | / | 0.459 | |
| 1ie9 | VDX | Vitamin D3 receptor | / | 0.458 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.458 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.458 | |
| 4nmd | FDA | Bifunctional protein PutA | / | 0.458 | |
| 4q0a | 4OA | Vitamin D3 receptor A | / | 0.458 | |
| 4ruo | BIV | Vitamin D3 receptor A | / | 0.458 | |
| 1rkg | VD1 | Vitamin D3 receptor | / | 0.457 | |
| 3l6j | Z90 | Alr2278 protein | / | 0.457 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.457 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.457 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.456 | |
| 2hb8 | MVD | Vitamin D3 receptor | / | 0.456 | |
| 2ieb | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.456 | |
| 3m7r | VDX | Vitamin D3 receptor | / | 0.456 | |
| 3v9v | 21L | Peroxisome proliferator-activated receptor gamma | / | 0.456 | |
| 3vtc | TK3 | Vitamin D3 receptor | / | 0.456 | |
| 4ema | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.456 | |
| 2aqk | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.455 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.455 | |
| 2zl9 | VDA | Vitamin D3 receptor | / | 0.454 | |
| 3a9w | NAD | NDP-sugar epimerase | / | 0.454 | |
| 3vtb | TKA | Vitamin D3 receptor | / | 0.454 | |
| 3w0i | O11 | Vitamin D3 receptor | / | 0.454 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.454 | |
| 4o70 | 1QK | Bromodomain-containing protein 4 | / | 0.454 | |
| 4rup | H97 | Vitamin D3 receptor A | / | 0.454 | |
| 3abi | NAD | Uncharacterized protein | / | 0.452 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.452 | |
| 1xuo | LA1 | Integrin alpha-L | / | 0.451 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.451 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.450 | |
| 2ykc | YKC | Heat shock protein HSP 90-alpha | / | 0.450 | |
| 2zla | VDB | Vitamin D3 receptor | / | 0.450 | |
| 3vev | 0H4 | Glucokinase | 2.7.1.2 | 0.450 | |
| 3vrt | YS2 | Vitamin D3 receptor | / | 0.450 | |
| 4jlj | 1NM | Deoxycytidine kinase | 2.7.1.74 | 0.450 | |
| 2pg0 | FAD | Acyl-CoA dehydrogenase | / | 0.449 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.449 | |
| 4dhy | S41 | Glucokinase | 2.7.1.2 | 0.449 | |
| 4g20 | 484 | Vitamin D3 receptor A | / | 0.449 | |
| 1guf | NDP | Enoyl-[acyl-carrier-protein] reductase 1, mitochondrial | 1.3.1.10 | 0.448 | |
| 3ad9 | NAD | Subunit alpha of sarocosine oxidase | / | 0.448 | |
| 3inw | JZB | Heat shock protein HSP 90-alpha | / | 0.448 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 3vt6 | 5YI | Vitamin D3 receptor | / | 0.448 | |
| 3w0c | 6DS | Vitamin D3 receptor | / | 0.448 | |
| 4r20 | AER | Cytochrome P450 family 17 polypeptide 2 | / | 0.448 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.447 | |
| 2pnj | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.447 | |
| 2ykj | YKJ | Heat shock protein HSP 90-alpha | / | 0.447 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.447 | |
| 4iae | 1DX | Alr2278 protein | / | 0.447 | |
| 4iui | 1GQ | Estrogen receptor | / | 0.447 | |
| 2iya | ZIO | Oleandomycin glycosyltransferase | / | 0.446 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.446 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.446 | |
| 3id8 | MRK | Glucokinase | 2.7.1.2 | 0.446 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.446 | |
| 3p6o | ETG | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.446 | |
| 3w0g | W07 | Vitamin D3 receptor | / | 0.446 | |
| 2znq | 401 | Peroxisome proliferator-activated receptor delta | / | 0.445 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.445 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.445 | |
| 2hbh | XE4 | Vitamin D3 receptor A | / | 0.444 | |
| 2om9 | AJA | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 2vzm | NRB | Cytochrome P450 monooxygenase PikC | / | 0.444 | |
| 3w0j | T08 | Vitamin D3 receptor | / | 0.444 | |
| 4o1m | NAD | Enoyl-acyl carrier reductase | / | 0.444 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.443 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.443 | |
| 3syi | FAD | Sulfide-quinone reductase | / | 0.443 | |
| 3w0h | W12 | Vitamin D3 receptor | / | 0.443 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 4jvb | 1M0 | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.443 | |
| 4kla | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.443 | |
| 4mle | VO1 | Glucokinase | 2.7.1.2 | 0.443 | |
| 4nkv | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.443 | |
| 1juv | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.442 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2r0c | FAD | Putative FAD-monooxygenase | / | 0.442 | |
| 3g4i | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 3ol5 | SAW | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.442 | |
| 1e5q | NDP | Saccharopine dehydrogenase [NADP(+), L-glutamate-forming] | 1.5.1.10 | 0.441 | |
| 1osv | CHC | Bile acid receptor | / | 0.441 | |
| 3irx | UDR | Gag-Pol polyprotein | 2.7.7.49 | 0.441 | |
| 3tnl | NAD | Shikimate dehydrogenase (NADP(+)) | / | 0.441 | |
| 4awq | 592 | Heat shock protein HSP 90-alpha | / | 0.441 | |
| 4h96 | 14Q | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3w5r | LOA | Vitamin D3 receptor | / | 0.440 | |
| 4g1y | 0VO | Vitamin D3 receptor A | / | 0.440 | |
| 4g2h | 0VQ | Vitamin D3 receptor A | / | 0.440 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.440 | |
| 4l8u | 9AZ | Serum albumin | / | 0.440 | |
| 4z63 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.440 |