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 |
|---|---|---|---|
| 3bej | MUF | Bile acid receptor |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3bej | MUF | Bile acid receptor | / | 1.000 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.507 | |
| 4q0a | 4OA | Vitamin D3 receptor A | / | 0.497 | |
| 1rdt | 570 | Peroxisome proliferator-activated receptor gamma | / | 0.495 | |
| 2hwr | DRD | Peroxisome proliferator-activated receptor gamma | / | 0.490 | |
| 3up3 | XCA | aceDAF-12 | / | 0.490 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.489 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.487 | |
| 3w0i | O11 | Vitamin D3 receptor | / | 0.487 | |
| 1s19 | MC9 | Vitamin D3 receptor | / | 0.486 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.486 | |
| 2has | C3O | Vitamin D3 receptor | / | 0.486 | |
| 3w5t | LHP | Vitamin D3 receptor | / | 0.485 | |
| 4nie | NBH | Nuclear receptor ROR-gamma | / | 0.485 | |
| 1bq1 | CB3 | Thymidylate synthase | / | 0.484 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.484 | |
| 3gbk | 2PQ | Peroxisome proliferator-activated receptor gamma | / | 0.484 | |
| 1ot7 | CHC | Bile acid receptor | / | 0.483 | |
| 1ot7 | IU5 | Bile acid receptor | / | 0.482 | |
| 2ath | 3EA | Peroxisome proliferator-activated receptor gamma | / | 0.482 | |
| 4itf | TFY | Vitamin D3 receptor | / | 0.481 | |
| 3w5r | LOA | Vitamin D3 receptor | / | 0.480 | |
| 2o4r | VD5 | Vitamin D3 receptor | / | 0.479 | |
| 2qo4 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.479 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.479 | |
| 3w0y | DS4 | Vitamin D3 receptor | / | 0.479 | |
| 2c7x | NRB | Cytochrome P450 monooxygenase PikC | / | 0.478 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.478 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.477 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.476 | |
| 3vt3 | VDX | Vitamin D3 receptor | / | 0.476 | |
| 1fm9 | 570 | Peroxisome proliferator-activated receptor gamma | / | 0.475 | |
| 3up0 | D7S | aceDAF-12 | / | 0.474 | |
| 3vru | YS3 | Vitamin D3 receptor | / | 0.474 | |
| 1osv | CHC | Bile acid receptor | / | 0.473 | |
| 1k74 | 544 | Peroxisome proliferator-activated receptor gamma | / | 0.472 | |
| 3w5q | 3KL | Vitamin D3 receptor | / | 0.472 | |
| 4g1y | 0VO | Vitamin D3 receptor A | / | 0.472 | |
| 2hc4 | VDX | Vitamin D3 receptor A | / | 0.471 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.471 | |
| 2hb8 | MVD | Vitamin D3 receptor | / | 0.470 | |
| 3kdu | NKS | Peroxisome proliferator-activated receptor alpha | / | 0.470 | |
| 4g20 | 484 | Vitamin D3 receptor A | / | 0.470 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.470 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.469 | |
| 3w0c | 6DS | Vitamin D3 receptor | / | 0.469 | |
| 1rkg | VD1 | Vitamin D3 receptor | / | 0.468 | |
| 1s0z | EB1 | Vitamin D3 receptor | / | 0.468 | |
| 2hb7 | O1C | Vitamin D3 receptor | / | 0.468 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.468 | |
| 1k7l | 544 | Peroxisome proliferator-activated receptor alpha | / | 0.467 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.467 | |
| 2rc6 | NAP | Ferredoxin--NADP reductase | / | 0.467 | |
| 2zlc | VDX | Vitamin D3 receptor | / | 0.467 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.467 | |
| 3vn2 | TLS | Peroxisome proliferator-activated receptor gamma | / | 0.467 | |
| 1n83 | CLR | Nuclear receptor ROR-alpha | / | 0.466 | |
| 3axw | TID | Casein kinase II subunit alpha | 2.7.11.1 | 0.466 | |
| 4f9m | FCM | Peroxisome proliferator-activated receptor gamma | / | 0.466 | |
| 4fjz | 4FJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.466 | |
| 2q5g | 1FA | Peroxisome proliferator-activated receptor delta | / | 0.465 | |
| 3gyt | DL4 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.465 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.465 | |
| 4ez8 | DHF | Thymidylate synthase | 2.1.1.45 | 0.465 | |
| 5bt4 | 2LO | Bromodomain-containing protein 4 | / | 0.465 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.464 | |
| 1ie9 | VDX | Vitamin D3 receptor | / | 0.464 | |
| 3dr1 | C5D | Vitamin D3 receptor A | / | 0.464 | |
| 3fco | IIG | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.464 | |
| 3qk0 | QK0 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.464 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.464 | |
| 4bcr | WY1 | Peroxisome proliferator-activated receptor alpha | / | 0.464 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.464 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.463 | |
| 1rk3 | VDX | Vitamin D3 receptor | / | 0.463 | |
| 3kyt | HC2 | Nuclear receptor ROR-gamma | / | 0.463 | |
| 3th8 | TH9 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.463 | |
| 3vt6 | 5YI | Vitamin D3 receptor | / | 0.463 | |
| 3vtc | TK3 | Vitamin D3 receptor | / | 0.463 | |
| 4hle | 17V | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.463 | |
| 2har | OCC | Vitamin D3 receptor | / | 0.462 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.462 | |
| 3mqe | 416 | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.462 | |
| 4g21 | 0VP | Vitamin D3 receptor A | / | 0.461 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.461 | |
| 4qe6 | JN3 | Bile acid receptor | / | 0.461 | |
| 1kyo | SMA | Cytochrome b | / | 0.460 | |
| 3cx5 | SMA | Cytochrome b | / | 0.460 | |
| 3gyu | DL7 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.460 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.460 | |
| 4i8v | BHF | Cytochrome P450 1A1 | 1.14.14.1 | 0.460 | |
| 3u8h | BHP | Phospholipase A2, membrane associated | / | 0.459 | |
| 3w0j | T08 | Vitamin D3 receptor | / | 0.459 | |
| 4g2h | 0VQ | Vitamin D3 receptor A | / | 0.458 | |
| 1eio | GCH | Gastrotropin | / | 0.457 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.457 | |
| 3d5f | L41 | Peroxisome proliferator-activated receptor delta | / | 0.457 | |
| 3vrv | YSD | Vitamin D3 receptor | / | 0.457 | |
| 3vt4 | 5YI | Vitamin D3 receptor | / | 0.457 | |
| 1rjk | VDZ | Vitamin D3 receptor | / | 0.456 | |
| 2oby | NAP | Quinone oxidoreductase PIG3 | 1 | 0.456 | |
| 3r5y | F42 | Uncharacterized protein | / | 0.456 | |
| 4c34 | STU | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.456 | |
| 4g1d | 0VK | Vitamin D3 receptor A | / | 0.456 | |
| 2hnz | PC0 | Gag-Pol polyprotein | 2.7.7.49 | 0.455 | |
| 3u4u | LNH | Casein kinase II subunit alpha | 2.7.11.1 | 0.455 | |
| 3ua5 | 06X | Cytochrome P450 2B6 | 1.14.13 | 0.455 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.455 | |
| 4ruj | VDX | Vitamin D3 receptor A | / | 0.455 | |
| 2nmt | NHM | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.454 | |
| 2w4q | CBW | Prostaglandin reductase 2 | 1.3.1.48 | 0.453 | |
| 3sp9 | IL2 | Peroxisome proliferator-activated receptor delta | / | 0.453 | |
| 1ezv | SMA | Cytochrome b | / | 0.452 | |
| 1i7i | AZ2 | Peroxisome proliferator-activated receptor gamma | / | 0.452 | |
| 2hbh | XE4 | Vitamin D3 receptor A | / | 0.452 | |
| 2yiu | SMA | Cytochrome b | / | 0.452 | |
| 4fhi | 0S4 | Vitamin D3 receptor A | / | 0.452 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.452 | |
| 4z9g | 1Q5 | Corticotropin-releasing factor receptor 1 | / | 0.452 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.451 | |
| 1l2j | ETC | Estrogen receptor beta | / | 0.450 | |
| 2aqk | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.450 | |
| 2i4z | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.450 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.450 | |
| 3vtb | TKA | Vitamin D3 receptor | / | 0.450 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.450 | |
| 2i4p | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.449 | |
| 2vf0 | F89 | Thymidylate synthase | / | 0.449 | |
| 2y46 | MIV | Mycinamicin IV hydroxylase/epoxidase | / | 0.449 | |
| 2ze2 | T27 | Gag-Pol polyprotein | 2.7.7.49 | 0.449 | |
| 3w0h | W12 | Vitamin D3 receptor | / | 0.449 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 2npa | MMB | Peroxisome proliferator-activated receptor alpha | / | 0.448 | |
| 2vzm | NRB | Cytochrome P450 monooxygenase PikC | / | 0.448 | |
| 3d7k | D7K | Benzaldehyde lyase | / | 0.448 | |
| 4h95 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.448 | |
| 4nmd | FDA | Bifunctional protein PutA | / | 0.448 | |
| 4rup | H97 | Vitamin D3 receptor A | / | 0.448 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 1db1 | VDX | Vitamin D3 receptor | / | 0.447 | |
| 1i7g | AZ2 | Peroxisome proliferator-activated receptor alpha | / | 0.447 | |
| 1p8d | CO1 | Oxysterols receptor LXR-beta | / | 0.447 | |
| 2hw2 | RFP | Rifampin ADP-ribosyl transferase | / | 0.447 | |
| 2y98 | MIV | Mycinamicin IV hydroxylase/epoxidase | / | 0.447 | |
| 3owk | 18E | Casein kinase II subunit alpha | 2.7.11.1 | 0.447 | |
| 3vrt | YS2 | Vitamin D3 receptor | / | 0.447 | |
| 4kla | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.447 | |
| 1cbr | REA | Cellular retinoic acid-binding protein 1 | / | 0.446 | |
| 1kb9 | SMA | Cytochrome b | / | 0.446 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.446 | |
| 1uyd | PU8 | Heat shock protein HSP 90-alpha | / | 0.446 | |
| 3h6k | 33T | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.446 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.446 | |
| 3t8x | T8X | T-cell surface glycoprotein CD1b | / | 0.446 | |
| 3zc3 | NAP | Ferredoxin--NADP reductase | 1.18.1.2 | 0.446 | |
| 4fhh | 0U3 | Vitamin D3 receptor A | / | 0.446 | |
| 4ib4 | ERM | 5-hydroxytryptamine receptor 2B | / | 0.446 | |
| 1n4s | CYS_VAL_ILE_LEU_GER | Geranylgeranyl transferase type-1 subunit beta | 2.5.1.59 | 0.445 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.445 | |
| 1zgy | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.445 | |
| 2pob | GW4 | Peroxisome proliferator-activated receptor gamma | / | 0.445 | |
| 4jv6 | 18F | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.445 | |
| 1zeo | C01 | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 2zl9 | VDA | Vitamin D3 receptor | / | 0.444 | |
| 3iae | D7K | Benzaldehyde lyase | / | 0.444 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.444 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.444 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.444 | |
| 4ge7 | 0K5 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.444 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.444 | |
| 4ruo | BIV | Vitamin D3 receptor A | / | 0.444 | |
| 1eny | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 1eup | ASD | 6-deoxyerythronolide B hydroxylase | / | 0.443 | |
| 1fml | RTL | Retinol dehydratase | / | 0.443 | |
| 1lri | CLR | Beta-elicitin cryptogein | / | 0.443 | |
| 1t0l | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.443 | |
| 1tvr | TB9 | Gag-Pol polyprotein | 2.7.7.49 | 0.443 | |
| 2ibz | SMA | Cytochrome b | / | 0.443 | |
| 2zb4 | 5OP | Prostaglandin reductase 2 | 1.3.1.48 | 0.443 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.443 | |
| 3t2y | FAD | Sulfide-quinone reductase | / | 0.443 | |
| 4cax | MYA | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.443 | |
| 4iui | 1GQ | Estrogen receptor | / | 0.443 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.443 | |
| 2j14 | GNI | Peroxisome proliferator-activated receptor delta | / | 0.442 | |
| 2q59 | 240 | Peroxisome proliferator-activated receptor gamma | / | 0.442 | |
| 2q9f | C3S | Cholesterol 24-hydroxylase | / | 0.442 | |
| 2zla | VDB | Vitamin D3 receptor | / | 0.442 | |
| 3v9y | 24L | Peroxisome proliferator-activated receptor gamma | / | 0.442 | |
| 4xld | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.442 | |
| 1s0x | C3S | Nuclear receptor ROR-alpha | / | 0.441 | |
| 1stc | STU | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.441 | |
| 3sn6 | P0G | Beta-2 adrenergic receptor | / | 0.441 | |
| 2o4j | VD4 | Vitamin D3 receptor | / | 0.440 | |
| 2znq | 401 | Peroxisome proliferator-activated receptor delta | / | 0.440 | |
| 3tmz | 06X | Cytochrome P450 2B4 | 1.14.14.1 | 0.440 | |
| 3tqh | NDP | Quinone oxidoreductase | / | 0.440 | |
| 3vjh | J35 | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 4i2p | G73 | Gag-Pol polyprotein | 2.7.7.49 | 0.440 | |
| 5cb3 | APR | O-acetyl-ADP-ribose deacetylase | / | 0.440 |