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 |
|---|---|---|---|
| 3gyt | DL4 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3gyt | DL4 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 1.000 | |
| 3gyu | DL7 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.757 | |
| 3up0 | D7S | aceDAF-12 | / | 0.634 | |
| 3up3 | XCA | aceDAF-12 | / | 0.581 | |
| 5k2c | ZMA | Adenosine receptor A2a | / | 0.489 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.488 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.487 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.482 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.481 | |
| 3eml | ZMA | Adenosine receptor A2a | / | 0.477 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.473 | |
| 2rc6 | NAP | Ferredoxin--NADP reductase | / | 0.473 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.472 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.471 | |
| 1osv | CHC | Bile acid receptor | / | 0.470 | |
| 1d3h | A26 | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.468 | |
| 4o7u | THF | Thymidylate synthase | / | 0.466 | |
| 2j3j | HC4 | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.465 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.464 | |
| 4a84 | DXC | Major pollen allergen Bet v 1-A | / | 0.464 | |
| 1dr3 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.463 | |
| 3zsh | 469 | Mitogen-activated protein kinase 14 | / | 0.463 | |
| 5iu8 | 6DZ | Adenosine receptor A2a | / | 0.463 | |
| 4qe6 | JN3 | Bile acid receptor | / | 0.462 | |
| 3ict | ADP | Coenzyme A disulfide reductase | / | 0.461 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.461 | |
| 5k2a | ZMA | Adenosine receptor A2a | / | 0.461 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.460 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.460 | |
| 5k2b | ZMA | Adenosine receptor A2a | / | 0.460 | |
| 2pr2 | DG1 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.458 | |
| 2zl9 | VDA | Vitamin D3 receptor | / | 0.458 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.457 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 4jbt | ASD | Cytochrome P450 monooxygenase | / | 0.457 | |
| 5iua | 6DX | Adenosine receptor A2a | / | 0.457 | |
| 3h0a | D30 | Peroxisome proliferator-activated receptor gamma | / | 0.456 | |
| 4l8u | 9AZ | Serum albumin | / | 0.456 | |
| 1rk3 | VDX | Vitamin D3 receptor | / | 0.455 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.455 | |
| 2z4y | 252 | Geranylgeranyl pyrophosphate synthase | / | 0.455 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.455 | |
| 4ez8 | DHF | Thymidylate synthase | 2.1.1.45 | 0.455 | |
| 4g2i | 0VQ | Vitamin D3 receptor | / | 0.455 | |
| 4pd6 | URI | Nucleoside permease | / | 0.455 | |
| 5jtb | ZMA | Adenosine receptor A2a | / | 0.455 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 1yc2 | NAD | NAD-dependent protein deacylase 2 | / | 0.454 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.454 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.454 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.454 | |
| 1p8d | CO1 | Oxysterols receptor LXR-beta | / | 0.453 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 3vwe | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.453 | |
| 2ym1 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.452 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 4pnm | NU1 | Tankyrase-2 | 2.4.2.30 | 0.452 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.452 | |
| 1s19 | MC9 | Vitamin D3 receptor | / | 0.451 | |
| 2ix5 | FAD | Acyl-coenzyme A oxidase 4, peroxisomal | 1.3.3.6 | 0.451 | |
| 2ntj | P1H | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.451 | |
| 2xw7 | NDP | Dihydrofolate reductase | / | 0.451 | |
| 3njo | PYV | Abscisic acid receptor PYR1 | / | 0.451 | |
| 1xuo | LA1 | Integrin alpha-L | / | 0.450 | |
| 3p9t | TCL | Repressor | / | 0.450 | |
| 3uax | NOS | Purine nucleoside phosphorylase DeoD-type | / | 0.450 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.450 | |
| 4hf4 | 15H | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.450 | |
| 5uvi | ZMA | Adenosine receptor A2a | / | 0.450 | |
| 1mxt | FAE | Cholesterol oxidase | 1.1.3.6 | 0.449 | |
| 1ot7 | CHC | Bile acid receptor | / | 0.449 | |
| 1tdu | CB3 | Thymidylate synthase | / | 0.449 | |
| 2ivp | ATP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.449 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.449 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.449 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 3ruk | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.448 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.448 | |
| 4m11 | MXM | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.448 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.448 | |
| 1h36 | R88 | Squalene--hopene cyclase | 4.2.1.129 | 0.447 | |
| 1udt | VIA | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.447 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.447 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.447 | |
| 1zeo | C01 | Peroxisome proliferator-activated receptor gamma | / | 0.447 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.447 | |
| 3bej | MUF | Bile acid receptor | / | 0.447 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.447 | |
| 3haz | FAD | Bifunctional protein PutA | / | 0.447 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.447 | |
| 4bbx | LKF | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.447 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.446 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.446 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.446 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.446 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.445 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.445 | |
| 3gmd | 2M3 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.445 | |
| 4cjx | 9L9 | C-1-tetrahydrofolate synthase, cytoplasmic, putative | / | 0.445 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 1rjk | VDZ | Vitamin D3 receptor | / | 0.444 | |
| 1uho | VDN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.444 | |
| 2b03 | TUD | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.444 | |
| 3had | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.444 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.444 | |
| 4da0 | GNG | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.444 | |
| 4gi2 | NAP | Crotonyl-CoA carboxylase/reductase | / | 0.444 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1n83 | CLR | Nuclear receptor ROR-alpha | / | 0.443 | |
| 1opb | RET | Retinol-binding protein 2 | / | 0.443 | |
| 1q1r | FAD | Putidaredoxin reductase | 1.18.1.5 | 0.443 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 4j6b | PLO | Cytochrome P450 monooxygenase | / | 0.443 | |
| 4jvb | 1M0 | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.443 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 1ml6 | GBX | Glutathione S-transferase A2 | 2.5.1.18 | 0.442 | |
| 1s0z | EB1 | Vitamin D3 receptor | / | 0.442 | |
| 2bxo | OPB | Serum albumin | / | 0.442 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.442 | |
| 3lfe | Z84 | Mitogen-activated protein kinase 14 | / | 0.442 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.442 | |
| 1cbr | REA | Cellular retinoic acid-binding protein 1 | / | 0.441 | |
| 1dr3 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1iyz | NDP | Probable quinone oxidoreductase | / | 0.441 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.441 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 3csd | EMO | Putative ketoacyl reductase | 1.3.1 | 0.441 | |
| 3wv9 | FEG | Hmd co-occurring protein HcgE | / | 0.441 | |
| 4h97 | 53S | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 4jv6 | 18F | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.441 | |
| 4jv8 | 1M1 | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.441 | |
| 4qzu | RTL | Retinol-binding protein 2 | / | 0.441 | |
| 4yfy | 0FX | VioF | / | 0.441 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.440 | |
| 2iod | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.440 | |
| 3bfb | 9OD | Pheromone-binding protein ASP1 | / | 0.440 | |
| 3vtb | TKA | Vitamin D3 receptor | / | 0.440 | |
| 3w0g | W07 | Vitamin D3 receptor | / | 0.440 | |
| 4g48 | PZB | Mycocyclosin synthase | 1.14.21.9 | 0.440 | |
| 4jvf | 17X | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.440 | |
| 4ktl | 1CQ | Cytochrome P450 | / | 0.440 |