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 |
|---|---|---|---|
| 4flp | JQ1 | Bromodomain testis-specific protein |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4flp | JQ1 | Bromodomain testis-specific protein | / | 1.000 | |
| 4uyg | 73B | Bromodomain-containing protein 2 | / | 0.617 | |
| 4a9o | A9O | Bromodomain-containing protein 2 | / | 0.600 | |
| 4alh | A9P | Bromodomain-containing protein 2 | / | 0.575 | |
| 4ogi | R78 | Bromodomain-containing protein 4 | / | 0.570 | |
| 4mr6 | 1K0 | Bromodomain-containing protein 2 | / | 0.567 | |
| 4c67 | L5S | Bromodomain-containing protein 4 | / | 0.566 | |
| 4a9n | A9N | Bromodomain-containing protein 2 | / | 0.564 | |
| 4j0s | 1H3 | Bromodomain-containing protein 4 | / | 0.561 | |
| 4uyf | 73B | Bromodomain-containing protein 2 | / | 0.560 | |
| 4hxs | 1A3 | Bromodomain-containing protein 4 | / | 0.550 | |
| 4lrg | 1XB | Bromodomain-containing protein 4 | / | 0.550 | |
| 4men | 25K | Bromodomain-containing protein 4 | / | 0.550 | |
| 4akn | S5B | Bromodomain-containing protein 2 | / | 0.549 | |
| 4nr5 | 2LL | CREB-binding protein | / | 0.548 | |
| 4o71 | CPB | Bromodomain-containing protein 4 | / | 0.548 | |
| 5bt5 | 2LO | Bromodomain-containing protein 2 | / | 0.548 | |
| 4bjx | 73B | Bromodomain-containing protein 4 | / | 0.545 | |
| 4mr4 | 1K0 | Bromodomain-containing protein 4 | / | 0.541 | |
| 4qzs | JQ1 | Bromodomain-containing protein 4 | / | 0.541 | |
| 4c66 | H4C | Bromodomain-containing protein 4 | / | 0.540 | |
| 4j0r | 1H2 | Bromodomain-containing protein 4 | / | 0.540 | |
| 2yem | WSH | Bromodomain-containing protein 4 | / | 0.539 | |
| 4bw2 | UTH | Bromodomain-containing protein 4 | / | 0.535 | |
| 4bw3 | 9BM | Bromodomain-containing protein 4 | / | 0.533 | |
| 4a9l | P9L | Bromodomain-containing protein 4 | / | 0.529 | |
| 4hxn | 1A7 | Bromodomain-containing protein 4 | / | 0.525 | |
| 4lr6 | 1XA | Bromodomain-containing protein 4 | / | 0.525 | |
| 2ydw | WSH | Bromodomain-containing protein 2 | / | 0.524 | |
| 4nqm | Y1Z | Bromodomain-containing protein 4 | / | 0.521 | |
| 3aqa | BYH | Bromodomain-containing protein 2 | / | 0.519 | |
| 4hby | 13F | Bromodomain-containing protein 4 | / | 0.518 | |
| 4hxr | 1A4 | Bromodomain-containing protein 4 | / | 0.517 | |
| 4meq | 25O | Bromodomain-containing protein 4 | / | 0.517 | |
| 2yek | EAM | Bromodomain-containing protein 2 | / | 0.514 | |
| 4hxo | 1A6 | Bromodomain-containing protein 4 | / | 0.513 | |
| 4o74 | R78 | Bromodomain-containing protein 4 | / | 0.513 | |
| 2yel | WSH | Bromodomain-containing protein 4 | / | 0.508 | |
| 4f3i | 0S6 | Bromodomain-containing protein 4 | / | 0.506 | |
| 4py6 | R78 | Bromodomain protein, putative | / | 0.504 | |
| 4nky | 3QZ | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.502 | |
| 4bw1 | S5B | Bromodomain-containing protein 4 | / | 0.499 | |
| 4mr5 | 1K0 | Bromodomain-containing protein 2 | / | 0.497 | |
| 3zyu | 1GH | Bromodomain-containing protein 4 | / | 0.491 | |
| 1og5 | SWF | Cytochrome P450 2C9 | / | 0.487 | |
| 4j1p | 1K0 | Bromodomain-containing protein 2 | / | 0.484 | |
| 4nkv | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.484 | |
| 4lyw | 21Q | Bromodomain-containing protein 4 | / | 0.480 | |
| 4hbw | 14Z | Bromodomain-containing protein 4 | / | 0.479 | |
| 3sp6 | IL2 | Peroxisome proliferator-activated receptor alpha | / | 0.476 | |
| 4alg | 1GH | Bromodomain-containing protein 2 | / | 0.476 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.476 | |
| 2aqh | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.475 | |
| 4mep | 24Y | Bromodomain-containing protein 4 | / | 0.475 | |
| 5bt4 | 2LO | Bromodomain-containing protein 4 | / | 0.474 | |
| 4o78 | SAV | Bromodomain-containing protein 4 | / | 0.473 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.472 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.471 | |
| 1beu | IPL | Tryptophan synthase alpha chain | / | 0.469 | |
| 2cib | CM6 | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.468 | |
| 4kne | 1CY | Dihydrofolate reductase | 1.5.1.3 | 0.468 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.467 | |
| 1jpa | ANP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.467 | |
| 2oci | TYC | Valacyclovir hydrolase | 3.1 | 0.467 | |
| 4j3i | 1K0 | Bromodomain-containing protein 4 | / | 0.467 | |
| 4awp | 99A | Heat shock protein HSP 90-alpha | / | 0.466 | |
| 1j3j | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.465 | |
| 1klk | PMD | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.465 | |
| 2v5a | LZL | Biotin carboxylase | 6.3.4.14 | 0.464 | |
| 4ead | 0NP | Thymidine phosphorylase | 2.4.2.4 | 0.464 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 4ir5 | IR5 | Bromodomain adjacent to zinc finger domain protein 2B | / | 0.462 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.460 | |
| 2w3v | TOP | Dihydrofolate reductase | / | 0.459 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.459 | |
| 4cfl | 8DQ | Bromodomain-containing protein 4 | / | 0.459 | |
| 4egn | TWO | Cytochrome P450 | / | 0.459 | |
| 4fhi | 0S4 | Vitamin D3 receptor A | / | 0.459 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.458 | |
| 2vzm | NRB | Cytochrome P450 monooxygenase PikC | / | 0.457 | |
| 3bfb | 9OD | Pheromone-binding protein ASP1 | / | 0.456 | |
| 3cgd | COA | Coenzyme A disulfide reductase | / | 0.456 | |
| 4jbt | ASD | Cytochrome P450 monooxygenase | / | 0.456 | |
| 1eny | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.455 | |
| 4j03 | FVS | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.455 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.455 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 1nvt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.454 | |
| 1s19 | MC9 | Vitamin D3 receptor | / | 0.454 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.454 | |
| 4mv8 | ACP | Biotin carboxylase | 6.3.4.14 | 0.454 | |
| 4yek | THM | Thymidine phosphorylase | / | 0.454 | |
| 3sn6 | P0G | Beta-2 adrenergic receptor | / | 0.454 | |
| 2qbm | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.453 | |
| 3nrr | D16 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.453 | |
| 4bw4 | 9B6 | Bromodomain-containing protein 4 | / | 0.453 | |
| 4h6r | FDA | Proline dehydrogenase | / | 0.453 | |
| 5ii2 | LU2 | Protein polybromo-1 | / | 0.453 | |
| 1ykd | CMP | Adenylate cyclase | / | 0.452 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.452 | |
| 3tk3 | CPZ | Cytochrome P450 2B4 | 1.14.14.1 | 0.452 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.452 | |
| 4l8u | 9AZ | Serum albumin | / | 0.452 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.451 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 3cwk | REA | Cellular retinoic acid-binding protein 2 | / | 0.451 | |
| 3ruk | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.451 | |
| 4y8w | STR | Steroid 21-hydroxylase | / | 0.451 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.451 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.450 | |
| 3t3q | 9PL | Cytochrome P450 2A6 | 1.14.13 | 0.450 | |
| 4hw2 | 19H | Induced myeloid leukemia cell differentiation protein Mcl-1 | / | 0.450 | |
| 1dna | CB3 | Thymidylate synthase | / | 0.449 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.449 | |
| 2z97 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 3tw6 | ADP | Pyruvate carboxylase | / | 0.449 | |
| 4l4d | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 1m9m | 6NI | Nitric oxide synthase, endothelial | 1.14.13.39 | 0.448 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.448 | |
| 2fgk | ATP | Alpha-hemolysin translocation ATP-binding protein HlyB | / | 0.448 | |
| 2hw2 | RFP | Rifampin ADP-ribosyl transferase | / | 0.448 | |
| 3mdv | CL6 | Cholesterol 24-hydroxylase | / | 0.448 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.448 | |
| 4awo | 99B | Heat shock protein HSP 90-alpha | / | 0.448 | |
| 4euf | NAD | Trans-2-enoyl-CoA reductase [NADH] | / | 0.448 | |
| 1rdt | 570 | Peroxisome proliferator-activated receptor gamma | / | 0.447 | |
| 2oax | SNL | Mineralocorticoid receptor | / | 0.447 | |
| 3ict | ADP | Coenzyme A disulfide reductase | / | 0.447 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.447 | |
| 3sn7 | 540 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.447 | |
| 3zdi | UGJ | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.447 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.447 | |
| 4gpj | 0Q1 | Bromodomain-containing protein 4 | / | 0.447 | |
| 4xe6 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.446 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.446 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.446 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.446 | |
| 3fwf | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 4ge4 | 0KE | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.446 | |
| 4i8v | BHF | Cytochrome P450 1A1 | 1.14.14.1 | 0.446 | |
| 4r20 | AER | Cytochrome P450 family 17 polypeptide 2 | / | 0.446 | |
| 1ppj | ANY | Cytochrome b | / | 0.445 | |
| 1uyu | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 2zax | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.445 | |
| 4c0b | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.445 | |
| 3qak | UKA | Adenosine receptor A2a | / | 0.445 | |
| 1diu | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1noo | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 2acw | UPG | Glycosyltransferase | / | 0.444 | |
| 2hb7 | O1C | Vitamin D3 receptor | / | 0.444 | |
| 2hk9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.444 | |
| 2idz | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.444 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.444 | |
| 4fgg | 0U5 | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.444 | |
| 4zm6 | ACO | N-acetyl-beta-D glucosaminidase | / | 0.444 | |
| 5ccc | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.443 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.443 | |
| 2has | C3O | Vitamin D3 receptor | / | 0.443 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 3c0i | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.443 | |
| 3gob | HXX | DdmC | / | 0.443 | |
| 3i1f | GCP | Translation initiation factor 2 subunit gamma | / | 0.443 | |
| 3pm1 | ET | HTH-type transcriptional regulator QacR | / | 0.443 | |
| 4qmx | H8H | Serine/threonine-protein kinase 24 | 2.7.11.1 | 0.443 | |
| 5cpb | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 5e8w | STU | TGF-beta receptor type-1 | 2.7.11.30 | 0.443 | |
| 2c31 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.442 | |
| 2h9i | EAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.442 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.442 | |
| 3c6u | M22 | Gag-Pol polyprotein | 2.7.7.49 | 0.442 | |
| 3cpp | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 3glm | COO | Glutaconyl-CoA decarboxylase alpha subunit | / | 0.442 | |
| 3ii4 | 3II | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.442 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.442 | |
| 3s7a | 684 | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3unj | 0BX | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.442 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 4ruj | VDX | Vitamin D3 receptor A | / | 0.442 | |
| 1bvr | THT | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.441 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.441 | |
| 2m56 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 2pmd | GNP | Translation initiation factor 2 subunit gamma | / | 0.441 | |
| 2qd3 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.441 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.441 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.441 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.441 | |
| 3lxi | CAM | Cytochrome P450 | / | 0.441 | |
| 3srq | Q19 | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3v9v | 21L | Peroxisome proliferator-activated receptor gamma | / | 0.441 | |
| 4fkr | 45K | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.441 | |
| 6cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.440 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 2pe0 | 39Z | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.440 | |
| 2pe2 | 464 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.440 | |
| 2wot | ZZG | TGF-beta receptor type-1 | 2.7.11.30 | 0.440 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.440 | |
| 3i59 | N6R | CRP-like cAMP-activated global transcriptional regulator | / | 0.440 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.440 |