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 |
|---|---|---|---|
| 1rx5 | DDF | Dihydrofolate reductase | 1.5.1.3 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1rx5 | DDF | Dihydrofolate reductase | 1.5.1.3 | 1.000 | |
| 1rx7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.752 | |
| 1rx6 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.666 | |
| 1rf7 | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.639 | |
| 1rx4 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.620 | |
| 1re7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.597 | |
| 5ccc | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.594 | |
| 1rx8 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.581 | |
| 4i13 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.579 | |
| 1dyi | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.575 | |
| 3och | 2MX | Dihydrofolate reductase | 1.5.1.3 | 0.573 | |
| 4ej1 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.566 | |
| 1dds | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.564 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.564 | |
| 4i1n | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.563 | |
| 1tdr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.558 | |
| 1ddr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.557 | |
| 1rc4 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.553 | |
| 1dra | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.552 | |
| 1jol | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.552 | |
| 1ra3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.551 | |
| 5hi6 | MTX | Dihydrofolate reductase | / | 0.544 | |
| 4x5j | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.541 | |
| 3eig | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.538 | |
| 4dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.538 | |
| 1jom | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.536 | |
| 5cc9 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.536 | |
| 1dr3 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.531 | |
| 1ra8 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.531 | |
| 3irm | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.531 | |
| 1rb3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.530 | |
| 4x5i | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.529 | |
| 1dyh | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.526 | |
| 1dyj | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.524 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.523 | |
| 1dhj | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.521 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.521 | |
| 1rb2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.520 | |
| 2drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.518 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.516 | |
| 2d0k | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.509 | |
| 1ia3 | TQ5 | Dihydrofolate reductase | 1.5.1.3 | 0.504 | |
| 4x5h | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.503 | |
| 1ia4 | TQ6 | Dihydrofolate reductase | 1.5.1.3 | 0.502 | |
| 1rd7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.497 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.496 | |
| 1drb | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.493 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.488 | |
| 1dhi | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.485 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.484 | |
| 1ao8 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.482 | |
| 3sgv | 2BJ | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.479 | |
| 4elb | 34S | Dihydrofolate reductase | / | 0.479 | |
| 4kne | 1CY | Dihydrofolate reductase | 1.5.1.3 | 0.479 | |
| 4xe6 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.479 | |
| 1dhf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.476 | |
| 1s3v | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.474 | |
| 2w9s | TOP | Dihydrofolate reductase type 1 from Tn4003 | 1.5.1.3 | 0.474 | |
| 1bzf | TMQ | Dihydrofolate reductase | 1.5.1.3 | 0.473 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.472 | |
| 3ar5 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.471 | |
| 3pz2 | 3PZ | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.471 | |
| 1cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.470 | |
| 3bac | 3B9 | DNA ligase | / | 0.468 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.468 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.468 | |
| 1jio | DEB | 6-deoxyerythronolide B hydroxylase | / | 0.467 | |
| 2azz | TCH | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.466 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.466 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.464 | |
| 1j3j | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.464 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.464 | |
| 3mdv | CL6 | Cholesterol 24-hydroxylase | / | 0.464 | |
| 3pm1 | ET | HTH-type transcriptional regulator QacR | / | 0.464 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.464 | |
| 3vt6 | 5YI | Vitamin D3 receptor | / | 0.464 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.464 | |
| 4enh | FVX | Cholesterol 24-hydroxylase | / | 0.463 | |
| 1u71 | MXA | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.461 | |
| 3s7a | 684 | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 4l9k | EHF | Serum albumin | / | 0.461 | |
| 1t88 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.460 | |
| 2qk8 | MTX | Dihydrofolate reductase | / | 0.460 | |
| 2w6z | L21 | Biotin carboxylase | 6.3.4.14 | 0.460 | |
| 3n0h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 1t86 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.459 | |
| 3ar4 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.459 | |
| 3t3r | 9PL | Cytochrome P450 2A6 | 1.14.13 | 0.459 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.458 | |
| 2qbo | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.458 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.458 | |
| 4ele | 31I | Dihydrofolate reductase | / | 0.458 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.458 | |
| 2zax | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.457 | |
| 4bgi | I4I | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.457 | |
| 4c1i | EH9 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.457 | |
| 4ge7 | 0K5 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.457 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.456 | |
| 1kt3 | RTL | Retinol-binding protein 4 | / | 0.456 | |
| 3jwc | EKB | Dihydrofolate reductase | / | 0.456 | |
| 3p99 | LNP | Lanosterol 14-alpha-demethylase | / | 0.456 | |
| 3fl8 | RAR | Dihydrofolate reductase | / | 0.455 | |
| 1t87 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.454 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.454 | |
| 3e6o | A55 | Nitric oxide synthase, inducible | 1.14.13.39 | 0.454 | |
| 2g1p | SAH | DNA adenine methylase | 2.1.1.72 | 0.453 | |
| 3l6j | Z90 | Alr2278 protein | / | 0.453 | |
| 4b7s | QLE | Cytochrome P450 monooxygenase PikC | / | 0.453 | |
| 4gbe | SAH | DNA adenine methylase | 2.1.1.72 | 0.453 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 1vi2 | NAD | Quinate/shikimate dehydrogenase | / | 0.452 | |
| 1xu9 | CPS | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.452 | |
| 2cd8 | PXI | Cytochrome P450 monooxygenase PikC | / | 0.452 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.452 | |
| 3zk5 | Z18 | Cytochrome P450 monooxygenase PikC | / | 0.452 | |
| 4e2d | FMN | Dehydrogenase | / | 0.452 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.452 | |
| 4rup | H97 | Vitamin D3 receptor A | / | 0.452 | |
| 1cqp | 803 | Integrin alpha-L | / | 0.451 | |
| 1jip | KTN | 6-deoxyerythronolide B hydroxylase | / | 0.451 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.451 | |
| 1zrz | BI1 | Protein kinase C iota type | 2.7.11.13 | 0.451 | |
| 2azy | CHD | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.451 | |
| 2y37 | A54 | Nitric oxide synthase, inducible | 1.14.13.39 | 0.451 | |
| 1fml | RTL | Retinol dehydratase | / | 0.450 | |
| 1qnf | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.450 | |
| 2a1n | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 2b00 | GCH | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.450 | |
| 2qbn | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 3s3v | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 4elb | 34R | Dihydrofolate reductase | / | 0.450 | |
| 4l8u | 9AZ | Serum albumin | / | 0.450 | |
| 4v2g | ITC | Tetracycline repressor protein class D | / | 0.450 | |
| 1diu | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 2bla | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.449 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.449 | |
| 2hc4 | VDX | Vitamin D3 receptor A | / | 0.449 | |
| 2y46 | MIV | Mycinamicin IV hydroxylase/epoxidase | / | 0.449 | |
| 3e7i | B2 | Nitric oxide synthase, inducible | 1.14.13.39 | 0.449 | |
| 3qly | 55V | Uncharacterized protein | / | 0.449 | |
| 4dpd | DHF | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.449 | |
| 4fkv | 61K | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.449 | |
| 4hfr | 14M | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.449 | |
| 2bl9 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.448 | |
| 2zb4 | 5OP | Prostaglandin reductase 2 | 1.3.1.48 | 0.448 | |
| 3kjs | DQ1 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.448 | |
| 3qg2 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.448 | |
| 3qlx | QLR | Uncharacterized protein | / | 0.448 | |
| 3sai | 9DR | Dihydrofolate reductase | / | 0.448 | |
| 4bge | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.448 | |
| 4bii | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.448 | |
| 4h95 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.447 | |
| 1m13 | HYF | Nuclear receptor subfamily 1 group I member 2 | / | 0.447 | |
| 2hb7 | O1C | Vitamin D3 receptor | / | 0.447 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.447 | |
| 2uxp | CLM | HTH-type transcriptional regulator TtgR | / | 0.447 | |
| 4e2b | FMN | Dehydrogenase | / | 0.447 | |
| 4h98 | 14Q | Uncharacterized protein | / | 0.447 | |
| 4n6h | EJ4 | Delta-type opioid receptor | / | 0.447 | |
| 1hvy | D16 | Thymidylate synthase | 2.1.1.45 | 0.446 | |
| 1jut | LYD | Thymidylate synthase | / | 0.446 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.446 | |
| 1tez | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.446 | |
| 2xwe | AMF | Glucosylceramidase | 3.2.1.45 | 0.446 | |
| 3zhq | TPP | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.446 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 4fjy | FJY | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.446 | |
| 4qi9 | MTX | Dihydrofolate reductase | / | 0.446 | |
| 1m9j | CLW | Nitric oxide synthase, endothelial | 1.14.13.39 | 0.445 | |
| 1nvr | STU | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.445 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.445 | |
| 2qbl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.445 | |
| 3c0i | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.445 | |
| 3cse | N22 | Uncharacterized protein | / | 0.445 | |
| 3g5h | YTT | Mycocyclosin synthase | 1.14.21.9 | 0.445 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.445 | |
| 4h6p | FMN | Chromate reductase | / | 0.445 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.445 | |
| 4nkv | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.445 | |
| 4yao | FMN | NADPH--cytochrome P450 reductase | / | 0.445 | |
| 1j3i | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.444 | |
| 2pul | ACP | Methylthioribose kinase | 2.7.1.100 | 0.444 | |
| 2q9f | C3S | Cholesterol 24-hydroxylase | / | 0.444 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.444 | |
| 3aba | FLI | Cytochrome P450 | / | 0.444 | |
| 3tvu | B37 | Acetyl-CoA carboxylase | / | 0.444 | |
| 4elg | 52J | Dihydrofolate reductase | / | 0.444 | |
| 4g2h | 0VQ | Vitamin D3 receptor A | / | 0.444 | |
| 4x5f | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.443 | |
| 1rx3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1s4d | SAH | Uroporphyrinogen-III C-methyltransferase | 2.1.1.107 | 0.443 | |
| 3jwm | 5WB | Dihydrofolate reductase | / | 0.443 | |
| 3qgt | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.443 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.443 | |
| 3t2k | FAD | Sulfide-quinone reductase | / | 0.443 | |
| 3t3q | 9PL | Cytochrome P450 2A6 | 1.14.13 | 0.443 | |
| 1e7q | NAP | GDP-L-fucose synthase | / | 0.442 | |
| 1q5d | EPB | Epothilone C/D epoxidase | 1.14 | 0.442 | |
| 1rd4 | L08 | Integrin alpha-L | / | 0.442 | |
| 1tdu | CB3 | Thymidylate synthase | / | 0.442 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 2w6q | OA5 | Biotin carboxylase | 6.3.4.14 | 0.442 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 3csd | EMO | Putative ketoacyl reductase | 1.3.1 | 0.442 | |
| 3lu8 | IQX | Serum albumin | / | 0.442 | |
| 3zsh | 469 | Mitogen-activated protein kinase 14 | / | 0.442 | |
| 4mv1 | ADP | Biotin carboxylase | 6.3.4.14 | 0.442 | |
| 4ruo | BIV | Vitamin D3 receptor A | / | 0.442 | |
| 4uyf | 73B | Bromodomain-containing protein 2 | / | 0.442 | |
| 5hs1 | VOR | Lanosterol 14-alpha demethylase | / | 0.442 | |
| 1eup | ASD | 6-deoxyerythronolide B hydroxylase | / | 0.441 | |
| 1kl2 | FON | Serine hydroxymethyltransferase | / | 0.441 | |
| 1klk | PMD | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1t85 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.441 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.441 | |
| 3qlr | QLR | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3wsb | RWZ | Farnesyltransferase, putative | / | 0.441 | |
| 4g21 | 0VP | Vitamin D3 receptor A | / | 0.441 | |
| 4ryv | ZEA | Protein LlR18A | / | 0.441 | |
| 1kij | NOV | DNA gyrase subunit B | / | 0.440 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.440 | |
| 2fzh | DH1 | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 2ktd | PUC | Prostaglandin-H2 D-isomerase | 5.3.99.2 | 0.440 | |
| 2o7o | DXT | Tetracycline repressor protein class D | / | 0.440 | |
| 2pau | D5M | 5'-deoxynucleotidase YfbR | / | 0.440 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.440 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.440 | |
| 2z97 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.440 | |
| 3cv9 | VDX | Vitamin D3 dihydroxylase | / | 0.440 | |
| 3eej | 53R | Uncharacterized protein | / | 0.440 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.440 | |
| 3w0j | T08 | Vitamin D3 receptor | / | 0.440 | |
| 4egn | TWO | Cytochrome P450 | / | 0.440 | |
| 4lb2 | DM5 | Serum albumin | / | 0.440 | |
| 4zow | CLM | Multidrug transporter MdfA | / | 0.440 |