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 |
|---|---|---|---|
| 3sa2 | 7DR | Dihydrofolate reductase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3sa2 | 7DR | Dihydrofolate reductase | / | 1.000 | |
| 3sa1 | 6DR | Dihydrofolate reductase | / | 0.642 | |
| 3sai | 9DR | Dihydrofolate reductase | / | 0.603 | |
| 4h98 | 14Q | Uncharacterized protein | / | 0.571 | |
| 1rx3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.569 | |
| 3jwm | 5WB | Dihydrofolate reductase | / | 0.569 | |
| 4fgg | 0U5 | Dihydrofolate reductase | 1.5.1.3 | 0.564 | |
| 3jwc | EKB | Dihydrofolate reductase | / | 0.562 | |
| 3eek | 53S | Uncharacterized protein | / | 0.558 | |
| 3cse | N22 | Uncharacterized protein | / | 0.557 | |
| 3fre | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.553 | |
| 4elg | 52J | Dihydrofolate reductase | / | 0.553 | |
| 3eel | 53T | Uncharacterized protein | / | 0.549 | |
| 3jw5 | TOP | Dihydrofolate reductase | / | 0.549 | |
| 3qlz | QLZ | Uncharacterized protein | / | 0.549 | |
| 4ele | 31I | Dihydrofolate reductase | / | 0.547 | |
| 3inv | C50 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.546 | |
| 3kjs | DQ1 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.543 | |
| 3srq | Q19 | Dihydrofolate reductase | 1.5.1.3 | 0.543 | |
| 4xe6 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.543 | |
| 3eem | 53V | Uncharacterized protein | / | 0.541 | |
| 3fl8 | RAR | Dihydrofolate reductase | / | 0.540 | |
| 1cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.538 | |
| 3td8 | D2R | Dihydrofolate reductase | 1.5.1.3 | 0.538 | |
| 3eej | 53R | Uncharacterized protein | / | 0.537 | |
| 2cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.536 | |
| 4elb | 34S | Dihydrofolate reductase | / | 0.536 | |
| 4p66 | MTX | Dihydrofolate reductase | / | 0.536 | |
| 1vj3 | TAB | Dihydrofolate reductase | 1.5.1.3 | 0.531 | |
| 2w3v | TOP | Dihydrofolate reductase | / | 0.531 | |
| 3ia4 | MTX | Dihydrofolate reductase | / | 0.531 | |
| 4x5g | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.531 | |
| 2zza | FOL | Dihydrofolate reductase | / | 0.527 | |
| 2fzi | DH3 | Dihydrofolate reductase | 1.5.1.3 | 0.526 | |
| 3qlx | QLR | Uncharacterized protein | / | 0.525 | |
| 1klk | PMD | Dihydrofolate reductase | 1.5.1.3 | 0.524 | |
| 1tdr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.522 | |
| 4h96 | 14Q | Dihydrofolate reductase | 1.5.1.3 | 0.522 | |
| 3dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.521 | |
| 2drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.520 | |
| 4h95 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.520 | |
| 1dra | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.519 | |
| 3qlw | N22 | Dihydrofolate reductase | 1.5.1.3 | 0.519 | |
| 4x5f | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.519 | |
| 3sh2 | 5DR | Dihydrofolate reductase | 1.5.1.3 | 0.518 | |
| 1m78 | CLZ | Dihydrofolate reductase | 1.5.1.3 | 0.513 | |
| 1df7 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.509 | |
| 1m7a | MQU | Dihydrofolate reductase | 1.5.1.3 | 0.508 | |
| 3fyw | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.508 | |
| 3qls | 55V | Dihydrofolate reductase | 1.5.1.3 | 0.508 | |
| 2fzh | DH1 | Dihydrofolate reductase | 1.5.1.3 | 0.507 | |
| 2w9s | TOP | Dihydrofolate reductase type 1 from Tn4003 | 1.5.1.3 | 0.507 | |
| 3dat | MTX | Dihydrofolate reductase | / | 0.507 | |
| 3qlr | QLR | Dihydrofolate reductase | 1.5.1.3 | 0.507 | |
| 3qly | 55V | Uncharacterized protein | / | 0.505 | |
| 4elb | 34R | Dihydrofolate reductase | / | 0.504 | |
| 4nx6 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.504 | |
| 3iro | 2CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.503 | |
| 4dph | P65 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.503 | |
| 3i8a | N22 | Dihydrofolate reductase | 1.5.1.3 | 0.501 | |
| 1ddr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.500 | |
| 1dyj | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.500 | |
| 4m2x | TMQ | Dihydrofolate reductase | 1.5.1.3 | 0.500 | |
| 1dg5 | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.499 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.499 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.499 | |
| 3frd | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.497 | |
| 3och | 2MX | Dihydrofolate reductase | 1.5.1.3 | 0.497 | |
| 3ix9 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.496 | |
| 1re7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.495 | |
| 1dg7 | WRB | Dihydrofolate reductase | 1.5.1.3 | 0.492 | |
| 1dhj | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.492 | |
| 1jol | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.492 | |
| 3jsu | KA5 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.492 | |
| 1j3k | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.489 | |
| 3srs | M23 | Dihydrofolate reductase | 1.5.1.3 | 0.489 | |
| 1s3y | TQT | Dihydrofolate reductase | 1.5.1.3 | 0.488 | |
| 2bl9 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.488 | |
| 2blc | CP7 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.488 | |
| 1j3i | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.486 | |
| 3cd2 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.486 | |
| 4h97 | 53S | Dihydrofolate reductase | 1.5.1.3 | 0.486 | |
| 1rc4 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.485 | |
| 2w3w | VG9 | Dihydrofolate reductase | / | 0.485 | |
| 3um6 | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.485 | |
| 4nx7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.485 | |
| 1rd7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.484 | |
| 3irn | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.484 | |
| 3jw3 | TOP | Dihydrofolate reductase | / | 0.484 | |
| 4kak | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.483 | |
| 1rb3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.482 | |
| 3clb | TMQ | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.482 | |
| 4fgh | 0U6 | Dihydrofolate reductase | 1.5.1.3 | 0.482 | |
| 5ccc | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.482 | |
| 2qk8 | MTX | Dihydrofolate reductase | / | 0.481 | |
| 4dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.481 | |
| 3sru | Q26 | Dihydrofolate reductase | 1.5.1.3 | 0.480 | |
| 4v2g | ITC | Tetracycline repressor protein class D | / | 0.480 | |
| 1dds | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.479 | |
| 2w9g | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.479 | |
| 2z97 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.479 | |
| 1lud | TRR | Dihydrofolate reductase | 1.5.1.3 | 0.478 | |
| 1rf7 | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.478 | |
| 3dau | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.477 | |
| 5hi6 | MTX | Dihydrofolate reductase | / | 0.477 | |
| 3dga | RJ1 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.476 | |
| 3k47 | D09 | Dihydrofolate reductase | 1.5.1.3 | 0.476 | |
| 3qfx | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.476 | |
| 4ixe | IXE | Dihydrofolate reductase | 1.5.1.3 | 0.476 | |
| 3fyv | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.475 | |
| 1aoe | GW3 | Dihydrofolate reductase | 1.5.1.3 | 0.473 | |
| 1ia2 | TQ4 | Dihydrofolate reductase | 1.5.1.3 | 0.473 | |
| 1rx8 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.473 | |
| 3s2a | 2NQ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.473 | |
| 4elf | 35I | Dihydrofolate reductase | / | 0.473 | |
| 1daj | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.472 | |
| 1j3j | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.472 | |
| 2y8l | ADP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.472 | |
| 1hfp | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.471 | |
| 3qaq | QAQ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.471 | |
| 3tq9 | MTX | Dihydrofolate reductase | / | 0.471 | |
| 3fy9 | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.469 | |
| 3sqy | Q11 | Dihydrofolate reductase | 1.5.1.3 | 0.469 | |
| 1drb | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.468 | |
| 1ly3 | COG | Dihydrofolate reductase | 1.5.1.3 | 0.467 | |
| 3srr | Q20 | Dihydrofolate reductase | 1.5.1.3 | 0.467 | |
| 3um5 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.467 | |
| 1e26 | GPB | Dihydrofolate reductase | 1.5.1.3 | 0.466 | |
| 1rb2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.466 | |
| 3tqb | FOL | Dihydrofolate reductase | / | 0.466 | |
| 4j6b | PLO | Cytochrome P450 monooxygenase | / | 0.466 | |
| 3srw | Q27 | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 3qgt | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.464 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 4ixf | IXF | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 4mv1 | ADP | Biotin carboxylase | 6.3.4.14 | 0.464 | |
| 3m08 | RAR | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.463 | |
| 4kbn | 25U | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 3eig | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 3r33 | 6ME | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 4kd7 | 9DR | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 3frf | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.461 | |
| 3fra | I2H | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 3nxo | D2B | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 4kfj | 1R0 | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 1diu | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 1og5 | SWF | Cytochrome P450 2C9 | / | 0.458 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.458 | |
| 4x5i | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 1ia1 | TQ3 | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 1kij | NOV | DNA gyrase subunit B | / | 0.457 | |
| 1m79 | MQ1 | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 2bla | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.457 | |
| 1cjc | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.456 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.455 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.455 | |
| 4ej1 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.454 | |
| 1dyi | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 2blb | CP7 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.453 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.452 | |
| 3c0g | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.452 | |
| 3ql3 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 1m13 | HYF | Nuclear receptor subfamily 1 group I member 2 | / | 0.451 | |
| 3tda | PN0 | Cytochrome P450 2D6 | / | 0.451 | |
| 4ixg | IXG | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 1boz | PRD | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.450 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 2e98 | B29 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.449 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.449 | |
| 3dg8 | RJ6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.449 | |
| 3t3q | 9PL | Cytochrome P450 2A6 | 1.14.13 | 0.449 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 4nkv | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.449 | |
| 3p99 | LNP | Lanosterol 14-alpha-demethylase | / | 0.448 | |
| 4fjy | FJY | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.448 | |
| 2has | C3O | Vitamin D3 receptor | / | 0.447 | |
| 2ykc | YKC | Heat shock protein HSP 90-alpha | / | 0.447 | |
| 3nrr | D16 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.447 | |
| 3sgv | 2BJ | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.447 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.447 | |
| 4jbt | ASD | Cytochrome P450 monooxygenase | / | 0.447 | |
| 5hs1 | VOR | Lanosterol 14-alpha demethylase | / | 0.447 | |
| 1e7v | LY2 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.446 | |
| 1rx7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 2chw | 039 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.446 | |
| 2vn0 | TDZ | Cytochrome P450 2C8 | / | 0.446 | |
| 3lu8 | IQX | Serum albumin | / | 0.446 | |
| 3rg9 | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.446 | |
| 4bfr | J82 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit beta isoform | 2.7.1.153 | 0.446 | |
| 4m7v | RAR | Dihydrofolate reductase | / | 0.446 | |
| 2hb7 | O1C | Vitamin D3 receptor | / | 0.445 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 4nr4 | 2LK | CREB-binding protein | / | 0.445 | |
| 2zl9 | VDA | Vitamin D3 receptor | / | 0.444 | |
| 4fjz | 4FJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.444 | |
| 5itz | LOC | Tubulin beta-2B chain | / | 0.444 | |
| 1ly4 | COQ | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 2hb8 | MVD | Vitamin D3 receptor | / | 0.443 | |
| 2y98 | MIV | Mycinamicin IV hydroxylase/epoxidase | / | 0.443 | |
| 3qg2 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.443 | |
| 4enh | FVX | Cholesterol 24-hydroxylase | / | 0.443 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.443 | |
| 1i58 | ACP | Chemotaxis protein CheA | 2.7.13.3 | 0.442 | |
| 1ie9 | VDX | Vitamin D3 receptor | / | 0.442 | |
| 1nq7 | ARL | Nuclear receptor ROR-beta | / | 0.442 | |
| 4aox | FAD | Steroid monooxygenase | / | 0.442 | |
| 4iui | 1GQ | Estrogen receptor | / | 0.442 | |
| 4jhz | 1KV | Beta-glucuronidase | 3.2.1.31 | 0.442 | |
| 4mv4 | ACP | Biotin carboxylase | 6.3.4.14 | 0.442 | |
| 4g1y | 0VO | Vitamin D3 receptor A | / | 0.441 | |
| 4l8u | 9AZ | Serum albumin | / | 0.441 | |
| 4muw | 2F4 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.441 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.441 | |
| 4x5j | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3dxj | NE6 | DNA-directed RNA polymerase subunit beta | / | 0.440 | |
| 3dxj | NE6 | DNA-directed RNA polymerase subunit beta' | / | 0.440 |