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 |
|---|---|---|---|
| 3qfx | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3qfx | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 1.000 | |
| 3rg9 | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.602 | |
| 3um5 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.594 | |
| 3inv | C50 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.586 | |
| 1dg5 | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.579 | |
| 4ixe | IXE | Dihydrofolate reductase | 1.5.1.3 | 0.576 | |
| 1klk | PMD | Dihydrofolate reductase | 1.5.1.3 | 0.575 | |
| 4h96 | 14Q | Dihydrofolate reductase | 1.5.1.3 | 0.572 | |
| 4h95 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.570 | |
| 3iro | 2CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.563 | |
| 1j3j | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.561 | |
| 3um6 | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.557 | |
| 1cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.554 | |
| 2bla | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.552 | |
| 3qlz | QLZ | Uncharacterized protein | / | 0.552 | |
| 3dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.550 | |
| 3qlr | QLR | Dihydrofolate reductase | 1.5.1.3 | 0.550 | |
| 2w3v | TOP | Dihydrofolate reductase | / | 0.549 | |
| 3qg2 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.549 | |
| 2bl9 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.548 | |
| 4h97 | 53S | Dihydrofolate reductase | 1.5.1.3 | 0.548 | |
| 3kjs | DQ1 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.546 | |
| 1vj3 | TAB | Dihydrofolate reductase | 1.5.1.3 | 0.545 | |
| 1ia1 | TQ3 | Dihydrofolate reductase | 1.5.1.3 | 0.542 | |
| 1dg7 | WRB | Dihydrofolate reductase | 1.5.1.3 | 0.541 | |
| 3qls | 55V | Dihydrofolate reductase | 1.5.1.3 | 0.541 | |
| 1aoe | GW3 | Dihydrofolate reductase | 1.5.1.3 | 0.539 | |
| 2blb | CP7 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.539 | |
| 3eek | 53S | Uncharacterized protein | / | 0.539 | |
| 1rx3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.536 | |
| 3jsu | KA5 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.536 | |
| 3qlw | N22 | Dihydrofolate reductase | 1.5.1.3 | 0.536 | |
| 3cse | N22 | Uncharacterized protein | / | 0.535 | |
| 1m78 | CLZ | Dihydrofolate reductase | 1.5.1.3 | 0.533 | |
| 4h98 | 14Q | Uncharacterized protein | / | 0.533 | |
| 1hfp | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.532 | |
| 3qgt | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.532 | |
| 3eej | 53R | Uncharacterized protein | / | 0.531 | |
| 3sh2 | 5DR | Dihydrofolate reductase | 1.5.1.3 | 0.531 | |
| 4dpd | DHF | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.530 | |
| 2fzi | DH3 | Dihydrofolate reductase | 1.5.1.3 | 0.529 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.527 | |
| 3td8 | D2R | Dihydrofolate reductase | 1.5.1.3 | 0.526 | |
| 2zza | FOL | Dihydrofolate reductase | / | 0.525 | |
| 2cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.524 | |
| 3irn | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.524 | |
| 3qly | 55V | Uncharacterized protein | / | 0.524 | |
| 3eem | 53V | Uncharacterized protein | / | 0.523 | |
| 3dga | RJ1 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.521 | |
| 3um8 | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.521 | |
| 4p66 | MTX | Dihydrofolate reductase | / | 0.518 | |
| 4xe6 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.518 | |
| 3dg8 | RJ6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.517 | |
| 1m7a | MQU | Dihydrofolate reductase | 1.5.1.3 | 0.516 | |
| 3irm | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.516 | |
| 1j3i | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.515 | |
| 2w3w | VG9 | Dihydrofolate reductase | / | 0.515 | |
| 5ccc | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.515 | |
| 1boz | PRD | Dihydrofolate reductase | 1.5.1.3 | 0.514 | |
| 3qlx | QLR | Uncharacterized protein | / | 0.512 | |
| 4m2x | TMQ | Dihydrofolate reductase | 1.5.1.3 | 0.512 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.508 | |
| 2blc | CP7 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.506 | |
| 1e26 | GPB | Dihydrofolate reductase | 1.5.1.3 | 0.505 | |
| 1qzf | FOL | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.504 | |
| 3i8a | N22 | Dihydrofolate reductase | 1.5.1.3 | 0.504 | |
| 4g8z | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.504 | |
| 3sa1 | 6DR | Dihydrofolate reductase | / | 0.501 | |
| 3eel | 53T | Uncharacterized protein | / | 0.500 | |
| 3ql3 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.500 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.500 | |
| 3fre | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.499 | |
| 4ixf | IXF | Dihydrofolate reductase | 1.5.1.3 | 0.499 | |
| 1daj | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.498 | |
| 3sai | 9DR | Dihydrofolate reductase | / | 0.498 | |
| 3srq | Q19 | Dihydrofolate reductase | 1.5.1.3 | 0.498 | |
| 2w3a | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.497 | |
| 4kfj | 1R0 | Dihydrofolate reductase | 1.5.1.3 | 0.497 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.496 | |
| 4dph | P65 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.496 | |
| 4nx6 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.495 | |
| 4kd7 | 9DR | Dihydrofolate reductase | 1.5.1.3 | 0.494 | |
| 1lud | TRR | Dihydrofolate reductase | 1.5.1.3 | 0.493 | |
| 2fzh | DH1 | Dihydrofolate reductase | 1.5.1.3 | 0.493 | |
| 4kbn | 25U | Dihydrofolate reductase | 1.5.1.3 | 0.492 | |
| 1dds | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.491 | |
| 4nx7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.491 | |
| 3sgy | 06W | Dihydrofolate reductase | 1.5.1.3 | 0.490 | |
| 3k47 | D09 | Dihydrofolate reductase | 1.5.1.3 | 0.489 | |
| 4dp3 | MMV | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.489 | |
| 4ixg | IXG | Dihydrofolate reductase | 1.5.1.3 | 0.488 | |
| 4x5f | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.488 | |
| 1ao8 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.487 | |
| 3eig | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.486 | |
| 3ia4 | MTX | Dihydrofolate reductase | / | 0.486 | |
| 4fgg | 0U5 | Dihydrofolate reductase | 1.5.1.3 | 0.486 | |
| 4x5g | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.485 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.484 | |
| 4m6l | 21V | Dihydrofolate reductase | 1.5.1.3 | 0.484 | |
| 1ddr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.483 | |
| 1s3y | TQT | Dihydrofolate reductase | 1.5.1.3 | 0.482 | |
| 7dfr | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.481 | |
| 4kak | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.480 | |
| 3jwm | 5WB | Dihydrofolate reductase | / | 0.478 | |
| 1j3k | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.476 | |
| 1re7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.475 | |
| 3cd2 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.474 | |
| 4p68 | MTX | Dihydrofolate reductase | / | 0.474 | |
| 1ia4 | TQ6 | Dihydrofolate reductase | 1.5.1.3 | 0.473 | |
| 1rb3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.473 | |
| 3jwc | EKB | Dihydrofolate reductase | / | 0.473 | |
| 1rx7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.472 | |
| 1tdr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.472 | |
| 3frf | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.472 | |
| 3nxt | D2E | Dihydrofolate reductase | 1.5.1.3 | 0.472 | |
| 3fy9 | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.470 | |
| 1ia3 | TQ5 | Dihydrofolate reductase | 1.5.1.3 | 0.469 | |
| 3sa2 | 7DR | Dihydrofolate reductase | / | 0.469 | |
| 4keb | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.469 | |
| 1ia2 | TQ4 | Dihydrofolate reductase | 1.5.1.3 | 0.468 | |
| 1dre | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.467 | |
| 1rh3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.467 | |
| 2jed | LG8 | Protein kinase C theta type | 2.7.11.13 | 0.467 | |
| 3nxo | D2B | Dihydrofolate reductase | 1.5.1.3 | 0.466 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.465 | |
| 3tqb | FOL | Dihydrofolate reductase | / | 0.465 | |
| 1diu | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 3qyo | Q24 | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 3r33 | 6ME | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 1dr4 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 2drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 3dau | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 3nxv | D2F | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 1ra2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 1szm | BI4 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.459 | |
| 3fyw | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 3jw5 | TOP | Dihydrofolate reductase | / | 0.459 | |
| 1ohj | COP | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 3fy8 | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 1hfr | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 3nxy | D2H | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 3ezp | B3N | Histone deacetylase 8 | 3.5.1.98 | 0.456 | |
| 3ghw | GHW | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 3ntz | 3TZ | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 3srs | M23 | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 4ej1 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 4o71 | CPB | Bromodomain-containing protein 4 | / | 0.456 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 3och | 2MX | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 3tq8 | TOP | Dihydrofolate reductase | / | 0.455 | |
| 4i13 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 1bzf | TMQ | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 1dyr | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 1ly4 | COQ | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 1dr3 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 1ly3 | COG | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 3fra | I2H | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 1jlc | FTC | Gag-Pol polyprotein | 2.7.7.49 | 0.451 | |
| 1kms | LIH | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 3sgv | 2BJ | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.451 | |
| 3srw | Q27 | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 1zky | 689 | Estrogen receptor | / | 0.450 | |
| 4gg7 | 0J8 | Hepatocyte growth factor receptor | 2.7.10.1 | 0.450 | |
| 1jol | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 1s3w | TQT | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 3srr | Q20 | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 4fhb | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 4oth | DRN | Serine/threonine-protein kinase N1 | / | 0.449 | |
| 1m79 | MQ1 | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1rx2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 3w0g | W07 | Vitamin D3 receptor | / | 0.448 | |
| 4l8u | 9AZ | Serum albumin | / | 0.448 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 4kjj | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 4lga | A2O | Abscisic acid receptor PYL2 | / | 0.447 | |
| 4x5j | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1dra | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 2nv6 | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.446 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.446 | |
| 3ns2 | PYV | Abscisic acid receptor PYL2 | / | 0.446 | |
| 4fjz | 4FJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.446 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.445 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.445 | |
| 3a4p | DFQ | Hepatocyte growth factor receptor | 2.7.10.1 | 0.445 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.445 | |
| 3o56 | ZG1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.445 | |
| 4r20 | AER | Cytochrome P450 family 17 polypeptide 2 | / | 0.445 | |
| 3bgq | VX2 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.444 | |
| 3sr5 | Q12 | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 4ele | 31I | Dihydrofolate reductase | / | 0.444 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1tbb | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.443 | |
| 4eil | FOL | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.443 | |
| 4elg | 52J | Dihydrofolate reductase | / | 0.443 | |
| 1y2c | 3DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 1y2d | 4DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.442 | |
| 3zku | HCV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 4i8v | BHF | Cytochrome P450 1A1 | 1.14.14.1 | 0.442 | |
| 1rd7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1rx8 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1u72 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3qlh | T27 | Gag-Pol polyprotein | 2.7.7.49 | 0.441 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 4j6b | PLO | Cytochrome P450 monooxygenase | / | 0.441 | |
| 1rb2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 2pr2 | DG1 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 4ddr | MMV | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.440 | |
| 4qa2 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.440 |