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 |
|---|---|---|---|
| 3jwc | EKB | Dihydrofolate reductase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3jwc | EKB | Dihydrofolate reductase | / | 1.000 | |
| 3sa1 | 6DR | Dihydrofolate reductase | / | 0.613 | |
| 4xe6 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.573 | |
| 3sa2 | 7DR | Dihydrofolate reductase | / | 0.565 | |
| 3sai | 9DR | Dihydrofolate reductase | / | 0.564 | |
| 3jwm | 5WB | Dihydrofolate reductase | / | 0.562 | |
| 4fgh | 0U6 | Dihydrofolate reductase | 1.5.1.3 | 0.559 | |
| 3sh2 | 5DR | Dihydrofolate reductase | 1.5.1.3 | 0.558 | |
| 4fgg | 0U5 | Dihydrofolate reductase | 1.5.1.3 | 0.554 | |
| 3eek | 53S | Uncharacterized protein | / | 0.553 | |
| 3jw5 | TOP | Dihydrofolate reductase | / | 0.553 | |
| 3fre | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.547 | |
| 3srq | Q19 | Dihydrofolate reductase | 1.5.1.3 | 0.547 | |
| 3frd | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.543 | |
| 2w3v | TOP | Dihydrofolate reductase | / | 0.542 | |
| 4h98 | 14Q | Uncharacterized protein | / | 0.540 | |
| 1dds | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.539 | |
| 3m08 | RAR | Dihydrofolate reductase | 1.5.1.3 | 0.538 | |
| 1cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.537 | |
| 3cse | N22 | Uncharacterized protein | / | 0.535 | |
| 4h96 | 14Q | Dihydrofolate reductase | 1.5.1.3 | 0.534 | |
| 3kjs | DQ1 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.533 | |
| 1klk | PMD | Dihydrofolate reductase | 1.5.1.3 | 0.532 | |
| 3fl8 | RAR | Dihydrofolate reductase | / | 0.532 | |
| 4elb | 34R | Dihydrofolate reductase | / | 0.531 | |
| 2w9s | TOP | Dihydrofolate reductase type 1 from Tn4003 | 1.5.1.3 | 0.530 | |
| 3td8 | D2R | Dihydrofolate reductase | 1.5.1.3 | 0.530 | |
| 3eel | 53T | Uncharacterized protein | / | 0.529 | |
| 1j3i | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.528 | |
| 3jw3 | TOP | Dihydrofolate reductase | / | 0.527 | |
| 3fyw | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.525 | |
| 3qlz | QLZ | Uncharacterized protein | / | 0.525 | |
| 3qls | 55V | Dihydrofolate reductase | 1.5.1.3 | 0.523 | |
| 1tdr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.521 | |
| 3qly | 55V | Uncharacterized protein | / | 0.521 | |
| 1rx3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.520 | |
| 3fra | I2H | Dihydrofolate reductase | 1.5.1.3 | 0.520 | |
| 4elb | 34S | Dihydrofolate reductase | / | 0.518 | |
| 1m7a | MQU | Dihydrofolate reductase | 1.5.1.3 | 0.517 | |
| 3eem | 53V | Uncharacterized protein | / | 0.517 | |
| 3qlx | QLR | Uncharacterized protein | / | 0.517 | |
| 3srr | Q20 | Dihydrofolate reductase | 1.5.1.3 | 0.517 | |
| 3srw | Q27 | Dihydrofolate reductase | 1.5.1.3 | 0.517 | |
| 4ele | 31I | Dihydrofolate reductase | / | 0.515 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.514 | |
| 3iro | 2CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.513 | |
| 3tq9 | MTX | Dihydrofolate reductase | / | 0.511 | |
| 3ia4 | MTX | Dihydrofolate reductase | / | 0.510 | |
| 3qlr | QLR | Dihydrofolate reductase | 1.5.1.3 | 0.510 | |
| 3sru | Q26 | Dihydrofolate reductase | 1.5.1.3 | 0.510 | |
| 2fzh | DH1 | Dihydrofolate reductase | 1.5.1.3 | 0.509 | |
| 2fzi | DH3 | Dihydrofolate reductase | 1.5.1.3 | 0.509 | |
| 3dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.509 | |
| 3dga | RJ1 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.509 | |
| 3inv | C50 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.509 | |
| 3qlw | N22 | Dihydrofolate reductase | 1.5.1.3 | 0.509 | |
| 1dg5 | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.508 | |
| 1re7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.508 | |
| 4m2x | TMQ | Dihydrofolate reductase | 1.5.1.3 | 0.508 | |
| 1diu | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.507 | |
| 1vj3 | TAB | Dihydrofolate reductase | 1.5.1.3 | 0.507 | |
| 4elg | 52J | Dihydrofolate reductase | / | 0.507 | |
| 2cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.506 | |
| 3eej | 53R | Uncharacterized protein | / | 0.506 | |
| 3fy9 | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.506 | |
| 3sgy | 06W | Dihydrofolate reductase | 1.5.1.3 | 0.506 | |
| 3frf | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.504 | |
| 3jsu | KA5 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.504 | |
| 4ixe | IXE | Dihydrofolate reductase | 1.5.1.3 | 0.503 | |
| 4p66 | MTX | Dihydrofolate reductase | / | 0.503 | |
| 2w9g | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.502 | |
| 1j3k | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.499 | |
| 2drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.496 | |
| 3tqb | FOL | Dihydrofolate reductase | / | 0.496 | |
| 4elh | 53I | Dihydrofolate reductase | / | 0.496 | |
| 1df7 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.495 | |
| 3srs | M23 | Dihydrofolate reductase | 1.5.1.3 | 0.495 | |
| 3dat | MTX | Dihydrofolate reductase | / | 0.493 | |
| 3um6 | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.493 | |
| 1aoe | GW3 | Dihydrofolate reductase | 1.5.1.3 | 0.492 | |
| 1dra | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.491 | |
| 3i8a | N22 | Dihydrofolate reductase | 1.5.1.3 | 0.491 | |
| 3cv9 | VDX | Vitamin D3 dihydroxylase | / | 0.489 | |
| 3irn | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.489 | |
| 4h95 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.489 | |
| 3irm | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.488 | |
| 5hi6 | MTX | Dihydrofolate reductase | / | 0.488 | |
| 1ia4 | TQ6 | Dihydrofolate reductase | 1.5.1.3 | 0.487 | |
| 1jol | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.487 | |
| 3fyv | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.487 | |
| 4nx6 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.486 | |
| 4x5f | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.486 | |
| 4x5i | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.486 | |
| 1m78 | CLZ | Dihydrofolate reductase | 1.5.1.3 | 0.484 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.483 | |
| 1ddr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.482 | |
| 3och | 2MX | Dihydrofolate reductase | 1.5.1.3 | 0.482 | |
| 1qzf | FOL | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.481 | |
| 4h97 | 53S | Dihydrofolate reductase | 1.5.1.3 | 0.481 | |
| 2qk8 | MTX | Dihydrofolate reductase | / | 0.480 | |
| 5ccc | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.480 | |
| 1dyj | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.479 | |
| 1drb | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.478 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.478 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.478 | |
| 4x5g | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.478 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.475 | |
| 1rb3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.475 | |
| 3cd2 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.475 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.475 | |
| 1dg7 | WRB | Dihydrofolate reductase | 1.5.1.3 | 0.474 | |
| 2bl9 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.473 | |
| 4dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.473 | |
| 4elf | 35I | Dihydrofolate reductase | / | 0.472 | |
| 4kjj | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.471 | |
| 1daj | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.470 | |
| 4dpd | DHF | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.470 | |
| 4x5j | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.470 | |
| 1dhj | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.469 | |
| 3um5 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.468 | |
| 1rx6 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.467 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.466 | |
| 1rf7 | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 3eig | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 1jom | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 2zza | FOL | Dihydrofolate reductase | / | 0.464 | |
| 1hfp | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 3clb | TMQ | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.463 | |
| 3lu8 | IQX | Serum albumin | / | 0.463 | |
| 3mdv | CL6 | Cholesterol 24-hydroxylase | / | 0.463 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.463 | |
| 3ua5 | 06X | Cytochrome P450 2B6 | 1.14.13 | 0.463 | |
| 4nx7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 3fy8 | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 3sqy | Q11 | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 4j6b | PLO | Cytochrome P450 monooxygenase | / | 0.462 | |
| 1dis | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 2blc | CP7 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.461 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.461 | |
| 2ydo | ADN | Adenosine receptor A2a | / | 0.461 | |
| 1zhz | ERG | Oxysterol-binding protein homolog 4 | / | 0.460 | |
| 3p99 | LNP | Lanosterol 14-alpha-demethylase | / | 0.459 | |
| 1ia3 | TQ5 | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 1rd7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 2vn0 | TDZ | Cytochrome P450 2C8 | / | 0.457 | |
| 1ia1 | TQ3 | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 1q5d | EPB | Epothilone C/D epoxidase | 1.14 | 0.455 | |
| 1rb2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.455 | |
| 2d29 | FAD | Acyl-CoA dehydrogenase | / | 0.455 | |
| 2z7g | EH9 | Adenosine deaminase | 3.5.4.4 | 0.455 | |
| 3l8s | BFF | Mitogen-activated protein kinase 14 | / | 0.455 | |
| 1phg | MYT | Camphor 5-monooxygenase | 1.14.15.1 | 0.454 | |
| 1uml | FR4 | Adenosine deaminase | 3.5.4.4 | 0.454 | |
| 2y98 | MIV | Mycinamicin IV hydroxylase/epoxidase | / | 0.454 | |
| 2nnh | REA | Cytochrome P450 2C8 | / | 0.453 | |
| 3th8 | TH9 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.453 | |
| 4qi9 | MTX | Dihydrofolate reductase | / | 0.453 | |
| 1zg3 | 2HI | Isoflavone 4'-O-methyltransferase | / | 0.452 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.452 | |
| 1e7v | LY2 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.451 | |
| 1iyz | NDP | Probable quinone oxidoreductase | / | 0.451 | |
| 2chw | 039 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.451 | |
| 3fwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.451 | |
| 3tda | PN0 | Cytochrome P450 2D6 | / | 0.451 | |
| 4hw3 | 19G | Induced myeloid leukemia cell differentiation protein Mcl-1 | / | 0.451 | |
| 4ixf | IXF | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 4l9q | 9TP | Serum albumin | / | 0.451 | |
| 1rx7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 4ixg | IXG | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 4k9v | 6AW | Cytochrome P450 3A4 | / | 0.450 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 2bbq | PFG | Thymidylate synthase | / | 0.449 | |
| 4ib4 | ERM | 5-hydroxytryptamine receptor 2B | / | 0.449 | |
| 1ly4 | COQ | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 2d0k | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 2ph5 | NAD | Homospermidine synthase | / | 0.448 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.448 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.448 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.448 | |
| 4nky | 3QZ | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.448 | |
| 1bzf | TMQ | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1cjc | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.447 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.447 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.447 | |
| 3p9t | TCL | Repressor | / | 0.447 | |
| 4g8z | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 4yt5 | H4M | H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ1338 | / | 0.447 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.446 | |
| 3nrr | D16 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.446 | |
| 1m79 | MQ1 | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 2cg5 | COA | L-aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase | 2.7.8 | 0.445 | |
| 3qaq | QAQ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.445 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.445 | |
| 4r20 | AER | Cytochrome P450 family 17 polypeptide 2 | / | 0.445 | |
| 1l8q | ADP | Chromosomal replication initiator protein DnaA | / | 0.444 | |
| 1mc5 | AHE | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.444 | |
| 2b37 | 8PS | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 3qg2 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.444 | |
| 3ql3 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.444 | |
| 3vtc | TK3 | Vitamin D3 receptor | / | 0.444 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.444 | |
| 1j3j | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.443 | |
| 1kij | NOV | DNA gyrase subunit B | / | 0.443 | |
| 1o5r | FR9 | Adenosine deaminase | 3.5.4.4 | 0.443 | |
| 2w3w | VG9 | Dihydrofolate reductase | / | 0.443 | |
| 3fl9 | TOP | Dihydrofolate reductase | / | 0.443 | |
| 3ix9 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 4kne | 1CY | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1e26 | GPB | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1jut | LYD | Thymidylate synthase | / | 0.442 | |
| 4f1s | F1S | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.442 | |
| 4hni | 16W | Casein kinase I isoform epsilon | 2.7.11.1 | 0.442 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.442 | |
| 1m13 | HYF | Nuclear receptor subfamily 1 group I member 2 | / | 0.441 | |
| 1qnf | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.441 | |
| 1qxl | FR8 | Adenosine deaminase | 3.5.4.4 | 0.441 | |
| 1s3v | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 2hm9 | TRR | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 2m56 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 4a99 | MIY | TetX family tetracycline inactivation enzyme | / | 0.441 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.441 | |
| 4ryv | ZEA | Protein LlR18A | / | 0.441 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.440 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2wuf | KEM | 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase | 3.7.1.17 | 0.440 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.440 | |
| 4ej1 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.440 |