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 |
|---|---|---|---|
| 3dau | MTX | Dihydrofolate reductase | 1.5.1.3 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3dau | MTX | Dihydrofolate reductase | 1.5.1.3 | 1.000 | |
| 2zza | FOL | Dihydrofolate reductase | / | 0.605 | |
| 3ia4 | MTX | Dihydrofolate reductase | / | 0.599 | |
| 4nx6 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.585 | |
| 1rx3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.583 | |
| 3cd2 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.570 | |
| 3ix9 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.568 | |
| 4nx7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.568 | |
| 2fzi | DH3 | Dihydrofolate reductase | 1.5.1.3 | 0.563 | |
| 3dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.560 | |
| 4x5g | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.558 | |
| 1jol | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.557 | |
| 2fzh | DH1 | Dihydrofolate reductase | 1.5.1.3 | 0.555 | |
| 2drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.554 | |
| 1vj3 | TAB | Dihydrofolate reductase | 1.5.1.3 | 0.553 | |
| 3och | 2MX | Dihydrofolate reductase | 1.5.1.3 | 0.552 | |
| 3irm | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.550 | |
| 3kjs | DQ1 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.550 | |
| 1m7a | MQU | Dihydrofolate reductase | 1.5.1.3 | 0.549 | |
| 3iro | 2CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.549 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.547 | |
| 3um6 | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.546 | |
| 1dra | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.541 | |
| 4ixg | IXG | Dihydrofolate reductase | 1.5.1.3 | 0.540 | |
| 1dg7 | WRB | Dihydrofolate reductase | 1.5.1.3 | 0.539 | |
| 3fy9 | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.537 | |
| 4h96 | 14Q | Dihydrofolate reductase | 1.5.1.3 | 0.536 | |
| 1aoe | GW3 | Dihydrofolate reductase | 1.5.1.3 | 0.535 | |
| 3qgt | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.535 | |
| 3qly | 55V | Uncharacterized protein | / | 0.535 | |
| 4ixe | IXE | Dihydrofolate reductase | 1.5.1.3 | 0.533 | |
| 1dyj | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.531 | |
| 4dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.531 | |
| 1daj | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.530 | |
| 1df7 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.530 | |
| 4ele | 31I | Dihydrofolate reductase | / | 0.529 | |
| 3sa2 | 7DR | Dihydrofolate reductase | / | 0.527 | |
| 3tq9 | MTX | Dihydrofolate reductase | / | 0.526 | |
| 3r33 | 6ME | Dihydrofolate reductase | 1.5.1.3 | 0.525 | |
| 1m78 | CLZ | Dihydrofolate reductase | 1.5.1.3 | 0.524 | |
| 2w3v | TOP | Dihydrofolate reductase | / | 0.524 | |
| 4h97 | 53S | Dihydrofolate reductase | 1.5.1.3 | 0.524 | |
| 1dg5 | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.523 | |
| 3qfx | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.523 | |
| 4dp3 | MMV | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.522 | |
| 1rg7 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.520 | |
| 4h95 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.520 | |
| 1tdr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.518 | |
| 3qg2 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.518 | |
| 3qlr | QLR | Dihydrofolate reductase | 1.5.1.3 | 0.518 | |
| 3um5 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.518 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.518 | |
| 1rb3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.517 | |
| 1cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.516 | |
| 1ly3 | COG | Dihydrofolate reductase | 1.5.1.3 | 0.516 | |
| 3eel | 53T | Uncharacterized protein | / | 0.515 | |
| 1dds | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.514 | |
| 1drb | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.514 | |
| 3qyo | Q24 | Dihydrofolate reductase | 1.5.1.3 | 0.513 | |
| 3qlw | N22 | Dihydrofolate reductase | 1.5.1.3 | 0.511 | |
| 1j3j | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.509 | |
| 4kjj | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.509 | |
| 3dat | MTX | Dihydrofolate reductase | / | 0.508 | |
| 3qlz | QLZ | Uncharacterized protein | / | 0.508 | |
| 3sa1 | 6DR | Dihydrofolate reductase | / | 0.508 | |
| 4dpd | DHF | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.508 | |
| 1dre | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.507 | |
| 1j3k | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.507 | |
| 1klk | PMD | Dihydrofolate reductase | 1.5.1.3 | 0.507 | |
| 4ixf | IXF | Dihydrofolate reductase | 1.5.1.3 | 0.507 | |
| 3td8 | D2R | Dihydrofolate reductase | 1.5.1.3 | 0.506 | |
| 3frd | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.505 | |
| 4x5f | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.505 | |
| 3fy8 | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.504 | |
| 3srq | Q19 | Dihydrofolate reductase | 1.5.1.3 | 0.504 | |
| 2blc | CP7 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.503 | |
| 2qk8 | MTX | Dihydrofolate reductase | / | 0.503 | |
| 4elf | 35I | Dihydrofolate reductase | / | 0.502 | |
| 1kms | LIH | Dihydrofolate reductase | 1.5.1.3 | 0.500 | |
| 3dga | RJ1 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.500 | |
| 3jwc | EKB | Dihydrofolate reductase | / | 0.499 | |
| 1ia1 | TQ3 | Dihydrofolate reductase | 1.5.1.3 | 0.498 | |
| 4dph | P65 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.498 | |
| 1m79 | MQ1 | Dihydrofolate reductase | 1.5.1.3 | 0.497 | |
| 4elb | 34S | Dihydrofolate reductase | / | 0.497 | |
| 2blb | CP7 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.496 | |
| 3inv | C50 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.496 | |
| 4m2x | TMQ | Dihydrofolate reductase | 1.5.1.3 | 0.496 | |
| 4xe6 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.496 | |
| 3eem | 53V | Uncharacterized protein | / | 0.495 | |
| 3fyw | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.495 | |
| 3jsu | KA5 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.495 | |
| 2cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.494 | |
| 3eek | 53S | Uncharacterized protein | / | 0.494 | |
| 1ddr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.493 | |
| 3qlx | QLR | Uncharacterized protein | / | 0.493 | |
| 3tqb | FOL | Dihydrofolate reductase | / | 0.493 | |
| 4elg | 52J | Dihydrofolate reductase | / | 0.493 | |
| 4p66 | MTX | Dihydrofolate reductase | / | 0.493 | |
| 2bla | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.491 | |
| 4h98 | 14Q | Uncharacterized protein | / | 0.491 | |
| 3frf | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.489 | |
| 3irn | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.489 | |
| 1j3i | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.488 | |
| 3sru | Q26 | Dihydrofolate reductase | 1.5.1.3 | 0.488 | |
| 1s3y | TQT | Dihydrofolate reductase | 1.5.1.3 | 0.487 | |
| 3jwm | 5WB | Dihydrofolate reductase | / | 0.487 | |
| 3qls | 55V | Dihydrofolate reductase | 1.5.1.3 | 0.487 | |
| 3jw5 | TOP | Dihydrofolate reductase | / | 0.486 | |
| 3um8 | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.486 | |
| 4fgg | 0U5 | Dihydrofolate reductase | 1.5.1.3 | 0.486 | |
| 3sai | 9DR | Dihydrofolate reductase | / | 0.483 | |
| 4eil | FOL | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.483 | |
| 5hi6 | MTX | Dihydrofolate reductase | / | 0.483 | |
| 3srw | Q27 | Dihydrofolate reductase | 1.5.1.3 | 0.482 | |
| 3cse | N22 | Uncharacterized protein | / | 0.481 | |
| 3fyv | XCF | Dihydrofolate reductase | 1.5.1.3 | 0.480 | |
| 4m6l | 21V | Dihydrofolate reductase | 1.5.1.3 | 0.480 | |
| 1ia2 | TQ4 | Dihydrofolate reductase | 1.5.1.3 | 0.479 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.479 | |
| 3eej | 53R | Uncharacterized protein | / | 0.479 | |
| 1e26 | GPB | Dihydrofolate reductase | 1.5.1.3 | 0.477 | |
| 3fre | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.477 | |
| 1rc4 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.473 | |
| 3clb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.473 | |
| 4ky4 | 04J | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.473 | |
| 4x5i | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.471 | |
| 2ay3 | MPP | Aromatic-amino-acid aminotransferase | 2.6.1.57 | 0.470 | |
| 1re7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.469 | |
| 3clb | TMQ | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.467 | |
| 3srs | M23 | Dihydrofolate reductase | 1.5.1.3 | 0.467 | |
| 2fzj | DH3 | Dihydrofolate reductase | 1.5.1.3 | 0.466 | |
| 4x5j | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.466 | |
| 1dyr | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 1ohk | COP | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 2qo4 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.463 | |
| 3m08 | RAR | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 4fgh | 0U6 | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 1zkl | IBM | High affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A | 3.1.4.53 | 0.462 | |
| 1ia3 | TQ5 | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 1ly4 | COQ | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 3a0i | AJI | Glucokinase | 2.7.1.2 | 0.458 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 4cuk | NAI | D-lactate dehydrogenase | / | 0.458 | |
| 1og5 | SWF | Cytochrome P450 2C9 | / | 0.457 | |
| 3sgy | 06W | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 3d80 | Q22 | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 3l3r | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 3sh2 | 5DR | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 4elb | 34R | Dihydrofolate reductase | / | 0.456 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.456 | |
| 3nrr | D16 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.455 | |
| 3jw3 | TOP | Dihydrofolate reductase | / | 0.454 | |
| 3srr | Q20 | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 1jom | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 1rb2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 4m7v | RAR | Dihydrofolate reductase | / | 0.453 | |
| 3fl9 | TOP | Dihydrofolate reductase | / | 0.452 | |
| 4m11 | MXM | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.452 | |
| 3eig | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 3gyf | 51P | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 3qaq | QAQ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.450 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.449 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 4fny | I3K | ALK tyrosine kinase receptor | 2.7.10.1 | 0.449 | |
| 3ddw | 055 | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.448 | |
| 3dho | B2M | Streptogramin A acetyltransferase | 2.3.1 | 0.448 | |
| 3koo | 24D | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.448 | |
| 4fhb | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1x2h | LPA | Lipoate-protein ligase A | 6.3.1.20 | 0.447 | |
| 3k47 | D09 | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1hfp | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 1z1f | STL | Resveratrol synthase | / | 0.446 | |
| 4g8z | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 2oci | TYC | Valacyclovir hydrolase | 3.1 | 0.445 | |
| 3sw8 | 5LI | Peptide deformylase | / | 0.445 | |
| 4i1n | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 2aqh | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 3new | 3NE | Mitogen-activated protein kinase 14 | / | 0.444 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.444 | |
| 4o70 | 1QK | Bromodomain-containing protein 4 | / | 0.444 | |
| 1db4 | 8IN | Phospholipase A2, membrane associated | / | 0.443 | |
| 1fml | RTL | Retinol dehydratase | / | 0.443 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.443 | |
| 2aq8 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.443 | |
| 3iqf | E4M | F420-dependent methylenetetrahydromethanopterin dehydrogenase | 1.5.98.1 | 0.443 | |
| 4bfr | J82 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit beta isoform | 2.7.1.153 | 0.443 | |
| 1e90 | MYC | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.442 | |
| 1ove | 358 | Mitogen-activated protein kinase 14 | / | 0.442 | |
| 2g2h | P16 | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.442 | |
| 2hm9 | TRR | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 2j2i | LY4 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.442 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.442 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.442 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.441 | |
| 2hw2 | RFP | Rifampin ADP-ribosyl transferase | / | 0.441 | |
| 2w9g | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3iqz | H4M | F420-dependent methylenetetrahydromethanopterin dehydrogenase | 1.5.98.1 | 0.441 | |
| 3vjh | J35 | Peroxisome proliferator-activated receptor gamma | / | 0.441 | |
| 3fra | I2H | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 4bbx | LKF | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 |