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 |
|---|---|---|---|
| 1kmv | LII | Dihydrofolate reductase | 1.5.1.3 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1kmv | LII | Dihydrofolate reductase | 1.5.1.3 | 1.000 | |
| 1kms | LIH | Dihydrofolate reductase | 1.5.1.3 | 0.688 | |
| 3gi2 | GHW | Dihydrofolate reductase | 1.5.1.3 | 0.605 | |
| 3ghw | GHW | Dihydrofolate reductase | 1.5.1.3 | 0.594 | |
| 3l3r | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.593 | |
| 1hfr | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.592 | |
| 2fzj | DH3 | Dihydrofolate reductase | 1.5.1.3 | 0.590 | |
| 2w3m | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.584 | |
| 4keb | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.583 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.581 | |
| 3ghv | GHC | Dihydrofolate reductase | 1.5.1.3 | 0.578 | |
| 3ntz | 3TZ | Dihydrofolate reductase | 1.5.1.3 | 0.578 | |
| 3gyf | 51P | Dihydrofolate reductase | 1.5.1.3 | 0.576 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.572 | |
| 4m6l | 21V | Dihydrofolate reductase | 1.5.1.3 | 0.570 | |
| 1u72 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.558 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.550 | |
| 1pd8 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.548 | |
| 3nu0 | 3TU | Dihydrofolate reductase | 1.5.1.3 | 0.548 | |
| 1ohj | COP | Dihydrofolate reductase | 1.5.1.3 | 0.546 | |
| 1mvt | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.545 | |
| 3s7a | 684 | Dihydrofolate reductase | 1.5.1.3 | 0.544 | |
| 4m6k | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.538 | |
| 1drf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.537 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.532 | |
| 1s3v | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.528 | |
| 1dhf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.526 | |
| 3d80 | Q22 | Dihydrofolate reductase | 1.5.1.3 | 0.522 | |
| 4eil | FOL | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.522 | |
| 3n0h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.521 | |
| 3s3v | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.519 | |
| 4ky4 | 04J | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.518 | |
| 3nrr | D16 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.516 | |
| 1yho | TRR | Dihydrofolate reductase | 1.5.1.3 | 0.503 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.501 | |
| 3k45 | 51P | Dihydrofolate reductase | 1.5.1.3 | 0.501 | |
| 4at3 | LTI | BDNF/NT-3 growth factors receptor | 2.7.10.1 | 0.498 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.495 | |
| 1ohk | COP | Dihydrofolate reductase | 1.5.1.3 | 0.494 | |
| 1u70 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.494 | |
| 4kbn | 25U | Dihydrofolate reductase | 1.5.1.3 | 0.488 | |
| 4kfj | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.488 | |
| 3k47 | D09 | Dihydrofolate reductase | 1.5.1.3 | 0.487 | |
| 1hfp | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.484 | |
| 1e26 | GPB | Dihydrofolate reductase | 1.5.1.3 | 0.483 | |
| 4kak | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.481 | |
| 3nxv | D2F | Dihydrofolate reductase | 1.5.1.3 | 0.480 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.477 | |
| 3g4i | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.473 | |
| 1boz | PRD | Dihydrofolate reductase | 1.5.1.3 | 0.472 | |
| 1daj | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.472 | |
| 3g58 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.472 | |
| 3qly | 55V | Uncharacterized protein | / | 0.472 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.470 | |
| 3iro | 2CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.470 | |
| 4dpd | DHF | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.470 | |
| 4g1n | NZT | Pyruvate kinase PKM | 2.7.1.40 | 0.470 | |
| 4kfj | 1R0 | Dihydrofolate reductase | 1.5.1.3 | 0.469 | |
| 1j3i | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.467 | |
| 1uho | VDN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.467 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.467 | |
| 4dbw | 511 | Aldo-keto reductase family 1 member C3 | / | 0.467 | |
| 1q9m | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.466 | |
| 4c1i | EH9 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.466 | |
| 1oyn | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.465 | |
| 3inv | C50 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.465 | |
| 1xoq | ROF | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.464 | |
| 2bak | AQZ | Mitogen-activated protein kinase 14 | / | 0.464 | |
| 2fzi | DH3 | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 3cse | N22 | Uncharacterized protein | / | 0.464 | |
| 3hu2 | AGS | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.464 | |
| 4a9y | AQZ | Mitogen-activated protein kinase 14 | / | 0.464 | |
| 4ixg | IXG | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 2fzh | DH1 | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 1dlr | MXA | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 2q15 | 3MR | Beta-secretase 1 | 3.4.23.46 | 0.462 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.461 | |
| 3iak | EV1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.461 | |
| 4dch | 4DC | Glucokinase | 2.7.1.2 | 0.461 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.460 | |
| 3itu | IBM | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.460 | |
| 4gtv | 7TR | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.460 | |
| 3sl6 | JN8 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.459 | |
| 3zku | HCV | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 1al7 | HST | Peroxisomal (S)-2-hydroxy-acid oxidase | 1.1.3.15 | 0.458 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.458 | |
| 4heu | 15J | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.458 | |
| 4ixe | IXE | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 4qa2 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.458 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 1eji | THF | Serine hydroxymethyltransferase, cytosolic | / | 0.456 | |
| 2fs4 | PZ1 | Renin | 3.4.23.15 | 0.456 | |
| 3c72 | CX1 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.456 | |
| 3o56 | ZG1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.456 | |
| 4qa0 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.456 | |
| 1ejb | INJ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.455 | |
| 1j3k | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.455 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.455 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.454 | |
| 3lfe | Z84 | Mitogen-activated protein kinase 14 | / | 0.454 | |
| 1dr4 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 1y2k | 7DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.453 | |
| 3hv3 | R49 | Mitogen-activated protein kinase 14 | / | 0.453 | |
| 4kd7 | 9DR | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 1ly3 | COG | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.452 | |
| 3gcq | 1BU | Mitogen-activated protein kinase 14 | / | 0.452 | |
| 4dbs | 0HV | Aldo-keto reductase family 1 member C3 | / | 0.452 | |
| 3clb | TMQ | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.451 | |
| 3d3p | 20A | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.451 | |
| 3k4s | 0MO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.451 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.451 | |
| 1w06 | W05 | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 2yne | YNE | Glycylpeptide N-tetradecanoyltransferase | / | 0.450 | |
| 4ddr | MMV | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.450 | |
| 1s3y | TQT | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 2wnb | C5P | CMP-N-acetylneuraminate-beta-galactosamide-alpha-2,3-sialyltransferase 1 | 2.4.99.4 | 0.448 | |
| 1klk | PMD | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1tbb | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.447 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.447 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.447 | |
| 1cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 1dls | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 1pz1 | NAP | General stress protein 69 | / | 0.446 | |
| 3jq8 | DX3 | Pteridine reductase, putative | / | 0.446 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.445 | |
| 1udt | VIA | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.445 | |
| 3d74 | NBB | Pheromone-binding protein ASP1 | / | 0.445 | |
| 4fcb | 0T7 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.445 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.444 | |
| 2iod | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.444 | |
| 2wjo | QUD | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.443 | |
| 1ro6 | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.443 | |
| 1zkn | IBM | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.443 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 2gvc | FAD | Thiol-specific monooxygenase | 1.14.13 | 0.443 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 3eig | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 3ns2 | PYV | Abscisic acid receptor PYL2 | / | 0.443 | |
| 4dph | P65 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.443 | |
| 5cc9 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 2h42 | VIA | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.442 | |
| 2j3j | HC4 | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.442 | |
| 3hxc | BD6 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.442 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3p9t | TCL | Repressor | / | 0.442 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.441 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1zkl | IBM | High affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A | 3.1.4.53 | 0.441 | |
| 3nj0 | PYV | Abscisic acid receptor PYL2 | / | 0.441 | |
| 3o57 | ZG2 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.441 | |
| 3o9l | LPN | Renin | 3.4.23.15 | 0.441 | |
| 3pz2 | 3PZ | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.441 | |
| 3u8h | BHP | Phospholipase A2, membrane associated | / | 0.441 | |
| 4bfy | ZVY | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 4jbt | ASD | Cytochrome P450 monooxygenase | / | 0.441 | |
| 4oex | 5EO | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.441 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.440 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2bla | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.440 | |
| 4lsj | LSJ | Glucocorticoid receptor | / | 0.440 | |
| 5d7q | 4I5 | NAD-dependent protein deacetylase sirtuin-2 | 3.5.1 | 0.440 | |
| 5kf2 | ACO | Predicted acetyltransferase | / | 0.440 |