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 |
|---|---|---|---|
| 5dkk | FMN | Predicted protein |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 5dkk | FMN | Predicted protein | / | 1.000 | |
| 3t50 | FMN | Blue-light-activated histidine kinase | 2.7.13.3 | 0.579 | |
| 3ue6 | FMN | Aureochrome1 | / | 0.573 | |
| 4hhd | FMN | Phototropin-1 | 2.7.11.1 | 0.570 | |
| 2z6d | FMN | Phototropin-2 | 2.7.11.1 | 0.565 | |
| 4eet | FMN | Phototropin-2 | 2.7.11.1 | 0.565 | |
| 5djt | FMN | NPH1-2 | / | 0.565 | |
| 5dju | FMN | NPH1-2 | / | 0.553 | |
| 3is2 | FAD | Vivid PAS protein VVD | / | 0.547 | |
| 4eep | FMN | Phototropin-2 | 2.7.11.1 | 0.544 | |
| 4eer | FMN | Phototropin-2 | 2.7.11.1 | 0.544 | |
| 3p7n | FMN | Light-activated DNA-binding protein EL222 | / | 0.525 | |
| 1n9n | FMN | Putative blue light receptor | / | 0.520 | |
| 2pr5 | FMN | Blue-light photoreceptor | / | 0.520 | |
| 2pd8 | FAD | Vivid PAS protein VVD | / | 0.518 | |
| 2pdt | FAD | Vivid PAS protein VVD | / | 0.512 | |
| 4wuj | FMN | Glycoside hydrolase family 15, cellulose signaling associated protein envoy | / | 0.508 | |
| 2xvv | 9DN | Serum albumin | / | 0.500 | |
| 3sw1 | FMN | Sensory box protein | / | 0.498 | |
| 5efw | FMN | NPH1-1 | / | 0.496 | |
| 4eeu | FMN | Phototropin-2 | 2.7.11.1 | 0.495 | |
| 2pd7 | FAD | Vivid PAS protein VVD | / | 0.494 | |
| 1g28 | FMN | PHY3 | / | 0.490 | |
| 3b9l | AZZ | Serum albumin | / | 0.487 | |
| 2z6c | FMN | Phototropin-1 | 2.7.11.1 | 0.482 | |
| 2xvw | 9NR | Serum albumin | / | 0.479 | |
| 4hj6 | FMN | LOV protein | / | 0.473 | |
| 3hwx | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.472 | |
| 3oet | NAD | Erythronate-4-phosphate dehydrogenase | / | 0.472 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.472 | |
| 2bxq | IMN | Serum albumin | / | 0.470 | |
| 4bls | APC | NTPase P4 | / | 0.470 | |
| 4h4q | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.470 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.467 | |
| 2ch6 | ADP | N-acetyl-D-glucosamine kinase | 2.7.1.59 | 0.467 | |
| 3hji | FAD | Vivid PAS protein VVD | / | 0.467 | |
| 1n9l | FMN | Putative blue light receptor | / | 0.466 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.466 | |
| 4fvq | ATP | Tyrosine-protein kinase JAK2 | / | 0.465 | |
| 2jlc | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.464 | |
| 3u2m | FAD | FAD-linked sulfhydryl oxidase ALR | 1.8.3.2 | 0.464 | |
| 5esd | TDP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.464 | |
| 2ehq | NAP | 1-pyrroline-5-carboxylate dehydrogenase | / | 0.463 | |
| 4ig0 | 1FG | Gag-Pol polyprotein | 2.7.7.49 | 0.462 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.461 | |
| 4hia | FMN | LOV protein | / | 0.461 | |
| 2abj | CBC | Branched-chain-amino-acid aminotransferase, cytosolic | 2.6.1.42 | 0.460 | |
| 4lb2 | DM5 | Serum albumin | / | 0.460 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.459 | |
| 1i24 | UPG | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.457 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.457 | |
| 4l4e | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.457 | |
| 2fvl | NAP | Aldo-keto reductase family 1 member C4 | 1.1.1.225 | 0.456 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.455 | |
| 4xzm | NAP | Aldo-keto reductase family 1 member B10 | 1.1.1 | 0.455 | |
| 1xkd | NAP | Isocitrate dehydrogenase [NADP] | / | 0.454 | |
| 4ees | FMN | Phototropin-2 | 2.7.11.1 | 0.454 | |
| 1uxj | NAD | Malate dehydrogenase | / | 0.453 | |
| 2ehu | NAD | 1-pyrroline-5-carboxylate dehydrogenase | / | 0.453 | |
| 2j40 | NAD | 1-pyrroline-5-carboxylate dehydrogenase | / | 0.453 | |
| 3w4k | 3LD | D-amino-acid oxidase | 1.4.3.3 | 0.453 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.452 | |
| 3s79 | ASD | Aromatase | 1.14.14.14 | 0.452 | |
| 4kfq | KFQ | Glutamate receptor ionotropic, NMDA 1 | / | 0.452 | |
| 3jvh | HHV | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.451 | |
| 5ej4 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.451 | |
| 5ej7 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.451 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.450 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 3t2v | KKJ | Peptidoglycan recognition protein 1 | / | 0.450 | |
| 4wuc | ANP | DNA gyrase subunit B | / | 0.450 | |
| 2v0u | FMN | NPH1-1 | / | 0.449 | |
| 1bxs | NAD | Retinal dehydrogenase 1 | 1.2.1.36 | 0.448 | |
| 1kqg | HQO | Formate dehydrogenase, nitrate-inducible, cytochrome b556(Fdn) subunit | / | 0.448 | |
| 1w49 | APC | NTPase P4 | / | 0.448 | |
| 1w4a | APC | NTPase P4 | / | 0.448 | |
| 1y2k | 7DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.448 | |
| 2fyp | RDE | Endoplasmin | / | 0.448 | |
| 2g37 | FAD | Proline dehydrogenase | / | 0.448 | |
| 3t9a | ANP | Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 | / | 0.448 | |
| 5cb5 | APR | O-acetyl-ADP-ribose deacetylase | / | 0.448 | |
| 1njf | AGS | DNA polymerase III subunit tau | 2.7.7.7 | 0.447 | |
| 1oya | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.447 | |
| 2bpo | NAP | NADPH--cytochrome P450 reductase | / | 0.447 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 1a9y | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.446 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.446 | |
| 1w06 | W05 | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 2qbo | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 4iah | 1DX | Alr2278 protein | / | 0.445 | |
| 1knu | YPA | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 1s60 | COA | Aminoglycoside N(6')-acetyltransferase type 1 | / | 0.444 | |
| 2aq8 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 2bxm | IMN | Serum albumin | / | 0.444 | |
| 3ruh | UD6 | UDP-N-acetylglucosamine 4-epimerase | / | 0.444 | |
| 4fvr | ATP | Tyrosine-protein kinase JAK2 | / | 0.444 | |
| 4yer | ADP | Antibiotic ABC transporter, ATP-binding protein, putative | / | 0.444 | |
| 5j3w | FMN | Sensory box protein | / | 0.444 | |
| 1eio | GCH | Gastrotropin | / | 0.443 | |
| 1sb8 | UD2 | WbpP | / | 0.443 | |
| 2q61 | SF1 | Peroxisome proliferator-activated receptor gamma | / | 0.443 | |
| 2z4s | ADP | Chromosomal replication initiator protein DnaA | / | 0.443 | |
| 3ics | ADP | Coenzyme A disulfide reductase | / | 0.443 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4kp7 | 1UQ | 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic | 1.1.1.267 | 0.443 | |
| 1f20 | NAP | Nitric oxide synthase, brain | 1.14.13.39 | 0.442 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.442 | |
| 2a1o | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.442 | |
| 4rpg | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.442 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.441 | |
| 1m3q | ANG | N-glycosylase/DNA lyase | 3.2.2 | 0.441 | |
| 1ot7 | IU5 | Bile acid receptor | / | 0.441 | |
| 1rx4 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.440 | |
| 2a4z | BYM | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.440 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.440 | |
| 2qen | ADP | Walker-Type ATPase | / | 0.440 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.440 | |
| 3ruq | ADP | Chaperonin | / | 0.440 | |
| 3zv6 | 4HB | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | 1.3.1.56 | 0.440 |