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 |
|---|---|---|---|
| 4hhd | FMN | Phototropin-1 | 2.7.11.1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4hhd | FMN | Phototropin-1 | 2.7.11.1 | 1.000 | |
| 4eer | FMN | Phototropin-2 | 2.7.11.1 | 0.620 | |
| 2pr5 | FMN | Blue-light photoreceptor | / | 0.598 | |
| 3ue6 | FMN | Aureochrome1 | / | 0.591 | |
| 5djt | FMN | NPH1-2 | / | 0.590 | |
| 2z6d | FMN | Phototropin-2 | 2.7.11.1 | 0.575 | |
| 5dju | FMN | NPH1-2 | / | 0.569 | |
| 5dkk | FMN | Predicted protein | / | 0.569 | |
| 3is2 | FAD | Vivid PAS protein VVD | / | 0.556 | |
| 4wuj | FMN | Glycoside hydrolase family 15, cellulose signaling associated protein envoy | / | 0.556 | |
| 4eet | FMN | Phototropin-2 | 2.7.11.1 | 0.555 | |
| 4eep | FMN | Phototropin-2 | 2.7.11.1 | 0.552 | |
| 2v1a | FMN | NPH1-1 | / | 0.544 | |
| 3t50 | FMN | Blue-light-activated histidine kinase | 2.7.13.3 | 0.540 | |
| 4eeu | FMN | Phototropin-2 | 2.7.11.1 | 0.538 | |
| 1n9l | FMN | Putative blue light receptor | / | 0.537 | |
| 1n9n | FMN | Putative blue light receptor | / | 0.525 | |
| 3p7n | FMN | Light-activated DNA-binding protein EL222 | / | 0.521 | |
| 1g28 | FMN | PHY3 | / | 0.519 | |
| 2v0u | FMN | NPH1-1 | / | 0.518 | |
| 4r38 | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.516 | |
| 4hj6 | FMN | LOV protein | / | 0.505 | |
| 5efw | FMN | NPH1-1 | / | 0.496 | |
| 2z6c | FMN | Phototropin-1 | 2.7.11.1 | 0.495 | |
| 5j4e | FMN | Sensory box protein | / | 0.492 | |
| 2mwg | FMN | Blue-light photoreceptor | / | 0.488 | |
| 3sw1 | FMN | Sensory box protein | / | 0.484 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.482 | |
| 4ees | FMN | Phototropin-2 | 2.7.11.1 | 0.478 | |
| 3f3s | NAD | Lambda-crystallin homolog | / | 0.476 | |
| 5j3w | FMN | Sensory box protein | / | 0.476 | |
| 1rx8 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.473 | |
| 2p4y | C03 | Peroxisome proliferator-activated receptor gamma | / | 0.472 | |
| 4a6n | FAD | TetX family tetracycline inactivation enzyme | / | 0.472 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.470 | |
| 1t87 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.470 | |
| 2qbo | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.469 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.468 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.467 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.466 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.465 | |
| 2xvw | 9NR | Serum albumin | / | 0.465 | |
| 2clq | STU | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.464 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.464 | |
| 4l4d | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.464 | |
| 1t88 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.463 | |
| 2qbn | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.462 | |
| 4hnb | FMN | LOV protein | / | 0.462 | |
| 1bdl | IM1 | Gag-Pol polyprotein | 3.4.23.16 | 0.461 | |
| 4hj3 | FMN | LOV protein | / | 0.461 | |
| 3t9a | ANP | Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 | / | 0.460 | |
| 4ajd | F04 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.460 | |
| 4bbx | LKF | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.460 | |
| 1ai9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 2m56 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.459 | |
| 3b9l | AZZ | Serum albumin | / | 0.459 | |
| 3hx4 | ANP | Calmodulin-domain protein kinase 1 | / | 0.459 | |
| 1y2b | DEE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.458 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.458 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.458 | |
| 4enh | FVX | Cholesterol 24-hydroxylase | / | 0.458 | |
| 4hj4 | FMN | LOV protein | / | 0.458 | |
| 4i02 | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.458 | |
| 1juv | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.457 | |
| 2qbl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.457 | |
| 2v4l | ABJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.457 | |
| 3sp9 | IL2 | Peroxisome proliferator-activated receptor delta | / | 0.457 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.456 | |
| 2q59 | 240 | Peroxisome proliferator-activated receptor gamma | / | 0.456 | |
| 2wey | EV1 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.456 | |
| 3ml8 | ML8 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.456 | |
| 1dd6 | MCI | Metallo-beta-lactamase type 2 | / | 0.455 | |
| 1m3q | ANG | N-glycosylase/DNA lyase | 3.2.2 | 0.455 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.455 | |
| 2ddo | ATP | Pyridoxine/pyridoxal/pyridoxamine kinase | / | 0.455 | |
| 2qbm | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.455 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 4ysw | FAD | Xanthine dehydrogenase/oxidase | / | 0.455 | |
| 1kqu | BR4 | Phospholipase A2, membrane associated | / | 0.454 | |
| 1kqw | RTL | Cellular retinol-binding protein type II | / | 0.454 | |
| 1kvs | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.454 | |
| 2iea | TDP | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.454 | |
| 2p9c | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.454 | |
| 3u9e | COA | Lmo1369 protein | / | 0.454 | |
| 4l17 | DNQ | Glutamate receptor 2 | / | 0.454 | |
| 3dv3 | MEK | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.453 | |
| 3e8x | NAP | BH1520 protein | / | 0.453 | |
| 4kp7 | 1UQ | 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic | 1.1.1.267 | 0.452 | |
| 1bdr | IM1 | Gag-Pol polyprotein | 3.4.23.16 | 0.451 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.451 | |
| 2gs7 | ANP | Epidermal growth factor receptor | 2.7.10.1 | 0.451 | |
| 2py3 | ACP | Fibroblast growth factor receptor 2 | / | 0.451 | |
| 3zv6 | 4HB | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | 1.3.1.56 | 0.451 | |
| 4ezk | 0SD | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.451 | |
| 4h8n | NDP | NADPH-dependent conjugated polyketone reductase C2 | / | 0.451 | |
| 4heu | 15J | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.451 | |
| 1f20 | FAD | Nitric oxide synthase, brain | 1.14.13.39 | 0.450 | |
| 1i58 | ACP | Chemotaxis protein CheA | 2.7.13.3 | 0.450 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 2zax | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.450 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.450 | |
| 1a72 | PAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.449 | |
| 1g4t | FTP | Thiamine-phosphate synthase | / | 0.449 | |
| 2a5u | QYT | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.449 | |
| 3itz | P66 | Mitogen-activated protein kinase 14 | / | 0.449 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 4lxh | C1E | Alpha/beta hydrolase fold | / | 0.449 | |
| 4u97 | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.449 | |
| 1udb | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.448 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.448 | |
| 3ruq | ADP | Chaperonin | / | 0.448 | |
| 3upf | 0BU | Polyprotein | / | 0.448 | |
| 3vvp | BNU | Uncharacterized protein | / | 0.448 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.447 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3nx2 | FER | Ferulic acid decarboxylase | / | 0.447 | |
| 3t99 | ADP | Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 | / | 0.447 | |
| 1l3i | SAH | Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) | / | 0.446 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 2p6l | SAH | Diphthine synthase | / | 0.446 | |
| 2qa2 | FAD | Polyketide oxygenase CabE | / | 0.446 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.446 | |
| 2vw5 | BC6 | ATP-dependent molecular chaperone HSP82 | / | 0.446 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.446 | |
| 4ajf | F03 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.446 | |
| 4avl | TMP | Polymerase acidic protein | / | 0.446 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.445 | |
| 2fm0 | M98 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.445 | |
| 2xvv | 9DN | Serum albumin | / | 0.445 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.445 | |
| 4ku2 | MYA | 3-oxoacyl-[ACP] synthase III | / | 0.445 | |
| 5eai | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 1f17 | NAI | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.444 | |
| 1n71 | COA | Aac(6')-Ii protein | / | 0.444 | |
| 1ro9 | 8BR | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.444 | |
| 2i4z | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 2j8z | NAP | Quinone oxidoreductase PIG3 | 1 | 0.444 | |
| 3cly | ACP | Fibroblast growth factor receptor 2 | / | 0.444 | |
| 3kji | ADP | CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC | / | 0.444 | |
| 3kjr | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.444 | |
| 3mdm | FJZ | Cholesterol 24-hydroxylase | / | 0.444 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.444 | |
| 4xzn | NAP | Aldo-keto reductase family 1 member B10 | 1.1.1 | 0.444 | |
| 1uho | VDN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.443 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.443 | |
| 1yqj | 6NP | Mitogen-activated protein kinase 14 | / | 0.443 | |
| 2fxv | 5GP | Xanthine phosphoribosyltransferase | 2.4.2.22 | 0.443 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 3v9v | 21L | Peroxisome proliferator-activated receptor gamma | / | 0.443 | |
| 3w5e | NVW | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.443 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.443 | |
| 4kuo | RBF | Putative blue-light photoreceptor | / | 0.443 | |
| 4pd6 | URI | Nucleoside permease | / | 0.443 | |
| 5hes | 032 | Mitogen-activated protein kinase kinase kinase 20 | 2.7.11.25 | 0.443 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 1lsj | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.442 | |
| 1z4i | UMP | 5'(3')-deoxyribonucleotidase, mitochondrial | 3.1.3 | 0.442 | |
| 2hma | SAM | tRNA-specific 2-thiouridylase MnmA | / | 0.442 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2wp9 | CBE | Succinate dehydrogenase iron-sulfur subunit | 1.3.5.1 | 0.442 | |
| 2wp9 | CBE | Succinate dehydrogenase cytochrome b556 subunit | / | 0.442 | |
| 3cpp | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 3gfe | P37 | Mitogen-activated protein kinase 14 | / | 0.442 | |
| 3lj3 | WYE | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.442 | |
| 3pju | C2E | Diguanylate cyclase/phosphodiesterase | / | 0.442 | |
| 4r3a | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.442 | |
| 4zzi | 1NS | NAD-dependent protein deacetylase sirtuin-1 | 3.5.1 | 0.442 | |
| 5cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1s3z | COA | Aminoglycoside N(6')-acetyltransferase type 1 | / | 0.441 | |
| 2chz | 093 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.441 | |
| 2gej | GDD | Phosphatidyl-myo-inositol mannosyltransferase | 2.4.1.57 | 0.441 | |
| 2psv | MUV | Protease | / | 0.441 | |
| 2y3r | TIR | TamL | / | 0.441 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.441 | |
| 3mt8 | 17T | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.441 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.441 | |
| 3s79 | ASD | Aromatase | 1.14.14.14 | 0.441 | |
| 4a6r | TA8 | Probable aminotransferase | / | 0.441 | |
| 4l4f | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.441 | |
| 4wso | NAD | Probable nicotinate-nucleotide adenylyltransferase | / | 0.441 | |
| 4xzm | NAP | Aldo-keto reductase family 1 member B10 | 1.1.1 | 0.441 | |
| 1sxj | AGS | Replication factor C subunit 1 | / | 0.440 | |
| 2bxq | IMN | Serum albumin | / | 0.440 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.440 | |
| 3cnt | FAD | Polyamine oxidase FMS1 | / | 0.440 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4c77 | N01 | Phenylacetone monooxygenase | 1.14.13.92 | 0.440 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.440 |