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 |
|---|---|---|---|
| 3l71 | AZO | Cytochrome b |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3l71 | AZO | Cytochrome b | / | 1.000 | |
| 3tgu | WF3 | Cytochrome b | / | 0.671 | |
| 3l70 | JZV | Cytochrome b | / | 0.633 | |
| 1sqp | MYX | Cytochrome b | / | 0.588 | |
| 1sqb | AZO | Cytochrome b | / | 0.577 | |
| 3h1j | SMA | Cytochrome b | / | 0.511 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.501 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.497 | |
| 4nc3 | ERM | 5-hydroxytryptamine receptor 2B | / | 0.496 | |
| 3bfa | 9OD | Odorant binding protein ASP1 | / | 0.489 | |
| 3aba | FLI | Cytochrome P450 | / | 0.487 | |
| 4o76 | 1M3 | Bromodomain-containing protein 4 | / | 0.487 | |
| 3ar4 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.486 | |
| 1zg3 | 2HI | Isoflavone 4'-O-methyltransferase | / | 0.480 | |
| 3p9t | TCL | Repressor | / | 0.480 | |
| 1og5 | SWF | Cytochrome P450 2C9 | / | 0.478 | |
| 1pp9 | SMA | Cytochrome b | / | 0.478 | |
| 1tdu | CB3 | Thymidylate synthase | / | 0.478 | |
| 3ar5 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.478 | |
| 4kla | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.478 | |
| 2e9d | B76 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.475 | |
| 3w1w | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.475 | |
| 3ar7 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.474 | |
| 2agv | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.473 | |
| 1ppj | SMA | Cytochrome b | / | 0.472 | |
| 3sgv | 2BJ | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.471 | |
| 1ai9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.470 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.469 | |
| 3gyt | DL4 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.469 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.469 | |
| 4ib4 | ERM | 5-hydroxytryptamine receptor 2B | / | 0.469 | |
| 2azy | CHD | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.468 | |
| 3njo | PYV | Abscisic acid receptor PYR1 | / | 0.468 | |
| 5k2b | ZMA | Adenosine receptor A2a | / | 0.468 | |
| 2acw | UPG | Glycosyltransferase | / | 0.467 | |
| 1tdu | DUR | Thymidylate synthase | / | 0.464 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.464 | |
| 2prh | 238 | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.463 | |
| 1lri | CLR | Beta-elicitin cryptogein | / | 0.462 | |
| 1ly4 | COQ | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 1yin | CM3 | Estrogen receptor | / | 0.462 | |
| 2azz | TCH | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.461 | |
| 2e9a | B28 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.461 | |
| 2jc6 | QPP | Calcium/calmodulin-dependent protein kinase type 1D | 2.7.11.17 | 0.461 | |
| 3ar6 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.461 | |
| 3sl6 | JN8 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.461 | |
| 4kfj | 1R0 | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.460 | |
| 2fto | CB3 | Thymidylate synthase | / | 0.459 | |
| 3fko | FKO | Mitogen-activated protein kinase 14 | / | 0.459 | |
| 1jut | LYD | Thymidylate synthase | / | 0.458 | |
| 2e99 | B08 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.458 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.458 | |
| 4bb5 | HD2 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.458 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 4jvb | 1M0 | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.458 | |
| 2dqs | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.457 | |
| 2hrc | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.457 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.457 | |
| 4qe6 | JN3 | Bile acid receptor | / | 0.457 | |
| 5d7q | 4I5 | NAD-dependent protein deacetylase sirtuin-2 | 3.5.1 | 0.457 | |
| 2cl5 | BIE | Catechol O-methyltransferase | 2.1.1.6 | 0.456 | |
| 3cyz | 9OD | Pheromone-binding protein ASP1 | / | 0.456 | |
| 3nx4 | NAP | Putative oxidoreductase | / | 0.456 | |
| 4dvq | 1CA | Cytochrome P450 11B2, mitochondrial | 1.14.15.4 | 0.456 | |
| 5uvi | ZMA | Adenosine receptor A2a | / | 0.456 | |
| 1ddt | APU | Diphtheria toxin | / | 0.455 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.455 | |
| 1ia1 | TQ3 | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 1w06 | W05 | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 2ynf | WHU | Gag-Pol polyprotein | 2.7.7.49 | 0.455 | |
| 4at0 | FAD | Possible succinate dehydrogenase | / | 0.455 | |
| 5bn3 | ADP | V-type ATP synthase alpha chain | / | 0.455 | |
| 5bn3 | ADP | NEQ263 | / | 0.455 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.455 | |
| 5cpb | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.455 | |
| 3tky | N7I | (Iso)eugenol O-methyltransferase | 2.1.1.146 | 0.454 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 4dqu | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.454 | |
| 4jv6 | 18F | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.454 | |
| 4pnm | NU1 | Tankyrase-2 | 2.4.2.30 | 0.454 | |
| 1s0x | C3S | Nuclear receptor ROR-alpha | / | 0.453 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.453 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.453 | |
| 2qd5 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.453 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 3bfb | 9OD | Pheromone-binding protein ASP1 | / | 0.453 | |
| 3eel | 53T | Uncharacterized protein | / | 0.453 | |
| 3irm | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.453 | |
| 4j6b | PLO | Cytochrome P450 monooxygenase | / | 0.453 | |
| 4nky | 3QZ | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.453 | |
| 4r20 | AER | Cytochrome P450 family 17 polypeptide 2 | / | 0.453 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 1rdt | L79 | Retinoic acid receptor RXR-alpha | / | 0.452 | |
| 3lfc | Z86 | Mitogen-activated protein kinase 14 | / | 0.452 | |
| 3uzc | T4E | Adenosine receptor A2a | / | 0.452 | |
| 1fwm | CB3 | Thymidylate synthase | / | 0.451 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.451 | |
| 1q5d | EPB | Epothilone C/D epoxidase | 1.14 | 0.451 | |
| 1tbb | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.451 | |
| 2b00 | GCH | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.451 | |
| 2b37 | 8PS | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.451 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.451 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.451 | |
| 3ctj | 320 | Hepatocyte growth factor receptor | 2.7.10.1 | 0.451 | |
| 4ubs | DIF | Pentalenic acid synthase | 1.14.15.11 | 0.451 | |
| 5k2a | ZMA | Adenosine receptor A2a | / | 0.451 | |
| 1al8 | DHP | Peroxisomal (S)-2-hydroxy-acid oxidase | 1.1.3.15 | 0.449 | |
| 1nqv | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.449 | |
| 1xuo | LA1 | Integrin alpha-L | / | 0.449 | |
| 2bxo | OPB | Serum albumin | / | 0.449 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.449 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.449 | |
| 2y46 | MIV | Mycinamicin IV hydroxylase/epoxidase | / | 0.449 | |
| 3cx5 | SMA | Cytochrome b | / | 0.449 | |
| 4jda | A9S | Abscisic acid receptor PYL3 | / | 0.449 | |
| 1m79 | MQ1 | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1zga | HMK | Isoflavone 4'-O-methyltransferase | / | 0.448 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.448 | |
| 2h2q | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.448 | |
| 2hm9 | TRR | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 3is9 | AC7 | Gag-Pol polyprotein | 2.7.7.49 | 0.448 | |
| 3oq1 | 3OQ | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.448 | |
| 3vjc | ZGA | Squalene synthase | 2.5.1.21 | 0.448 | |
| 3zia | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.448 | |
| 4h4m | 494 | Gag-Pol polyprotein | 2.7.7.49 | 0.448 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.448 | |
| 4zas | TYD | CalS13 | / | 0.448 | |
| 5k2c | ZMA | Adenosine receptor A2a | / | 0.448 | |
| 2blc | CP7 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.447 | |
| 3cv9 | VDX | Vitamin D3 dihydroxylase | / | 0.447 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.447 | |
| 3wd9 | QPC | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.447 | |
| 3zsh | 469 | Mitogen-activated protein kinase 14 | / | 0.447 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.447 | |
| 5jtb | ZMA | Adenosine receptor A2a | / | 0.447 | |
| 1bvr | THT | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.446 | |
| 1enz | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.446 | |
| 3fu9 | KIB | Laccase-1 | 1.10.3.2 | 0.446 | |
| 3nwl | NDP | Catalase | 1.11.1.6 | 0.446 | |
| 3pn1 | IVH | DNA ligase | / | 0.446 | |
| 4hw3 | 19G | Induced myeloid leukemia cell differentiation protein Mcl-1 | / | 0.446 | |
| 4iui | 1GQ | Estrogen receptor | / | 0.446 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.446 | |
| 1cdo | NAD | Alcohol dehydrogenase 1 | 1.1.1.1 | 0.445 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.445 | |
| 1wrl | TFP | Troponin C, slow skeletal and cardiac muscles | / | 0.445 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.445 | |
| 2ydo | ADN | Adenosine receptor A2a | / | 0.445 | |
| 4dsc | A8S | Abscisic acid receptor PYL3 | / | 0.445 | |
| 5d7p | OCZ | NAD-dependent protein deacetylase sirtuin-2 | 3.5.1 | 0.445 | |
| 1ia3 | TQ5 | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1qv1 | CZH | Obelin | / | 0.444 | |
| 2aib | ERG | Beta-elicitin cinnamomin | / | 0.444 | |
| 2pr2 | DG1 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 2vrb | NAP | Triphenylmethane reductase | / | 0.444 | |
| 3bqd | DAY | Glucocorticoid receptor | / | 0.444 | |
| 3td8 | D2R | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 4ez7 | 2AN | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.444 | |
| 4jbt | ASD | Cytochrome P450 monooxygenase | / | 0.444 | |
| 4qa2 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.444 | |
| 4u95 | MIY | Multidrug efflux pump subunit AcrB | / | 0.444 | |
| 1fdw | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.443 | |
| 1p44 | GEQ | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 2imf | TOM | 2-hydroxychromene-2-carboxylate isomerase | 5.99.1.4 | 0.443 | |
| 2p7z | OHT | Estrogen-related receptor gamma | / | 0.443 | |
| 3t8x | T8X | T-cell surface glycoprotein CD1b | / | 0.443 | |
| 4e0u | 0MV | Cyclic dipeptide N-prenyltransferase | / | 0.443 | |
| 4egn | TWO | Cytochrome P450 | / | 0.443 | |
| 4equ | G6I | Serine/threonine-protein kinase 10 | 2.7.11.1 | 0.443 | |
| 3rey | XAC | Adenosine receptor A2a | / | 0.443 | |
| 1dgb | NDP | Catalase | 1.11.1.6 | 0.442 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.442 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.442 | |
| 1ro6 | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.442 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.442 | |
| 1ysx | 4EB | Serum albumin | / | 0.442 | |
| 3g4i | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 4boe | CLR | Japanin | / | 0.442 | |
| 2jed | LG8 | Protein kinase C theta type | 2.7.11.13 | 0.441 | |
| 2p15 | EZT | Estrogen receptor | / | 0.441 | |
| 2qjy | SMA | Cytochrome b | / | 0.441 | |
| 3anl | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.441 | |
| 3byz | H11 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.441 | |
| 3gyu | DL7 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.441 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.441 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.441 | |
| 4ajw | VWN | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform | 2.7.1.153 | 0.441 | |
| 4bfp | SWY | Tankyrase-2 | 2.4.2.30 | 0.441 | |
| 4bqp | VMY | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 1diu | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1y2k | 7DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.440 | |
| 2zev | B71 | Geranylgeranyl pyrophosphate synthase | / | 0.440 | |
| 3drp | R8E | Gag-Pol polyprotein | 2.7.7.49 | 0.440 | |
| 3fco | IIG | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.440 | |
| 3tvx | PNX | cAMP-specific 3',5'-cyclic phosphodiesterase 4A | 3.1.4.53 | 0.440 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.440 | |
| 4cjx | 9L9 | C-1-tetrahydrofolate synthase, cytoplasmic, putative | / | 0.440 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.440 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 4g1n | NZT | Pyruvate kinase PKM | 2.7.1.40 | 0.440 | |
| 4hyf | 1AK | Tankyrase-2 | 2.4.2.30 | 0.440 | |
| 4pv5 | CBW | Lactoylglutathione lyase | 4.4.1.5 | 0.440 |