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 |
|---|---|---|---|
| 2lbd | REA | Retinoic acid receptor gamma |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2lbd | REA | Retinoic acid receptor gamma | / | 1.000 | |
| 1fd0 | 254 | Retinoic acid receptor gamma | / | 0.676 | |
| 4dm6 | TTB | Retinoic acid receptor beta | / | 0.676 | |
| 1fcx | 184 | Retinoic acid receptor gamma | / | 0.675 | |
| 1fcy | 564 | Retinoic acid receptor gamma | / | 0.658 | |
| 4dm8 | REA | Retinoic acid receptor beta | / | 0.658 | |
| 1exa | 394 | Retinoic acid receptor gamma | / | 0.613 | |
| 1xdk | REA | Retinoic acid receptor beta | / | 0.589 | |
| 1diu | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.512 | |
| 2pnc | CLU | Primary amine oxidase, liver isozyme | / | 0.502 | |
| 1q5d | EPB | Epothilone C/D epoxidase | 1.14 | 0.497 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.496 | |
| 4ele | 31I | Dihydrofolate reductase | / | 0.495 | |
| 1iyz | NDP | Probable quinone oxidoreductase | / | 0.493 | |
| 4elb | 34R | Dihydrofolate reductase | / | 0.493 | |
| 2j9l | ATP | H(+)/Cl(-) exchange transporter 5 | / | 0.492 | |
| 2hm9 | TRR | Dihydrofolate reductase | 1.5.1.3 | 0.491 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.490 | |
| 1dis | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.489 | |
| 1h36 | R88 | Squalene--hopene cyclase | 4.2.1.129 | 0.489 | |
| 4b1f | KRH | Glutamate racemase | / | 0.487 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.486 | |
| 4elf | 35I | Dihydrofolate reductase | / | 0.485 | |
| 3fmz | 2T1 | Retinol-binding protein 4 | / | 0.484 | |
| 3irm | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.484 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.484 | |
| 3t8x | T8X | T-cell surface glycoprotein CD1b | / | 0.484 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.484 | |
| 2cul | FAD | GidA-related protein | / | 0.483 | |
| 4gi2 | NAP | Crotonyl-CoA carboxylase/reductase | / | 0.483 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.483 | |
| 2xc3 | RT8 | Steroid C26-monooxygenase | 1.14.13.141 | 0.482 | |
| 2ydo | ADN | Adenosine receptor A2a | / | 0.482 | |
| 4pnm | NU1 | Tankyrase-2 | 2.4.2.30 | 0.480 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.479 | |
| 4o1m | NAD | Enoyl-acyl carrier reductase | / | 0.479 | |
| 3up3 | XCA | aceDAF-12 | / | 0.478 | |
| 4bb5 | HD2 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.477 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.477 | |
| 2xkc | 4VQ | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.476 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.475 | |
| 3fl9 | TOP | Dihydrofolate reductase | / | 0.475 | |
| 4b8u | IBK | 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase | 4.2.1.59 | 0.475 | |
| 1ezf | IN0 | Squalene synthase | 2.5.1.21 | 0.474 | |
| 1fdu | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.474 | |
| 4cjx | 9L9 | C-1-tetrahydrofolate synthase, cytoplasmic, putative | / | 0.474 | |
| 2lf1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.473 | |
| 1bzf | TMQ | Dihydrofolate reductase | 1.5.1.3 | 0.472 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.472 | |
| 4elg | 52J | Dihydrofolate reductase | / | 0.472 | |
| 2q4w | FAD | Cytokinin dehydrogenase 7 | 1.5.99.12 | 0.471 | |
| 2yki | YKI | Heat shock protein HSP 90-alpha | / | 0.471 | |
| 3ihg | FAD | Aklavinone 12-hydroxylase RdmE | / | 0.471 | |
| 1drf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.469 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.469 | |
| 4mfb | 29T | Gag-Pol polyprotein | 2.7.7.49 | 0.469 | |
| 1dhf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.468 | |
| 1n4s | CYS_VAL_ILE_LEU_GER | Geranylgeranyl transferase type-1 subunit beta | 2.5.1.59 | 0.468 | |
| 2qk8 | MTX | Dihydrofolate reductase | / | 0.468 | |
| 3fl8 | RAR | Dihydrofolate reductase | / | 0.468 | |
| 3inv | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.468 | |
| 4elb | 34S | Dihydrofolate reductase | / | 0.468 | |
| 1o6r | R19 | Squalene--hopene cyclase | 4.2.1.129 | 0.466 | |
| 1yc2 | NAD | NAD-dependent protein deacylase 2 | / | 0.466 | |
| 2qd5 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.466 | |
| 4eil | FOL | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.466 | |
| 1d3h | A26 | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.465 | |
| 1s7g | NAD | NAD-dependent protein deacylase 2 | / | 0.465 | |
| 3byz | H11 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.465 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.464 | |
| 3eig | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 3pm9 | FAD | Putative oxidoreductase | / | 0.464 | |
| 4gki | 0JN | Aminoglycoside 3'-phosphotransferase AphA1-IAB | / | 0.464 | |
| 1fds | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.463 | |
| 2ntj | P1H | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.463 | |
| 2qo6 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.463 | |
| 3iw8 | HIZ | Mitogen-activated protein kinase 14 | / | 0.463 | |
| 1rd4 | L08 | Integrin alpha-L | / | 0.462 | |
| 2bkt | RPF | Renin | 3.4.23.15 | 0.462 | |
| 2iod | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.462 | |
| 2ydv | NEC | Adenosine receptor A2a | / | 0.462 | |
| 3n0h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.462 | |
| 4jbt | ASD | Cytochrome P450 monooxygenase | / | 0.462 | |
| 2bel | CBO | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.461 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.461 | |
| 4b0j | 3MQ | 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase | 4.2.1.59 | 0.461 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.461 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.460 | |
| 3sfh | 1DI | Histone deacetylase 8 | 3.5.1.98 | 0.460 | |
| 2bxo | OPB | Serum albumin | / | 0.459 | |
| 3is9 | AC7 | Gag-Pol polyprotein | 2.7.7.49 | 0.459 | |
| 3lfc | Z86 | Mitogen-activated protein kinase 14 | / | 0.459 | |
| 3qlh | T27 | Gag-Pol polyprotein | 2.7.7.49 | 0.459 | |
| 1j3j | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.458 | |
| 1o6q | R17 | Squalene--hopene cyclase | 4.2.1.129 | 0.458 | |
| 2ykj | YKJ | Heat shock protein HSP 90-alpha | / | 0.458 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.457 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.457 | |
| 1xu7 | CPS | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.457 | |
| 2azz | TCH | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.457 | |
| 3anm | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.457 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.457 | |
| 1ia4 | TQ6 | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 2h2q | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.456 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.456 | |
| 3hxf | BD9 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.456 | |
| 3vwe | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.456 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 4j6b | PLO | Cytochrome P450 monooxygenase | / | 0.456 | |
| 1fel | FEN | Retinol-binding protein 4 | / | 0.455 | |
| 1n4h | REA | Nuclear receptor ROR-beta | / | 0.455 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.455 | |
| 2gvc | FAD | Thiol-specific monooxygenase | 1.14.13 | 0.455 | |
| 4fc0 | 0T2 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.455 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.455 | |
| 2e0n | SAH | Precorrin-2 C20-methyltransferase | / | 0.454 | |
| 3gyu | DL7 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.454 | |
| 3up0 | D7S | aceDAF-12 | / | 0.454 | |
| 4bqu | CLR | Japanin | / | 0.454 | |
| 4elh | 53I | Dihydrofolate reductase | / | 0.454 | |
| 5dp2 | NAP | CurF | / | 0.454 | |
| 5hi6 | MTX | Dihydrofolate reductase | / | 0.454 | |
| 1rf7 | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 2b00 | GCH | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.453 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.453 | |
| 3p9t | TCL | Repressor | / | 0.453 | |
| 1x1d | SAH | C-20 methyltransferase | / | 0.452 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.452 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.452 | |
| 2zb8 | IMN | Prostaglandin reductase 2 | 1.3.1.48 | 0.452 | |
| 2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.452 | |
| 3aba | FLI | Cytochrome P450 | / | 0.452 | |
| 4ej1 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 5cto | NTD | 4-hydroxyphenylpyruvate dioxygenase | 1.13.11.27 | 0.452 | |
| 2b35 | TCL | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.451 | |
| 2e48 | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.451 | |
| 3dg8 | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.451 | |
| 3glu | LYS_VAL_MET | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | 3.5.1 | 0.451 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.450 | |
| 4awo | 99B | Heat shock protein HSP 90-alpha | / | 0.450 | |
| 4dhy | S41 | Glucokinase | 2.7.1.2 | 0.450 | |
| 1gky | 5GP | Guanylate kinase | 2.7.4.8 | 0.449 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.449 | |
| 3bxx | QUE | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.449 | |
| 4i42 | 1HA | 1,4-dihydroxy-2-naphthoyl-CoA synthase | / | 0.449 | |
| 4o76 | 1M3 | Bromodomain-containing protein 4 | / | 0.449 | |
| 4qi9 | MTX | Dihydrofolate reductase | / | 0.449 | |
| 1uy8 | PU5 | Heat shock protein HSP 90-alpha | / | 0.448 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 2p1t | 3TN | Retinoic acid receptor RXR-alpha | / | 0.448 | |
| 3ox4 | NAD | Alcohol dehydrogenase 2 | 1.1.1.1 | 0.448 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.448 | |
| 1xuo | LA1 | Integrin alpha-L | / | 0.447 | |
| 2p4i | MR9 | Angiopoietin-1 receptor | 2.7.10.1 | 0.447 | |
| 2rjp | 886 | A disintegrin and metalloproteinase with thrombospondin motifs 4 | 3.4.24.82 | 0.447 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.447 | |
| 3h6k | 33T | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.447 | |
| 3s3v | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 3tky | N7I | (Iso)eugenol O-methyltransferase | 2.1.1.146 | 0.447 | |
| 3w5e | NVW | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.447 | |
| 1jom | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 1uyh | PU0 | Heat shock protein HSP 90-alpha | / | 0.446 | |
| 2vna | NAP | Prostaglandin reductase 2 | 1.3.1.48 | 0.446 | |
| 2yhu | WHF | Pteridine reductase | / | 0.446 | |
| 3irx | UDR | Gag-Pol polyprotein | 2.7.7.49 | 0.446 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.446 | |
| 4iwv | 1J9 | Glucokinase | 2.7.1.2 | 0.446 | |
| 5emh | NAP | Iridoid synthase | 1.3.1.99 | 0.446 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 1h35 | R01 | Squalene--hopene cyclase | 4.2.1.129 | 0.445 | |
| 1j3k | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.445 | |
| 3bfb | 9OD | Pheromone-binding protein ASP1 | / | 0.445 | |
| 3elu | SAM | Methyltransferase | / | 0.445 | |
| 3kpk | FAD | Sulfide-quinone reductase | / | 0.445 | |
| 4klr | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.445 | |
| 4xbf | FAD | Lysine-specific histone demethylase 1A | 1 | 0.445 | |
| 1b87 | ACO | Aac(6')-Ii protein | / | 0.444 | |
| 1dds | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 3sso | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.444 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.444 | |
| 4ifv | T27 | Gag-Pol polyprotein | 2.7.7.49 | 0.444 | |
| 1mvt | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1p44 | GEQ | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.443 | |
| 2psw | COA | N-alpha-acetyltransferase 50 | / | 0.443 | |
| 3g49 | 3G4 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.443 | |
| 4b5n | FMN | NAD(P)H:flavin oxidoreductase Sye4 | / | 0.443 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.443 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.443 | |
| 4ksp | 1SU | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.443 | |
| 4rw6 | 494 | Gag-Pol polyprotein | 2.7.7.49 | 0.443 | |
| 5ab6 | CAA | Nonspecific lipid-transfer protein, putative | / | 0.443 | |
| 1fp1 | HCC | Isoliquiritigenin 2'-O-methyltransferase | / | 0.442 | |
| 1zg3 | 2HI | Isoflavone 4'-O-methyltransferase | / | 0.442 | |
| 2aib | ERG | Beta-elicitin cinnamomin | / | 0.442 | |
| 2fs4 | PZ1 | Renin | 3.4.23.15 | 0.442 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.442 | |
| 3g4g | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 3ix9 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 4r20 | AER | Cytochrome P450 family 17 polypeptide 2 | / | 0.442 | |
| 1ayp | INB | Phospholipase A2, membrane associated | / | 0.441 | |
| 1nzy | BCA | 4-chlorobenzoyl coenzyme A dehalogenase | 3.8.1.7 | 0.441 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.441 | |
| 2b36 | 5PP | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 3cxh | SMA | Cytochrome b | / | 0.441 | |
| 4ajg | F07 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.441 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.441 | |
| 4g31 | 0WH | Eukaryotic translation initiation factor 2-alpha kinase 3 | 2.7.11.1 | 0.441 | |
| 4id5 | T27 | Gag-Pol polyprotein | 2.7.7.49 | 0.441 | |
| 4wdb | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.441 | |
| 5ab7 | MLC | Nonspecific lipid-transfer protein, putative | / | 0.441 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1cdo | NAD | Alcohol dehydrogenase 1 | 1.1.1.1 | 0.440 | |
| 1uyd | PU8 | Heat shock protein HSP 90-alpha | / | 0.440 | |
| 1w22 | NHB | Histone deacetylase 8 | 3.5.1.98 | 0.440 | |
| 3dei | RXB | Caspase-3 | 3.4.22.56 | 0.440 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.440 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.440 | |
| 3w8w | FAD | Putative FAD-dependent oxygenase EncM | / | 0.440 | |
| 4cax | 646 | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.440 | |
| 4gg1 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.440 | |
| 4nie | NBH | Nuclear receptor ROR-gamma | / | 0.440 | |
| 5dcy | NAP | Iridoid synthase | 1.3.1.99 | 0.440 | |
| 5uvi | ZMA | Adenosine receptor A2a | / | 0.440 |