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 |
|---|---|---|---|
| 1uhl | MEI | Retinoic acid receptor RXR-beta |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1uhl | MEI | Retinoic acid receptor RXR-beta | / | 1.000 | |
| 1k74 | 9CR | Retinoic acid receptor RXR-alpha | / | 0.594 | |
| 3uvv | REA | Retinoic acid receptor RXR-alpha | / | 0.583 | |
| 1fby | REA | Retinoic acid receptor RXR-alpha | / | 0.582 | |
| 1fm6 | 9CR | Retinoic acid receptor RXR-alpha | / | 0.570 | |
| 2p1v | 5TN | Retinoic acid receptor RXR-alpha | / | 0.563 | |
| 1rdt | L79 | Retinoic acid receptor RXR-alpha | / | 0.558 | |
| 2p1u | 4TN | Retinoic acid receptor RXR-alpha | / | 0.558 | |
| 3oap | REA | Retinoic acid receptor RXR-alpha | / | 0.556 | |
| 1mzn | BM6 | Retinoic acid receptor RXR-alpha | / | 0.545 | |
| 3h0a | 9RA | Retinoic acid receptor RXR-alpha | / | 0.543 | |
| 4k6i | 9RA | Retinoic acid receptor RXR-alpha | / | 0.542 | |
| 4m8h | R4M | Retinoic acid receptor RXR-alpha | / | 0.541 | |
| 1xls | REA | Retinoic acid receptor RXR-alpha | / | 0.539 | |
| 2p1t | 3TN | Retinoic acid receptor RXR-alpha | / | 0.539 | |
| 1mvc | BM6 | Retinoic acid receptor RXR-alpha | / | 0.537 | |
| 4k4j | 1O8 | Retinoic acid receptor RXR-alpha | / | 0.532 | |
| 4m8e | 29V | Retinoic acid receptor RXR-alpha | / | 0.530 | |
| 1xiu | REA | Retinoic acid receptor RXR | / | 0.527 | |
| 2acl | REA | Retinoic acid receptor RXR-alpha | / | 0.512 | |
| 3fc6 | REA | Retinoic acid receptor RXR-alpha | / | 0.512 | |
| 1fm9 | 9CR | Retinoic acid receptor RXR-alpha | / | 0.507 | |
| 3fal | REA | Retinoic acid receptor RXR-alpha | / | 0.501 | |
| 1og5 | SWF | Cytochrome P450 2C9 | / | 0.489 | |
| 3fco | IIG | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.482 | |
| 3uza | T4G | Adenosine receptor A2a | / | 0.481 | |
| 1q5d | EPB | Epothilone C/D epoxidase | 1.14 | 0.480 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.478 | |
| 5ai5 | BSU | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.478 | |
| 4j6b | PLO | Cytochrome P450 monooxygenase | / | 0.477 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.477 | |
| 1ia3 | TQ5 | Dihydrofolate reductase | 1.5.1.3 | 0.474 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.473 | |
| 2aqh | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.472 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.469 | |
| 2h2q | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.469 | |
| 5bn3 | ADP | V-type ATP synthase alpha chain | / | 0.468 | |
| 5bn3 | ADP | NEQ263 | / | 0.468 | |
| 2h55 | DZ8 | Heat shock protein HSP 90-alpha | / | 0.467 | |
| 3uzc | T4E | Adenosine receptor A2a | / | 0.467 | |
| 3bxx | QUE | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.466 | |
| 3qg2 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.466 | |
| 1l2j | ETC | Estrogen receptor beta | / | 0.465 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.465 | |
| 2ydo | ADN | Adenosine receptor A2a | / | 0.465 | |
| 3lfc | Z86 | Mitogen-activated protein kinase 14 | / | 0.465 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 1u2g | APR | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.464 | |
| 2p15 | EZT | Estrogen receptor | / | 0.464 | |
| 3jsu | KA5 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.464 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 3njo | PYV | Abscisic acid receptor PYR1 | / | 0.463 | |
| 3vjc | ZGA | Squalene synthase | 2.5.1.21 | 0.463 | |
| 1tbb | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.462 | |
| 1y2k | 7DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.462 | |
| 3t8x | T8X | T-cell surface glycoprotein CD1b | / | 0.462 | |
| 5cpb | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.461 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.460 | |
| 2zb4 | 5OP | Prostaglandin reductase 2 | 1.3.1.48 | 0.460 | |
| 5d7p | OCZ | NAD-dependent protein deacetylase sirtuin-2 | 3.5.1 | 0.460 | |
| 1fpq | SAM | Isoliquiritigenin 2'-O-methyltransferase | / | 0.459 | |
| 1j3j | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.459 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.459 | |
| 4fjz | 4FJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.459 | |
| 2bxq | IMN | Serum albumin | / | 0.458 | |
| 4j03 | FVS | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.458 | |
| 4zas | TYD | CalS13 | / | 0.458 | |
| 1e7a | PFL | Serum albumin | / | 0.457 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 4bii | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.457 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 3hbb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.456 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.456 | |
| 3p9t | TCL | Repressor | / | 0.456 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 4lsj | LSJ | Glucocorticoid receptor | / | 0.456 | |
| 1ia4 | TQ6 | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 3iqe | H4M | F420-dependent methylenetetrahydromethanopterin dehydrogenase | 1.5.98.1 | 0.455 | |
| 3um5 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.455 | |
| 4dpd | DHF | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.455 | |
| 4fex | 0TO | Aminoglycoside 3'-phosphotransferase AphA1-IAB | / | 0.455 | |
| 1q9m | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.454 | |
| 1xuo | LA1 | Integrin alpha-L | / | 0.454 | |
| 3b9l | AZZ | Serum albumin | / | 0.454 | |
| 3oey | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.454 | |
| 3qgt | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.454 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.453 | |
| 2b36 | 5PP | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.453 | |
| 2rab | NAD | Glutathione amide reductase | / | 0.453 | |
| 3pwh | ZMA | Adenosine receptor A2a | / | 0.453 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.452 | |
| 2xvv | 9DN | Serum albumin | / | 0.452 | |
| 2z97 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 3l8s | BFF | Mitogen-activated protein kinase 14 | / | 0.452 | |
| 3r3b | 4CO | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.452 | |
| 3um8 | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.452 | |
| 4qa0 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.452 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.451 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 1tsd | F89 | Thymidylate synthase | / | 0.451 | |
| 3kjs | DQ1 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.451 | |
| 3um6 | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.451 | |
| 4h4m | 494 | Gag-Pol polyprotein | 2.7.7.49 | 0.451 | |
| 4klr | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.451 | |
| 1uyk | PUX | Heat shock protein HSP 90-alpha | / | 0.450 | |
| 2yke | YKE | Heat shock protein HSP 90-alpha | / | 0.450 | |
| 3ar7 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.450 | |
| 3koo | 24D | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.450 | |
| 3ngl | NAP | Bifunctional protein FolD | / | 0.450 | |
| 4fjy | FJY | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.450 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.450 | |
| 4pnm | NU1 | Tankyrase-2 | 2.4.2.30 | 0.450 | |
| 1xor | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.449 | |
| 3qly | 55V | Uncharacterized protein | / | 0.449 | |
| 4zqc | F6F | Tryptophan synthase alpha chain | / | 0.449 | |
| 1mc5 | AHE | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.448 | |
| 1x2h | LPA | Lipoate-protein ligase A | 6.3.1.20 | 0.448 | |
| 1zga | HMK | Isoflavone 4'-O-methyltransferase | / | 0.448 | |
| 2y98 | MIV | Mycinamicin IV hydroxylase/epoxidase | / | 0.448 | |
| 3k4s | 0MO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.448 | |
| 4jvm | XDI | Estrogen sulfotransferase | 2.8.2.4 | 0.448 | |
| 4kne | 1CY | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.448 | |
| 5akk | 1P8 | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.448 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.447 | |
| 2aqi | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.447 | |
| 2aqk | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.447 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.447 | |
| 2pui | ADP | Methylthioribose kinase | 2.7.1.100 | 0.447 | |
| 3anm | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.447 | |
| 3inv | C50 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.447 | |
| 3ua5 | 06X | Cytochrome P450 2B6 | 1.14.13 | 0.447 | |
| 3wav | DWV | Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 | 3.1.4.39 | 0.447 | |
| 4gg7 | 0J8 | Hepatocyte growth factor receptor | 2.7.10.1 | 0.447 | |
| 3rfm | CFF | Adenosine receptor A2a | / | 0.447 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 1ppj | ANY | Cytochrome b | / | 0.446 | |
| 1vru | AAP | Gag-Pol polyprotein | 2.7.7.49 | 0.446 | |
| 1y2c | 3DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.446 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 2hb7 | O1C | Vitamin D3 receptor | / | 0.446 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 3is9 | AC7 | Gag-Pol polyprotein | 2.7.7.49 | 0.446 | |
| 4at3 | LTI | BDNF/NT-3 growth factors receptor | 2.7.10.1 | 0.446 | |
| 4euf | NAD | Trans-2-enoyl-CoA reductase [NADH] | / | 0.446 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.446 | |
| 4nc3 | ERM | 5-hydroxytryptamine receptor 2B | / | 0.446 | |
| 1bvr | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 1dr3 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.445 | |
| 2qd5 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.445 | |
| 4bfr | J82 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit beta isoform | 2.7.1.153 | 0.445 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 4h96 | 14Q | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 4i42 | 1HA | 1,4-dihydroxy-2-naphthoyl-CoA synthase | / | 0.445 | |
| 4p6w | MOF | Glucocorticoid receptor | / | 0.445 | |
| 5bn4 | ANP | V-type ATP synthase alpha chain | / | 0.445 | |
| 2bxm | IMN | Serum albumin | / | 0.444 | |
| 2has | C3O | Vitamin D3 receptor | / | 0.444 | |
| 2idz | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 2zlc | VDX | Vitamin D3 receptor | / | 0.444 | |
| 3ar4 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.444 | |
| 3bjh | NBB | Odorant binding protein ASP1 | / | 0.444 | |
| 3eek | 53S | Uncharacterized protein | / | 0.444 | |
| 3irm | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.444 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 2c9d | PHR | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.443 | |
| 2imf | TOM | 2-hydroxychromene-2-carboxylate isomerase | 5.99.1.4 | 0.443 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 2vss | ACO | Hydroxycinnamoyl-CoA hydratase-lyase | 4.1.2.41 | 0.443 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.443 | |
| 3zze | 6XP | Hepatocyte growth factor receptor | 2.7.10.1 | 0.443 | |
| 4ap1 | NAP | Steroid monooxygenase | / | 0.443 | |
| 1eny | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.442 | |
| 2pup | ADP | Methylthioribose kinase | 2.7.1.100 | 0.442 | |
| 3csd | EMO | Putative ketoacyl reductase | 1.3.1 | 0.442 | |
| 3irn | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.442 | |
| 3oew | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.442 | |
| 4iui | 1GQ | Estrogen receptor | / | 0.442 | |
| 4jbt | ASD | Cytochrome P450 monooxygenase | / | 0.442 | |
| 1dhf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.441 | |
| 1xdk | REA | Retinoic acid receptor beta | / | 0.441 | |
| 1y2d | 4DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.441 | |
| 2a1n | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 2blc | CP7 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.441 | |
| 2h9i | EAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 3eig | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 4ajw | VWN | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform | 2.7.1.153 | 0.441 | |
| 4bgi | I4I | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 4c3y | ANB | 3-ketosteroid dehydrogenase | / | 0.441 | |
| 4ruo | BIV | Vitamin D3 receptor A | / | 0.441 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 5jtb | ZMA | Adenosine receptor A2a | / | 0.441 | |
| 1olm | VTQ | SEC14-like protein 2 | / | 0.440 | |
| 1rd4 | L08 | Integrin alpha-L | / | 0.440 | |
| 2fm0 | M98 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.440 | |
| 2w3v | TOP | Dihydrofolate reductase | / | 0.440 | |
| 2xvw | 9NR | Serum albumin | / | 0.440 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.440 | |
| 3gkj | HC3 | Niemann-Pick C1 protein | / | 0.440 | |
| 3iro | 2CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.440 | |
| 4l9q | 9TP | Serum albumin | / | 0.440 | |
| 5iu8 | 6DZ | Adenosine receptor A2a | / | 0.440 |