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 |
|---|---|---|---|
| 2har | OCC | Vitamin D3 receptor |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2har | OCC | Vitamin D3 receptor | / | 1.000 | |
| 1ie9 | VDX | Vitamin D3 receptor | / | 0.751 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.734 | |
| 1s19 | MC9 | Vitamin D3 receptor | / | 0.728 | |
| 2hb7 | O1C | Vitamin D3 receptor | / | 0.722 | |
| 1s0z | EB1 | Vitamin D3 receptor | / | 0.711 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.700 | |
| 3m7r | VDX | Vitamin D3 receptor | / | 0.698 | |
| 3w0c | 6DS | Vitamin D3 receptor | / | 0.694 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.693 | |
| 1rk3 | VDX | Vitamin D3 receptor | / | 0.687 | |
| 1db1 | VDX | Vitamin D3 receptor | / | 0.683 | |
| 1rkg | VD1 | Vitamin D3 receptor | / | 0.682 | |
| 4itf | TFY | Vitamin D3 receptor | / | 0.678 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.674 | |
| 2hc4 | VDX | Vitamin D3 receptor A | / | 0.670 | |
| 2zl9 | VDA | Vitamin D3 receptor | / | 0.670 | |
| 3vrv | YSD | Vitamin D3 receptor | / | 0.667 | |
| 3w0y | DS4 | Vitamin D3 receptor | / | 0.667 | |
| 4g1y | 0VO | Vitamin D3 receptor A | / | 0.667 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.666 | |
| 2zlc | VDX | Vitamin D3 receptor | / | 0.665 | |
| 4rup | H97 | Vitamin D3 receptor A | / | 0.665 | |
| 2hbh | XE4 | Vitamin D3 receptor A | / | 0.664 | |
| 2o4j | VD4 | Vitamin D3 receptor | / | 0.663 | |
| 2o4r | VD5 | Vitamin D3 receptor | / | 0.663 | |
| 4g1d | 0VK | Vitamin D3 receptor A | / | 0.663 | |
| 3vt6 | 5YI | Vitamin D3 receptor | / | 0.660 | |
| 2has | C3O | Vitamin D3 receptor | / | 0.659 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.659 | |
| 2zla | VDB | Vitamin D3 receptor | / | 0.657 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.656 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.656 | |
| 4fhh | 0U3 | Vitamin D3 receptor A | / | 0.653 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.651 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.651 | |
| 3dr1 | C5D | Vitamin D3 receptor A | / | 0.650 | |
| 3vt3 | VDX | Vitamin D3 receptor | / | 0.650 | |
| 2hb8 | MVD | Vitamin D3 receptor | / | 0.649 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.649 | |
| 4fhi | 0S4 | Vitamin D3 receptor A | / | 0.648 | |
| 4g21 | 0VP | Vitamin D3 receptor A | / | 0.645 | |
| 4g2h | 0VQ | Vitamin D3 receptor A | / | 0.644 | |
| 3w0j | T08 | Vitamin D3 receptor | / | 0.642 | |
| 4g20 | 484 | Vitamin D3 receptor A | / | 0.642 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.641 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.639 | |
| 3vru | YS3 | Vitamin D3 receptor | / | 0.636 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.636 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.634 | |
| 3vrt | YS2 | Vitamin D3 receptor | / | 0.632 | |
| 4ruj | VDX | Vitamin D3 receptor A | / | 0.631 | |
| 3vt4 | 5YI | Vitamin D3 receptor | / | 0.628 | |
| 3w5r | LOA | Vitamin D3 receptor | / | 0.628 | |
| 1rjk | VDZ | Vitamin D3 receptor | / | 0.625 | |
| 3vtb | TKA | Vitamin D3 receptor | / | 0.621 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.621 | |
| 4q0a | 4OA | Vitamin D3 receptor A | / | 0.621 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.620 | |
| 4ruo | BIV | Vitamin D3 receptor A | / | 0.617 | |
| 3w5t | LHP | Vitamin D3 receptor | / | 0.616 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.614 | |
| 3w0i | O11 | Vitamin D3 receptor | / | 0.608 | |
| 3w0g | W07 | Vitamin D3 receptor | / | 0.607 | |
| 3vtc | TK3 | Vitamin D3 receptor | / | 0.602 | |
| 3w0h | W12 | Vitamin D3 receptor | / | 0.597 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.595 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.595 | |
| 3w5q | 3KL | Vitamin D3 receptor | / | 0.573 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.465 | |
| 2j3k | NAP | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.465 | |
| 3g4i | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.465 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.464 | |
| 1guf | NDP | Enoyl-[acyl-carrier-protein] reductase 1, mitochondrial | 1.3.1.10 | 0.463 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.463 | |
| 1hw5 | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.462 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.462 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.460 | |
| 4xuh | SFI | Peroxisome proliferator-activated receptor gamma | / | 0.460 | |
| 1osv | CHC | Bile acid receptor | / | 0.459 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.459 | |
| 4hfr | 14M | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.459 | |
| 4l8u | 9AZ | Serum albumin | / | 0.459 | |
| 3cge | COA | Coenzyme A disulfide reductase | / | 0.458 | |
| 2fto | CB3 | Thymidylate synthase | / | 0.457 | |
| 2nry | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.457 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.456 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.456 | |
| 3csd | EMO | Putative ketoacyl reductase | 1.3.1 | 0.456 | |
| 5ecc | NAP | Dehydrofolate reductase type I | / | 0.456 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.455 | |
| 3fco | IIG | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.455 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.455 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.454 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.454 | |
| 3iup | NDP | Possible NADH oxidoreductase | / | 0.454 | |
| 3zux | TCH | Transporter | / | 0.454 | |
| 4geb | 0LD | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.454 | |
| 5ify | UMP | Glucose-1-phosphate thymidylyltransferase | / | 0.454 | |
| 1lco | PPY | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.453 | |
| 3mnr | SD1 | Heat shock protein HSP 90-alpha | / | 0.453 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.453 | |
| 4jvf | 17X | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.453 | |
| 2vn0 | TDZ | Cytochrome P450 2C8 | / | 0.452 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.452 | |
| 4ryv | ZEA | Protein LlR18A | / | 0.452 | |
| 5ai5 | BSU | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.452 | |
| 1uyf | PU1 | Heat shock protein HSP 90-alpha | / | 0.451 | |
| 1f4f | TP3 | Thymidylate synthase | / | 0.450 | |
| 1pjk | ANP | Casein kinase II subunit alpha | 2.7.11.1 | 0.450 | |
| 2qbl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 3byz | H11 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.450 | |
| 3icr | FAD | Coenzyme A disulfide reductase | / | 0.450 | |
| 3zep | 1NX | Tyrosine-protein kinase JAK3 | 2.7.10.2 | 0.450 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.450 | |
| 4jvb | 1M0 | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.450 | |
| 4nxu | ADP | Mitochondrial dynamics protein MID51 | / | 0.450 | |
| 4o0r | X4Z | Serine/threonine-protein kinase PAK 1 | 2.7.11.1 | 0.450 | |
| 4rph | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.450 | |
| 1ie4 | T44 | Transthyretin | / | 0.449 | |
| 2fy5 | SOP | Choline O-acetyltransferase | 2.3.1.6 | 0.449 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.449 | |
| 4ge4 | 0KE | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.449 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.448 | |
| 4a6b | QG8 | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 4awo | 99B | Heat shock protein HSP 90-alpha | / | 0.448 | |
| 2i4p | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.447 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 3tqh | NDP | Quinone oxidoreductase | / | 0.447 | |
| 4j03 | FVS | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.447 | |
| 2ww4 | ADP | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | 2.7.1.148 | 0.446 | |
| 2ykj | YKJ | Heat shock protein HSP 90-alpha | / | 0.446 | |
| 2zb4 | 5OP | Prostaglandin reductase 2 | 1.3.1.48 | 0.446 | |
| 3gbu | ATP | Uncharacterized sugar kinase PH1459 | 2.7.1 | 0.446 | |
| 3stu | DK3 | Methylketone synthase I | / | 0.446 | |
| 4h6r | FDA | Proline dehydrogenase | / | 0.446 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.446 | |
| 4rpg | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.446 | |
| 4wdb | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.446 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.445 | |
| 1og5 | SWF | Cytochrome P450 2C9 | / | 0.445 | |
| 2nru | T12 | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.445 | |
| 2z97 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.445 | |
| 4hfm | NAP | 2-alkenal reductase (NADP(+)-dependent) | / | 0.445 | |
| 4l4a | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.444 | |
| 3poz | 03P | Epidermal growth factor receptor | 2.7.10.1 | 0.444 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.444 | |
| 5eai | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1ot7 | IU5 | Bile acid receptor | / | 0.443 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.443 | |
| 3aty | FMN | Prostaglandin F2a synthase | / | 0.443 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.443 | |
| 3mdv | CL6 | Cholesterol 24-hydroxylase | / | 0.443 | |
| 4nh8 | 2LC | Heat shock protein HSP 90-alpha | / | 0.443 | |
| 1fp2 | HMO | Isoflavone-7-O-methyltransferase 8 | 2.1.1.150 | 0.442 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 1nq7 | ARL | Nuclear receptor ROR-beta | / | 0.442 | |
| 1xkk | FMM | Epidermal growth factor receptor | 2.7.10.1 | 0.442 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.442 | |
| 2vss | ACO | Hydroxycinnamoyl-CoA hydratase-lyase | 4.1.2.41 | 0.442 | |
| 3w33 | W19 | Epidermal growth factor receptor | 2.7.10.1 | 0.442 | |
| 4bbx | LKF | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.442 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.442 | |
| 1sn5 | T3 | Transthyretin | / | 0.441 | |
| 1uyh | PU0 | Heat shock protein HSP 90-alpha | / | 0.441 | |
| 1xuo | LA1 | Integrin alpha-L | / | 0.441 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.441 | |
| 2go4 | TUX | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.441 | |
| 2i4j | DRJ | Peroxisome proliferator-activated receptor gamma | / | 0.441 | |
| 2j8z | NAP | Quinone oxidoreductase PIG3 | 1 | 0.441 | |
| 3w5e | NVW | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.441 | |
| 3wd9 | QPC | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.441 | |
| 4a6c | QG9 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 4kf1 | HT5 | Aryldialkylphosphatase | 3.1.8.1 | 0.441 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.441 | |
| 1jip | KTN | 6-deoxyerythronolide B hydroxylase | / | 0.440 | |
| 1s60 | COA | Aminoglycoside N(6')-acetyltransferase type 1 | / | 0.440 | |
| 2o7p | NAP | Riboflavin biosynthesis protein RibD | / | 0.440 | |
| 2yke | YKE | Heat shock protein HSP 90-alpha | / | 0.440 | |
| 3bej | MUF | Bile acid receptor | / | 0.440 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.440 | |
| 3w32 | W32 | Epidermal growth factor receptor | 2.7.10.1 | 0.440 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.440 | |
| 4g2i | 0VQ | Vitamin D3 receptor | / | 0.440 | |
| 4ge7 | 0K5 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.440 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.440 | |
| 4jbt | ASD | Cytochrome P450 monooxygenase | / | 0.440 | |
| 4nky | 3QZ | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.440 | |
| 4rqu | NAD | Alcohol dehydrogenase class-P | / | 0.440 |