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 |
|---|---|---|---|
| 3w0i | O11 | Vitamin D3 receptor |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3w0i | O11 | Vitamin D3 receptor | / | 1.000 | |
| 3vt4 | 5YI | Vitamin D3 receptor | / | 0.658 | |
| 3vt3 | VDX | Vitamin D3 receptor | / | 0.656 | |
| 3vtb | TKA | Vitamin D3 receptor | / | 0.654 | |
| 3w0g | W07 | Vitamin D3 receptor | / | 0.647 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.643 | |
| 4g1d | 0VK | Vitamin D3 receptor A | / | 0.635 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.632 | |
| 3vrv | YSD | Vitamin D3 receptor | / | 0.629 | |
| 3w0h | W12 | Vitamin D3 receptor | / | 0.628 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.626 | |
| 3vt6 | 5YI | Vitamin D3 receptor | / | 0.626 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.624 | |
| 3w0y | DS4 | Vitamin D3 receptor | / | 0.624 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.623 | |
| 4fhi | 0S4 | Vitamin D3 receptor A | / | 0.623 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.620 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.619 | |
| 1rkg | VD1 | Vitamin D3 receptor | / | 0.619 | |
| 1rk3 | VDX | Vitamin D3 receptor | / | 0.618 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.618 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.618 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.616 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.615 | |
| 1rjk | VDZ | Vitamin D3 receptor | / | 0.612 | |
| 2o4j | VD4 | Vitamin D3 receptor | / | 0.612 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.612 | |
| 2has | C3O | Vitamin D3 receptor | / | 0.611 | |
| 2o4r | VD5 | Vitamin D3 receptor | / | 0.610 | |
| 4g20 | 484 | Vitamin D3 receptor A | / | 0.610 | |
| 4ruj | VDX | Vitamin D3 receptor A | / | 0.609 | |
| 2zla | VDB | Vitamin D3 receptor | / | 0.608 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.608 | |
| 1s19 | MC9 | Vitamin D3 receptor | / | 0.606 | |
| 3vrt | YS2 | Vitamin D3 receptor | / | 0.606 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.604 | |
| 1db1 | VDX | Vitamin D3 receptor | / | 0.602 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.602 | |
| 4fhh | 0U3 | Vitamin D3 receptor A | / | 0.602 | |
| 3vru | YS3 | Vitamin D3 receptor | / | 0.601 | |
| 2har | OCC | Vitamin D3 receptor | / | 0.600 | |
| 1s0z | EB1 | Vitamin D3 receptor | / | 0.598 | |
| 2zl9 | VDA | Vitamin D3 receptor | / | 0.597 | |
| 2hb8 | MVD | Vitamin D3 receptor | / | 0.596 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.596 | |
| 4itf | TFY | Vitamin D3 receptor | / | 0.596 | |
| 2zlc | VDX | Vitamin D3 receptor | / | 0.595 | |
| 4g21 | 0VP | Vitamin D3 receptor A | / | 0.592 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.590 | |
| 4g1y | 0VO | Vitamin D3 receptor A | / | 0.589 | |
| 3w5r | LOA | Vitamin D3 receptor | / | 0.587 | |
| 4q0a | 4OA | Vitamin D3 receptor A | / | 0.586 | |
| 4ruo | BIV | Vitamin D3 receptor A | / | 0.586 | |
| 2hb7 | O1C | Vitamin D3 receptor | / | 0.585 | |
| 2hc4 | VDX | Vitamin D3 receptor A | / | 0.584 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.584 | |
| 3w0j | T08 | Vitamin D3 receptor | / | 0.583 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.582 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.580 | |
| 3w5t | LHP | Vitamin D3 receptor | / | 0.579 | |
| 4g2h | 0VQ | Vitamin D3 receptor A | / | 0.579 | |
| 1ie9 | VDX | Vitamin D3 receptor | / | 0.578 | |
| 3dr1 | C5D | Vitamin D3 receptor A | / | 0.578 | |
| 3w0c | 6DS | Vitamin D3 receptor | / | 0.568 | |
| 4rup | H97 | Vitamin D3 receptor A | / | 0.566 | |
| 2hbh | XE4 | Vitamin D3 receptor A | / | 0.564 | |
| 3vtc | TK3 | Vitamin D3 receptor | / | 0.560 | |
| 3m7r | VDX | Vitamin D3 receptor | / | 0.553 | |
| 3w5q | 3KL | Vitamin D3 receptor | / | 0.529 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.483 | |
| 4l8u | 9AZ | Serum albumin | / | 0.474 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.472 | |
| 3zux | TCH | Transporter | / | 0.472 | |
| 4hfr | 14M | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.471 | |
| 2qo4 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.469 | |
| 4yaf | FAD | NADPH--cytochrome P450 reductase | / | 0.465 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.463 | |
| 2y3r | TRK | TamL | / | 0.462 | |
| 4l9q | 9TP | Serum albumin | / | 0.462 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.460 | |
| 4o70 | 1QK | Bromodomain-containing protein 4 | / | 0.458 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.457 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.455 | |
| 3lu8 | IQX | Serum albumin | / | 0.455 | |
| 4y8w | STR | Steroid 21-hydroxylase | / | 0.455 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.454 | |
| 3g4i | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.454 | |
| 3w8w | FAD | Putative FAD-dependent oxygenase EncM | / | 0.454 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.453 | |
| 1zmc | NAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.453 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.453 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.452 | |
| 4jvf | 17X | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.452 | |
| 1xuo | LA1 | Integrin alpha-L | / | 0.451 | |
| 2eq6 | FAD | Dihydrolipoyl dehydrogenase | / | 0.451 | |
| 2q9f | C3S | Cholesterol 24-hydroxylase | / | 0.451 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.451 | |
| 4nxv | GDP | Mitochondrial dynamics protein MID51 | / | 0.450 | |
| 1jq5 | NAD | Glycerol dehydrogenase | 1.1.1.6 | 0.449 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.449 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.449 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.449 | |
| 2w9s | TOP | Dihydrofolate reductase type 1 from Tn4003 | 1.5.1.3 | 0.449 | |
| 4geb | 0LD | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.449 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.449 | |
| 1jio | DEB | 6-deoxyerythronolide B hydroxylase | / | 0.448 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.448 | |
| 3mdv | CL6 | Cholesterol 24-hydroxylase | / | 0.448 | |
| 1k7l | 544 | Peroxisome proliferator-activated receptor alpha | / | 0.447 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.447 | |
| 3a99 | ANP | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.447 | |
| 4ead | 0NP | Thymidine phosphorylase | 2.4.2.4 | 0.447 | |
| 4ez8 | DHF | Thymidylate synthase | 2.1.1.45 | 0.447 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.447 | |
| 1k6t | XN1 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 2q59 | 240 | Peroxisome proliferator-activated receptor gamma | / | 0.446 | |
| 4jv8 | 1M1 | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.446 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.445 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.445 | |
| 3d7k | D7K | Benzaldehyde lyase | / | 0.445 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.445 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.445 | |
| 5ecc | NAP | Dehydrofolate reductase type I | / | 0.445 | |
| 1dg8 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1osv | CHC | Bile acid receptor | / | 0.444 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.444 | |
| 2vn0 | TDZ | Cytochrome P450 2C8 | / | 0.444 | |
| 3d5f | L41 | Peroxisome proliferator-activated receptor delta | / | 0.444 | |
| 1fp2 | HMO | Isoflavone-7-O-methyltransferase 8 | 2.1.1.150 | 0.443 | |
| 1ie4 | T44 | Transthyretin | / | 0.443 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.443 | |
| 3iae | D7K | Benzaldehyde lyase | / | 0.443 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.443 | |
| 4pkh | ADP | Actin, alpha skeletal muscle | / | 0.443 | |
| 4qi5 | FAD | Cellobiose dehydrogenase | / | 0.443 | |
| 1fm6 | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.442 | |
| 1guf | NDP | Enoyl-[acyl-carrier-protein] reductase 1, mitochondrial | 1.3.1.10 | 0.442 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.442 | |
| 4g2i | 0VQ | Vitamin D3 receptor | / | 0.442 | |
| 4iae | 1DX | Alr2278 protein | / | 0.442 | |
| 4jvb | 1M0 | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.442 | |
| 1zmd | NAI | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.441 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.441 | |
| 3bej | MUF | Bile acid receptor | / | 0.441 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.441 | |
| 2z97 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 3fco | IIG | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.440 | |
| 3iaa | TYD | CalG2 | / | 0.440 | |
| 3koo | 24D | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.440 | |
| 3tqh | NDP | Quinone oxidoreductase | / | 0.440 | |
| 4a33 | MYA | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.440 | |
| 4nxu | ADP | Mitochondrial dynamics protein MID51 | / | 0.440 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.440 | |
| 5kjc | PFB | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.440 |