sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 3w0i | O11 | Vitamin D3 receptor |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3w0i | O11 | Vitamin D3 receptor | / | 1.000 | |
| 3vt3 | VDX | Vitamin D3 receptor | / | 0.658 | |
| 3vtb | TKA | Vitamin D3 receptor | / | 0.657 | |
| 3vt4 | 5YI | Vitamin D3 receptor | / | 0.656 | |
| 3w0g | W07 | Vitamin D3 receptor | / | 0.649 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.645 | |
| 4g1d | 0VK | Vitamin D3 receptor A | / | 0.638 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.632 | |
| 3vrv | YSD | Vitamin D3 receptor | / | 0.632 | |
| 3w0h | W12 | Vitamin D3 receptor | / | 0.628 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.626 | |
| 3vt6 | 5YI | Vitamin D3 receptor | / | 0.625 | |
| 3w0y | DS4 | Vitamin D3 receptor | / | 0.625 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.624 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.623 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.623 | |
| 4fhi | 0S4 | Vitamin D3 receptor A | / | 0.623 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.622 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.621 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.620 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.619 | |
| 1rk3 | VDX | Vitamin D3 receptor | / | 0.618 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.618 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.618 | |
| 1rjk | VDZ | Vitamin D3 receptor | / | 0.612 | |
| 2o4j | VD4 | Vitamin D3 receptor | / | 0.612 | |
| 2has | C3O | Vitamin D3 receptor | / | 0.611 | |
| 4g20 | 484 | Vitamin D3 receptor A | / | 0.611 | |
| 1rkg | VD1 | Vitamin D3 receptor | / | 0.610 | |
| 2o4r | VD5 | Vitamin D3 receptor | / | 0.610 | |
| 2zla | VDB | Vitamin D3 receptor | / | 0.610 | |
| 1s19 | MC9 | Vitamin D3 receptor | / | 0.609 | |
| 4ruj | VDX | Vitamin D3 receptor A | / | 0.609 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.608 | |
| 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 | |
| 2zl9 | VDA | Vitamin D3 receptor | / | 0.601 | |
| 3vru | YS3 | Vitamin D3 receptor | / | 0.601 | |
| 2har | OCC | Vitamin D3 receptor | / | 0.600 | |
| 1s0z | EB1 | Vitamin D3 receptor | / | 0.598 | |
| 2hb8 | MVD | Vitamin D3 receptor | / | 0.596 | |
| 2zlc | VDX | Vitamin D3 receptor | / | 0.596 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.596 | |
| 4itf | TFY | Vitamin D3 receptor | / | 0.596 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.594 | |
| 4g21 | 0VP | Vitamin D3 receptor A | / | 0.594 | |
| 3vrt | YS2 | Vitamin D3 receptor | / | 0.592 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.592 | |
| 4ruo | BIV | Vitamin D3 receptor A | / | 0.591 | |
| 4g1y | 0VO | Vitamin D3 receptor A | / | 0.589 | |
| 3w5r | LOA | Vitamin D3 receptor | / | 0.588 | |
| 4q0a | 4OA | Vitamin D3 receptor A | / | 0.587 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.586 | |
| 2hb7 | O1C | Vitamin D3 receptor | / | 0.585 | |
| 2hc4 | VDX | Vitamin D3 receptor A | / | 0.584 | |
| 3w0j | T08 | Vitamin D3 receptor | / | 0.584 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.583 | |
| 3dr1 | C5D | Vitamin D3 receptor A | / | 0.580 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.580 | |
| 4g2h | 0VQ | Vitamin D3 receptor A | / | 0.580 | |
| 3w5t | LHP | Vitamin D3 receptor | / | 0.579 | |
| 1ie9 | VDX | Vitamin D3 receptor | / | 0.578 | |
| 4rup | H97 | Vitamin D3 receptor A | / | 0.569 | |
| 2hbh | XE4 | Vitamin D3 receptor A | / | 0.568 | |
| 3w0c | 6DS | Vitamin D3 receptor | / | 0.568 | |
| 3vtc | TK3 | Vitamin D3 receptor | / | 0.561 | |
| 3m7r | VDX | Vitamin D3 receptor | / | 0.553 | |
| 3w5q | 3KL | Vitamin D3 receptor | / | 0.531 | |
| 4hfr | 14M | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.477 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.470 | |
| 3g4i | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.465 | |
| 4l9q | 9TP | Serum albumin | / | 0.464 | |
| 2qo4 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.463 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.463 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.462 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.461 | |
| 1jq5 | NAD | Glycerol dehydrogenase | 1.1.1.6 | 0.460 | |
| 3jqp | A2P | Ferredoxin--NADP reductase, apicoplast | / | 0.458 | |
| 4nxv | GDP | Mitochondrial dynamics protein MID51 | / | 0.458 | |
| 2pob | GW4 | Peroxisome proliferator-activated receptor gamma | / | 0.457 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.455 | |
| 4o70 | 1QK | Bromodomain-containing protein 4 | / | 0.455 | |
| 5itz | LOC | Tubulin beta-2B chain | / | 0.453 | |
| 3lu8 | IQX | Serum albumin | / | 0.452 | |
| 4jvf | 17X | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.452 | |
| 1xuo | LA1 | Integrin alpha-L | / | 0.451 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.450 | |
| 3czr | 3CZ | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.450 | |
| 3fco | IIG | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.450 | |
| 1k6t | XN1 | Gag-Pol polyprotein | 3.4.23.16 | 0.449 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.449 | |
| 4ead | 0NP | Thymidine phosphorylase | 2.4.2.4 | 0.449 | |
| 4ez8 | DHF | Thymidylate synthase | 2.1.1.45 | 0.449 | |
| 2nnh | REA | Cytochrome P450 2C8 | / | 0.446 | |
| 1guf | NDP | Enoyl-[acyl-carrier-protein] reductase 1, mitochondrial | 1.3.1.10 | 0.445 | |
| 2hwr | DRD | Peroxisome proliferator-activated receptor gamma | / | 0.445 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.445 | |
| 3c0g | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.445 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.445 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.444 | |
| 3d5f | L41 | Peroxisome proliferator-activated receptor delta | / | 0.444 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.444 | |
| 4jvb | 1M0 | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.444 | |
| 4cy8 | FDA | 2-hydroxybiphenyl-3-monooxygenase | / | 0.443 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.443 | |
| 4l9k | EHF | Serum albumin | / | 0.443 | |
| 4nxw | ADP | Mitochondrial dynamics protein MID51 | / | 0.443 | |
| 1osv | CHC | Bile acid receptor | / | 0.442 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.442 | |
| 2bel | CBO | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.442 | |
| 3bej | MUF | Bile acid receptor | / | 0.442 | |
| 3t2k | FAD | Sulfide-quinone reductase | / | 0.442 | |
| 4jlj | 1NM | Deoxycytidine kinase | 2.7.1.74 | 0.442 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.441 | |
| 2c7x | NRB | Cytochrome P450 monooxygenase PikC | / | 0.441 | |
| 2ntv | P1H | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.441 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.441 | |
| 3t14 | FAD | Sulfide-quinone reductase | / | 0.441 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.441 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.441 | |
| 4nxu | ADP | Mitochondrial dynamics protein MID51 | / | 0.441 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.441 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.441 | |
| 4r20 | AER | Cytochrome P450 family 17 polypeptide 2 | / | 0.441 | |
| 1k74 | 544 | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 2wuf | KEM | 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase | 3.7.1.17 | 0.440 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.440 | |
| 4l8u | 9AZ | Serum albumin | / | 0.440 |