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 |
|---|---|---|---|
| 3h0a | 9RA | Retinoic acid receptor RXR-alpha |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3h0a | 9RA | Retinoic acid receptor RXR-alpha | / | 1.000 | |
| 1mzn | BM6 | Retinoic acid receptor RXR-alpha | / | 0.569 | |
| 4k6i | 9RA | Retinoic acid receptor RXR-alpha | / | 0.563 | |
| 1rdt | L79 | Retinoic acid receptor RXR-alpha | / | 0.547 | |
| 1fm9 | 9CR | Retinoic acid receptor RXR-alpha | / | 0.543 | |
| 1uhl | MEI | Retinoic acid receptor RXR-beta | / | 0.543 | |
| 1k74 | 9CR | Retinoic acid receptor RXR-alpha | / | 0.541 | |
| 3uvv | REA | Retinoic acid receptor RXR-alpha | / | 0.540 | |
| 1fby | REA | Retinoic acid receptor RXR-alpha | / | 0.539 | |
| 2p1u | 4TN | Retinoic acid receptor RXR-alpha | / | 0.536 | |
| 2p1v | 5TN | Retinoic acid receptor RXR-alpha | / | 0.536 | |
| 4k4j | 1O8 | Retinoic acid receptor RXR-alpha | / | 0.530 | |
| 1mvc | BM6 | Retinoic acid receptor RXR-alpha | / | 0.526 | |
| 3oap | REA | Retinoic acid receptor RXR-alpha | / | 0.525 | |
| 1fm6 | 9CR | Retinoic acid receptor RXR-alpha | / | 0.523 | |
| 1xls | REA | Retinoic acid receptor RXR-alpha | / | 0.515 | |
| 4m8e | 29V | Retinoic acid receptor RXR-alpha | / | 0.513 | |
| 4m8h | R4M | Retinoic acid receptor RXR-alpha | / | 0.511 | |
| 1xiu | REA | Retinoic acid receptor RXR | / | 0.507 | |
| 3fc6 | REA | Retinoic acid receptor RXR-alpha | / | 0.504 | |
| 2acl | REA | Retinoic acid receptor RXR-alpha | / | 0.498 | |
| 3fal | REA | Retinoic acid receptor RXR-alpha | / | 0.498 | |
| 2p1t | 3TN | Retinoic acid receptor RXR-alpha | / | 0.489 | |
| 2y98 | MIV | Mycinamicin IV hydroxylase/epoxidase | / | 0.484 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.474 | |
| 2uxp | CLM | HTH-type transcriptional regulator TtgR | / | 0.469 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.469 | |
| 2j14 | GNI | Peroxisome proliferator-activated receptor delta | / | 0.468 | |
| 2xvv | 9DN | Serum albumin | / | 0.468 | |
| 2xvw | 9NR | Serum albumin | / | 0.465 | |
| 3p99 | LNP | Lanosterol 14-alpha-demethylase | / | 0.465 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.461 | |
| 4apu | A2K | Progesterone receptor | / | 0.460 | |
| 2hwr | DRD | Peroxisome proliferator-activated receptor gamma | / | 0.459 | |
| 3dd1 | 25D | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.459 | |
| 2y46 | MIV | Mycinamicin IV hydroxylase/epoxidase | / | 0.458 | |
| 1eio | GCH | Gastrotropin | / | 0.457 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.457 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.456 | |
| 3kjs | DQ1 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.456 | |
| 3mdm | FJZ | Cholesterol 24-hydroxylase | / | 0.456 | |
| 4uym | VOR | 14-alpha sterol demethylase Cyp51B | / | 0.456 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.455 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.455 | |
| 1uy6 | PU3 | Heat shock protein HSP 90-alpha | / | 0.454 | |
| 2hw2 | RFP | Rifampin ADP-ribosyl transferase | / | 0.454 | |
| 2wpw | ACO | Orf14 | / | 0.454 | |
| 3vev | 0H4 | Glucokinase | 2.7.1.2 | 0.454 | |
| 1fml | RTL | Retinol dehydratase | / | 0.453 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.453 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.452 | |
| 2wpx | ACO | Orf14 | / | 0.452 | |
| 2xc3 | RT8 | Steroid C26-monooxygenase | 1.14.13.141 | 0.452 | |
| 3d3e | D3E | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.452 | |
| 3d5f | L41 | Peroxisome proliferator-activated receptor delta | / | 0.452 | |
| 3d78 | NBB | Pheromone-binding protein ASP1 | / | 0.452 | |
| 1dxo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.451 | |
| 1xuo | LA1 | Integrin alpha-L | / | 0.451 | |
| 3q0g | BCO | Probable enoyl-CoA hydratase echA8 | 4.2.1.17 | 0.451 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 1fm9 | 570 | Peroxisome proliferator-activated receptor gamma | / | 0.450 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.450 | |
| 3fbu | COA | Acetyltransferase, GNAT family | / | 0.450 | |
| 3vtc | TK3 | Vitamin D3 receptor | / | 0.450 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.450 | |
| 2hnz | PC0 | Gag-Pol polyprotein | 2.7.7.49 | 0.449 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.449 | |
| 4iui | 1GQ | Estrogen receptor | / | 0.449 | |
| 4boe | CLR | Japanin | / | 0.448 | |
| 2om9 | AJA | Peroxisome proliferator-activated receptor gamma | / | 0.447 | |
| 3b9l | AZZ | Serum albumin | / | 0.447 | |
| 3k9u | ACO | Spermidine N(1)-acetyltransferase | / | 0.447 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.447 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.447 | |
| 2iod | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.446 | |
| 2q66 | ATP | Poly(A) polymerase | 2.7.7.19 | 0.446 | |
| 3cse | N22 | Uncharacterized protein | / | 0.446 | |
| 4gg7 | 0J8 | Hepatocyte growth factor receptor | 2.7.10.1 | 0.446 | |
| 1mp0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.445 | |
| 2uxh | QUE | HTH-type transcriptional regulator TtgR | / | 0.445 | |
| 3th8 | TH9 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.445 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.445 | |
| 5hs1 | VOR | Lanosterol 14-alpha demethylase | / | 0.445 | |
| 5kgp | ACO | Predicted acetyltransferase | / | 0.445 | |
| 3uko | NAD | Alcohol dehydrogenase class-3 | / | 0.444 | |
| 4fhi | 0S4 | Vitamin D3 receptor A | / | 0.444 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.443 | |
| 2hrc | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.443 | |
| 3u8h | BHP | Phospholipase A2, membrane associated | / | 0.443 | |
| 3pwh | ZMA | Adenosine receptor A2a | / | 0.443 | |
| 1uyk | PUX | Heat shock protein HSP 90-alpha | / | 0.442 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.442 | |
| 2qd3 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.442 | |
| 2vxo | XMP | GMP synthase [glutamine-hydrolyzing] | 6.3.5.2 | 0.442 | |
| 3inv | C50 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.442 | |
| 4ok1 | 198 | Androgen receptor | / | 0.442 | |
| 2ath | 3EA | Peroxisome proliferator-activated receptor gamma | / | 0.441 | |
| 3hz5 | Z64 | Heat shock protein HSP 90-alpha | / | 0.441 | |
| 3vjh | J35 | Peroxisome proliferator-activated receptor gamma | / | 0.441 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.441 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.441 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.441 | |
| 4zm6 | ACO | N-acetyl-beta-D glucosaminidase | / | 0.441 | |
| 1k74 | 544 | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 1kb9 | SMA | Cytochrome b | / | 0.440 | |
| 1uy7 | PU4 | Heat shock protein HSP 90-alpha | / | 0.440 | |
| 2ibz | SMA | Cytochrome b | / | 0.440 | |
| 2pnj | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.440 | |
| 3rpn | GTX | Glutathione S-transferase kappa 1 | 2.5.1.18 | 0.440 | |
| 4j03 | FVS | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.440 | |
| 5bt4 | 2LO | Bromodomain-containing protein 4 | / | 0.440 |