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 |
|---|---|---|---|
| 1sr7 | MOF | Progesterone receptor |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1sr7 | MOF | Progesterone receptor | / | 1.000 | |
| 4p6w | MOF | Glucocorticoid receptor | / | 0.579 | |
| 1sqn | NDR | Progesterone receptor | / | 0.573 | |
| 1p93 | DEX | Glucocorticoid receptor | / | 0.554 | |
| 2w8y | 486 | Progesterone receptor | / | 0.542 | |
| 3zrb | ORC | Progesterone receptor | / | 0.538 | |
| 2w8y | NDR | Progesterone receptor | / | 0.531 | |
| 4a2j | AS0 | Progesterone receptor | / | 0.530 | |
| 4uda | DEX | Mineralocorticoid receptor | / | 0.528 | |
| 2ovm | AS0 | Progesterone receptor | / | 0.522 | |
| 3d90 | NOG | Progesterone receptor | / | 0.520 | |
| 2oax | SNL | Mineralocorticoid receptor | / | 0.517 | |
| 4apu | A2K | Progesterone receptor | / | 0.514 | |
| 3zrb | OR8 | Progesterone receptor | / | 0.513 | |
| 4apu | OR8 | Progesterone receptor | / | 0.510 | |
| 2ab2 | SNL | Mineralocorticoid receptor | / | 0.505 | |
| 1zuc | T98 | Progesterone receptor | / | 0.503 | |
| 3zr7 | OR8 | Progesterone receptor | / | 0.501 | |
| 4p6x | HCY | Glucocorticoid receptor | / | 0.501 | |
| 2a3i | C0R | Mineralocorticoid receptor | / | 0.500 | |
| 4udc | DEX | Glucocorticoid receptor | / | 0.499 | |
| 2aax | PDN | Mineralocorticoid receptor | / | 0.498 | |
| 4lsj | LSJ | Glucocorticoid receptor | / | 0.497 | |
| 1ya3 | STR | Mineralocorticoid receptor | / | 0.494 | |
| 1e3k | R18 | Progesterone receptor | / | 0.492 | |
| 4y8w | STR | Steroid 21-hydroxylase | / | 0.492 | |
| 2aa2 | AS4 | Mineralocorticoid receptor | / | 0.489 | |
| 2aa5 | STR | Mineralocorticoid receptor | / | 0.489 | |
| 2aa6 | STR | Mineralocorticoid receptor | / | 0.488 | |
| 3zra | ORB | Progesterone receptor | / | 0.487 | |
| 1gs4 | ZK5 | Androgen receptor | / | 0.486 | |
| 1m2z | DEX | Glucocorticoid receptor | / | 0.486 | |
| 5akk | 1P8 | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.483 | |
| 3l6j | Z90 | Alr2278 protein | / | 0.482 | |
| 2x7g | PVB | SRSF protein kinase 2 | 2.7.11.1 | 0.480 | |
| 3uvv | REA | Retinoic acid receptor RXR-alpha | / | 0.480 | |
| 4j03 | FVS | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.480 | |
| 2abi | 1CA | Mineralocorticoid receptor | / | 0.479 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.476 | |
| 3vhu | SNL | Mineralocorticoid receptor | / | 0.476 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.473 | |
| 3mdv | CL6 | Cholesterol 24-hydroxylase | / | 0.472 | |
| 2ylp | TES | Androgen receptor | / | 0.471 | |
| 4q0a | 4OA | Vitamin D3 receptor A | / | 0.471 | |
| 2q9f | C3S | Cholesterol 24-hydroxylase | / | 0.469 | |
| 4o71 | CPB | Bromodomain-containing protein 4 | / | 0.469 | |
| 3gyu | DL7 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.468 | |
| 4oea | DHT | Androgen receptor | / | 0.468 | |
| 2pix | DHT | Androgen receptor | / | 0.467 | |
| 2q7i | TES | Androgen receptor | / | 0.467 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.467 | |
| 4i2q | 1BT | Gag-Pol polyprotein | 2.7.7.49 | 0.467 | |
| 2hw2 | RFP | Rifampin ADP-ribosyl transferase | / | 0.466 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.466 | |
| 1osv | CHC | Bile acid receptor | / | 0.465 | |
| 2ylq | TES | Androgen receptor | / | 0.464 | |
| 4nky | 3QZ | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.464 | |
| 3a60 | STU | Ribosomal protein S6 kinase beta-1 | 2.7.11.1 | 0.463 | |
| 3d75 | NBB | Pheromone-binding protein ASP1 | / | 0.463 | |
| 3tmz | 06X | Cytochrome P450 2B4 | 1.14.14.1 | 0.463 | |
| 2o4r | VD5 | Vitamin D3 receptor | / | 0.461 | |
| 2zlc | VDX | Vitamin D3 receptor | / | 0.461 | |
| 3gyt | DL4 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.461 | |
| 3of2 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.461 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.461 | |
| 3zqt | TES | Androgen receptor | / | 0.461 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.461 | |
| 1db1 | VDX | Vitamin D3 receptor | / | 0.460 | |
| 1xiu | REA | Retinoic acid receptor RXR | / | 0.460 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.460 | |
| 1fml | RTL | Retinol dehydratase | / | 0.459 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.459 | |
| 2pkl | DHT | Androgen receptor | / | 0.459 | |
| 2q7k | TES | Androgen receptor | / | 0.459 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.459 | |
| 2p15 | EZT | Estrogen receptor | / | 0.458 | |
| 2pir | DHT | Androgen receptor | / | 0.458 | |
| 3tk3 | CPZ | Cytochrome P450 2B4 | 1.14.14.1 | 0.458 | |
| 4iae | 1DX | Alr2278 protein | / | 0.458 | |
| 1fm6 | 9CR | Retinoic acid receptor RXR-alpha | / | 0.457 | |
| 2aib | ERG | Beta-elicitin cinnamomin | / | 0.457 | |
| 2has | C3O | Vitamin D3 receptor | / | 0.457 | |
| 3ua5 | 06X | Cytochrome P450 2B6 | 1.14.13 | 0.457 | |
| 4uyg | 73B | Bromodomain-containing protein 2 | / | 0.457 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.456 | |
| 1og5 | SWF | Cytochrome P450 2C9 | / | 0.456 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.456 | |
| 3g49 | 3G4 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.456 | |
| 1nhz | 486 | Glucocorticoid receptor | / | 0.455 | |
| 1s9q | OHT | Estrogen-related receptor gamma | / | 0.455 | |
| 3w5r | LOA | Vitamin D3 receptor | / | 0.455 | |
| 4ivy | 1GT | Estrogen receptor | / | 0.455 | |
| 4jbt | ASD | Cytochrome P450 monooxygenase | / | 0.455 | |
| 1l2j | ETC | Estrogen receptor beta | / | 0.454 | |
| 3vt6 | 5YI | Vitamin D3 receptor | / | 0.454 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.454 | |
| 1s19 | MC9 | Vitamin D3 receptor | / | 0.453 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.453 | |
| 2ama | DHT | Androgen receptor | / | 0.453 | |
| 2amb | 17H | Androgen receptor | / | 0.453 | |
| 3vru | YS3 | Vitamin D3 receptor | / | 0.453 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.453 | |
| 1ddu | CB3 | Thymidylate synthase | / | 0.452 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.452 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.452 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 3vtb | TKA | Vitamin D3 receptor | / | 0.452 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.452 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.451 | |
| 1m79 | MQ1 | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.451 | |
| 2acl | REA | Retinoic acid receptor RXR-alpha | / | 0.451 | |
| 2bj4 | OHT | Estrogen receptor | / | 0.451 | |
| 2hb7 | O1C | Vitamin D3 receptor | / | 0.451 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 3kyt | HC2 | Nuclear receptor ROR-gamma | / | 0.451 | |
| 4ejh | 0QA | Cytochrome P450 2A13 | 1.14.14.1 | 0.451 | |
| 4nie | NBH | Nuclear receptor ROR-gamma | / | 0.451 | |
| 4ruo | BIV | Vitamin D3 receptor A | / | 0.451 | |
| 1fby | REA | Retinoic acid receptor RXR-alpha | / | 0.450 | |
| 1zeo | C01 | Peroxisome proliferator-activated receptor gamma | / | 0.450 | |
| 2aqk | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.450 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.450 | |
| 3mne | DEX | Glucocorticoid receptor | / | 0.450 | |
| 3w0c | 6DS | Vitamin D3 receptor | / | 0.450 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 4fhi | 0S4 | Vitamin D3 receptor A | / | 0.450 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.450 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.450 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.450 | |
| 1ie9 | VDX | Vitamin D3 receptor | / | 0.449 | |
| 2aa7 | 1CA | Mineralocorticoid receptor | / | 0.449 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 2y46 | MIV | Mycinamicin IV hydroxylase/epoxidase | / | 0.449 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 3beg | ANP | SRSF protein kinase 1 | 2.7.11.1 | 0.449 | |
| 3tdl | 11D | Serum albumin | / | 0.449 | |
| 3vtc | TK3 | Vitamin D3 receptor | / | 0.449 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.449 | |
| 4isk | 1JY | Thymidylate synthase | / | 0.449 | |
| 4iv4 | 1GS | Estrogen receptor | / | 0.449 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.449 | |
| 1fdu | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.448 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 1t65 | DHT | Androgen receptor | / | 0.448 | |
| 1t7r | DHT | Androgen receptor | / | 0.448 | |
| 2ao6 | R18 | Androgen receptor | / | 0.448 | |
| 2har | OCC | Vitamin D3 receptor | / | 0.448 | |
| 2hb8 | MVD | Vitamin D3 receptor | / | 0.448 | |
| 2vf0 | F89 | Thymidylate synthase | / | 0.448 | |
| 3vrv | YSD | Vitamin D3 receptor | / | 0.448 | |
| 1rk3 | VDX | Vitamin D3 receptor | / | 0.447 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.447 | |
| 1t79 | DHT | Androgen receptor | / | 0.447 | |
| 2iod | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.447 | |
| 2p1v | 5TN | Retinoic acid receptor RXR-alpha | / | 0.447 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.447 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.447 | |
| 1al8 | DHP | Peroxisomal (S)-2-hydroxy-acid oxidase | 1.1.3.15 | 0.446 | |
| 2hc4 | VDX | Vitamin D3 receptor A | / | 0.446 | |
| 3mno | DEX | Glucocorticoid receptor | / | 0.446 | |
| 3ns2 | PYV | Abscisic acid receptor PYL2 | / | 0.446 | |
| 4i8v | BHF | Cytochrome P450 1A1 | 1.14.14.1 | 0.446 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.446 | |
| 5doz | NDP | JamJ | / | 0.446 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.445 | |
| 2e9c | B75 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.445 | |
| 2zl9 | VDA | Vitamin D3 receptor | / | 0.445 | |
| 3fco | IIG | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.445 | |
| 3mdm | FJZ | Cholesterol 24-hydroxylase | / | 0.445 | |
| 4fjz | 4FJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.445 | |
| 4k7a | DHT | Androgen receptor | / | 0.445 | |
| 4mcv | 29K | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.445 | |
| 5k2b | ZMA | Adenosine receptor A2a | / | 0.445 | |
| 1dhj | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.444 | |
| 1t7f | DHT | Androgen receptor | / | 0.444 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.444 | |
| 2y98 | MIV | Mycinamicin IV hydroxylase/epoxidase | / | 0.444 | |
| 2yhd | TES | Androgen receptor | / | 0.444 | |
| 3c0g | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.444 | |
| 3irx | UDR | Gag-Pol polyprotein | 2.7.7.49 | 0.444 | |
| 3nj0 | PYV | Abscisic acid receptor PYL2 | / | 0.444 | |
| 3up0 | D7S | aceDAF-12 | / | 0.444 | |
| 3v8w | 0G2 | Tyrosine-protein kinase ITK/TSK | 2.7.10.2 | 0.444 | |
| 4enh | FVX | Cholesterol 24-hydroxylase | / | 0.444 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.444 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.444 | |
| 4nkv | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.444 | |
| 1jip | KTN | 6-deoxyerythronolide B hydroxylase | / | 0.443 | |
| 1n83 | CLR | Nuclear receptor ROR-alpha | / | 0.443 | |
| 1p44 | GEQ | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.443 | |
| 2ath | 3EA | Peroxisome proliferator-activated receptor gamma | / | 0.443 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 2bw7 | ECS | Adenylate cyclase | / | 0.443 | |
| 2fzh | DH1 | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 2hrc | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.443 | |
| 2q8s | L92 | Peroxisome proliferator-activated receptor gamma | / | 0.443 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.443 | |
| 3ijd | C2F | Methylenetetrahydrofolate reductase | / | 0.443 | |
| 3p6o | ETG | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.443 | |
| 5l7d | CLR | Smoothened homolog | / | 0.443 | |
| 1b4v | FAD | Cholesterol oxidase | 1.1.3.6 | 0.442 | |
| 1nde | MON | Estrogen receptor beta | / | 0.442 | |
| 1y9r | 1CA | Mineralocorticoid receptor | / | 0.442 | |
| 2aq8 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.442 | |
| 2piu | DHT | Androgen receptor | / | 0.442 | |
| 2pr2 | DG1 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.442 | |
| 2vzm | NRB | Cytochrome P450 monooxygenase PikC | / | 0.442 | |
| 3fls | FLS | Mitogen-activated protein kinase 14 | / | 0.442 | |
| 3vt3 | VDX | Vitamin D3 receptor | / | 0.442 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.442 | |
| 4nm9 | FAD | Bifunctional protein PutA | / | 0.442 | |
| 4oha | HFT | Androgen receptor | / | 0.442 | |
| 1i7i | AZ2 | Peroxisome proliferator-activated receptor gamma | / | 0.441 | |
| 1mxt | FAE | Cholesterol oxidase | 1.1.3.6 | 0.441 | |
| 1rdt | L79 | Retinoic acid receptor RXR-alpha | / | 0.441 | |
| 2aqh | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 2pio | DHT | Androgen receptor | / | 0.441 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.441 | |
| 3p9t | TCL | Repressor | / | 0.441 | |
| 3t14 | FAD | Sulfide-quinone reductase | / | 0.441 | |
| 4bqp | VMY | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1ot7 | CHC | Bile acid receptor | / | 0.440 | |
| 1phg | MYT | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 2j0m | 4ST | Focal adhesion kinase 1 | 2.7.10.2 | 0.440 | |
| 2jc6 | QPP | Calcium/calmodulin-dependent protein kinase type 1D | 2.7.11.17 | 0.440 | |
| 2yne | NHW | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 | |
| 3dho | B2M | Streptogramin A acetyltransferase | 2.3.1 | 0.440 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.440 | |
| 4iw8 | KN3 | Estrogen receptor | / | 0.440 | |
| 4kla | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.440 |