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 |
|---|---|---|---|
| 2o4j | VD4 | Vitamin D3 receptor |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2o4j | VD4 | Vitamin D3 receptor | / | 1.000 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.884 | |
| 2o4r | VD5 | Vitamin D3 receptor | / | 0.836 | |
| 3vru | YS3 | Vitamin D3 receptor | / | 0.750 | |
| 1rkg | VD1 | Vitamin D3 receptor | / | 0.726 | |
| 2hb7 | O1C | Vitamin D3 receptor | / | 0.717 | |
| 3vrv | YSD | Vitamin D3 receptor | / | 0.709 | |
| 1rjk | VDZ | Vitamin D3 receptor | / | 0.708 | |
| 2has | C3O | Vitamin D3 receptor | / | 0.708 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.700 | |
| 1s0z | EB1 | Vitamin D3 receptor | / | 0.697 | |
| 2hc4 | VDX | Vitamin D3 receptor A | / | 0.696 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.695 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.694 | |
| 2zl9 | VDA | Vitamin D3 receptor | / | 0.694 | |
| 1s19 | MC9 | Vitamin D3 receptor | / | 0.693 | |
| 2har | OCC | Vitamin D3 receptor | / | 0.692 | |
| 2zlc | VDX | Vitamin D3 receptor | / | 0.692 | |
| 4g1d | 0VK | Vitamin D3 receptor A | / | 0.692 | |
| 4rup | H97 | Vitamin D3 receptor A | / | 0.691 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.690 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.690 | |
| 3w0j | T08 | Vitamin D3 receptor | / | 0.689 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.689 | |
| 2hb8 | MVD | Vitamin D3 receptor | / | 0.687 | |
| 1db1 | VDX | Vitamin D3 receptor | / | 0.684 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.684 | |
| 4fhh | 0U3 | Vitamin D3 receptor A | / | 0.683 | |
| 4g20 | 484 | Vitamin D3 receptor A | / | 0.677 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.676 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.676 | |
| 1ie9 | VDX | Vitamin D3 receptor | / | 0.675 | |
| 4g21 | 0VP | Vitamin D3 receptor A | / | 0.675 | |
| 1rk3 | VDX | Vitamin D3 receptor | / | 0.674 | |
| 2zla | VDB | Vitamin D3 receptor | / | 0.673 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.673 | |
| 3vt3 | VDX | Vitamin D3 receptor | / | 0.671 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.671 | |
| 3vt4 | 5YI | Vitamin D3 receptor | / | 0.670 | |
| 3vt6 | 5YI | Vitamin D3 receptor | / | 0.670 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.670 | |
| 4ruj | VDX | Vitamin D3 receptor A | / | 0.670 | |
| 3dr1 | C5D | Vitamin D3 receptor A | / | 0.669 | |
| 3vtb | TKA | Vitamin D3 receptor | / | 0.669 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.669 | |
| 4itf | TFY | Vitamin D3 receptor | / | 0.667 | |
| 2hbh | XE4 | Vitamin D3 receptor A | / | 0.666 | |
| 3w0y | DS4 | Vitamin D3 receptor | / | 0.666 | |
| 3vrt | YS2 | Vitamin D3 receptor | / | 0.665 | |
| 4fhi | 0S4 | Vitamin D3 receptor A | / | 0.665 | |
| 4g1y | 0VO | Vitamin D3 receptor A | / | 0.664 | |
| 3vtc | TK3 | Vitamin D3 receptor | / | 0.660 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.659 | |
| 3w0i | O11 | Vitamin D3 receptor | / | 0.659 | |
| 4ruo | BIV | Vitamin D3 receptor A | / | 0.659 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.657 | |
| 4g2h | 0VQ | Vitamin D3 receptor A | / | 0.657 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.656 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.653 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.652 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.651 | |
| 3w0c | 6DS | Vitamin D3 receptor | / | 0.647 | |
| 3w0h | W12 | Vitamin D3 receptor | / | 0.645 | |
| 3w0g | W07 | Vitamin D3 receptor | / | 0.639 | |
| 3m7r | VDX | Vitamin D3 receptor | / | 0.638 | |
| 4q0a | 4OA | Vitamin D3 receptor A | / | 0.637 | |
| 3w5q | 3KL | Vitamin D3 receptor | / | 0.625 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.623 | |
| 3w5t | LHP | Vitamin D3 receptor | / | 0.623 | |
| 3w5r | LOA | Vitamin D3 receptor | / | 0.619 | |
| 4g2i | 0VQ | Vitamin D3 receptor | / | 0.522 | |
| 4hfr | 14M | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.515 | |
| 3fco | IIG | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.497 | |
| 3czr | 3CZ | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.496 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.486 | |
| 3d5f | L41 | Peroxisome proliferator-activated receptor delta | / | 0.482 | |
| 3bej | MUF | Bile acid receptor | / | 0.477 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.476 | |
| 3up0 | D7S | aceDAF-12 | / | 0.476 | |
| 2ykj | YKJ | Heat shock protein HSP 90-alpha | / | 0.475 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.474 | |
| 2qo4 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.473 | |
| 1p8d | CO1 | Oxysterols receptor LXR-beta | / | 0.471 | |
| 1guf | NDP | Enoyl-[acyl-carrier-protein] reductase 1, mitochondrial | 1.3.1.10 | 0.470 | |
| 3oq1 | 3OQ | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.470 | |
| 4l9k | EHF | Serum albumin | / | 0.469 | |
| 2nnh | REA | Cytochrome P450 2C8 | / | 0.468 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.468 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.467 | |
| 3g49 | 3G4 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.467 | |
| 4iah | 1DX | Alr2278 protein | / | 0.466 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.466 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.465 | |
| 1uyf | PU1 | Heat shock protein HSP 90-alpha | / | 0.465 | |
| 2nq8 | ZID | Enoyl-ACP reductase | / | 0.465 | |
| 2nry | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.464 | |
| 4enh | FVX | Cholesterol 24-hydroxylase | / | 0.464 | |
| 2pr2 | DG1 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.463 | |
| 2qo6 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.463 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.463 | |
| 4jvb | 1M0 | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.463 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.462 | |
| 1f5f | DHT | Sex hormone-binding globulin | / | 0.462 | |
| 2wuf | KEM | 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase | 3.7.1.17 | 0.462 | |
| 2ev9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.461 | |
| 3anl | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.461 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.461 | |
| 1z6t | ADP | Apoptotic protease-activating factor 1 | / | 0.460 | |
| 3lkh | LT6 | Genome polyprotein | 2.7.7.48 | 0.460 | |
| 4kxn | 6K6 | 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 | / | 0.460 | |
| 4l9q | 9TP | Serum albumin | / | 0.460 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.459 | |
| 3up3 | XCA | aceDAF-12 | / | 0.459 | |
| 4dhy | S41 | Glucokinase | 2.7.1.2 | 0.459 | |
| 4o0r | X4Z | Serine/threonine-protein kinase PAK 1 | 2.7.11.1 | 0.459 | |
| 5itz | LOC | Tubulin beta-2B chain | / | 0.459 | |
| 1zga | HMK | Isoflavone 4'-O-methyltransferase | / | 0.457 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.457 | |
| 1fml | RTL | Retinol dehydratase | / | 0.456 | |
| 1l2j | ETC | Estrogen receptor beta | / | 0.456 | |
| 1lhv | NOG | Sex hormone-binding globulin | / | 0.456 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.456 | |
| 1zid | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.456 | |
| 3mnr | SD1 | Heat shock protein HSP 90-alpha | / | 0.456 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.456 | |
| 3d3e | D3E | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.455 | |
| 1m13 | HYF | Nuclear receptor subfamily 1 group I member 2 | / | 0.454 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.454 | |
| 3p3c | 3P3 | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.454 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.453 | |
| 2ykc | YKC | Heat shock protein HSP 90-alpha | / | 0.453 | |
| 2yke | YKE | Heat shock protein HSP 90-alpha | / | 0.453 | |
| 3beg | ANP | SRSF protein kinase 1 | 2.7.11.1 | 0.453 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.453 | |
| 1ppj | SMA | Cytochrome b | / | 0.452 | |
| 1ysx | 4EB | Serum albumin | / | 0.452 | |
| 3g4i | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.452 | |
| 3gyu | DL7 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.452 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.451 | |
| 1ie4 | T44 | Transthyretin | / | 0.451 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.451 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.451 | |
| 3byz | H11 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.451 | |
| 3wd7 | COA | Acridone synthase | / | 0.451 | |
| 3zk5 | Z18 | Cytochrome P450 monooxygenase PikC | / | 0.451 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.451 | |
| 4okt | 198 | Androgen receptor | / | 0.451 | |
| 1nyt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.450 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 2ntv | P1H | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.450 | |
| 2o7p | NAP | Riboflavin biosynthesis protein RibD | / | 0.450 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 2w6o | OA3 | Biotin carboxylase | 6.3.4.14 | 0.450 | |
| 3ijd | C2F | Methylenetetrahydrofolate reductase | / | 0.450 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.450 | |
| 4r20 | AER | Cytochrome P450 family 17 polypeptide 2 | / | 0.450 | |
| 5k2b | ZMA | Adenosine receptor A2a | / | 0.450 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.449 | |
| 1nq7 | ARL | Nuclear receptor ROR-beta | / | 0.449 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.449 | |
| 2w9s | TOP | Dihydrofolate reductase type 1 from Tn4003 | 1.5.1.3 | 0.449 | |
| 3nj0 | PYV | Abscisic acid receptor PYL2 | / | 0.449 | |
| 2aib | ERG | Beta-elicitin cinnamomin | / | 0.448 | |
| 2lba | CHO | Fatty acid binding protein 6 | / | 0.448 | |
| 3c0g | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.448 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.448 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.448 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.448 | |
| 4ly9 | 1YY | Glucokinase regulatory protein | / | 0.448 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.448 | |
| 4u9z | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.448 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 1zeo | C01 | Peroxisome proliferator-activated receptor gamma | / | 0.447 | |
| 2vd5 | BI8 | Myotonin-protein kinase | 2.7.11.1 | 0.447 | |
| 2vzm | NRB | Cytochrome P450 monooxygenase PikC | / | 0.447 | |
| 3cgc | COA | Coenzyme A disulfide reductase | / | 0.447 | |
| 3gyt | DL4 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.447 | |
| 3mg3 | ECH | Orange carotenoid-binding protein | / | 0.447 | |
| 1jip | KTN | 6-deoxyerythronolide B hydroxylase | / | 0.446 | |
| 1zg3 | 2HI | Isoflavone 4'-O-methyltransferase | / | 0.446 | |
| 3w32 | W32 | Epidermal growth factor receptor | 2.7.10.1 | 0.446 | |
| 4o1m | NAD | Enoyl-acyl carrier reductase | / | 0.446 | |
| 1fds | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.445 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.445 | |
| 2wot | ZZG | TGF-beta receptor type-1 | 2.7.11.30 | 0.445 | |
| 2zb4 | 5OP | Prostaglandin reductase 2 | 1.3.1.48 | 0.445 | |
| 2zb8 | IMN | Prostaglandin reductase 2 | 1.3.1.48 | 0.445 | |
| 3l8s | BFF | Mitogen-activated protein kinase 14 | / | 0.445 | |
| 4fjz | 4FJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.445 | |
| 4h95 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 5ag6 | MYA | Glycylpeptide N-tetradecanoyltransferase | / | 0.445 | |
| 1opb | RET | Retinol-binding protein 2 | / | 0.444 | |
| 1sn5 | T3 | Transthyretin | / | 0.444 | |
| 3ey4 | 352 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.444 | |
| 3lu8 | IQX | Serum albumin | / | 0.444 | |
| 4nmk | NAP | Aldehyde dehydrogenase | / | 0.444 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.444 | |
| 5koi | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.444 | |
| 1iyz | NDP | Probable quinone oxidoreductase | / | 0.443 | |
| 1ju6 | LYA | Thymidylate synthase | 2.1.1.45 | 0.443 | |
| 1rf9 | DBR | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 1uyh | PU0 | Heat shock protein HSP 90-alpha | / | 0.443 | |
| 2fto | CB3 | Thymidylate synthase | / | 0.443 | |
| 2om9 | AJA | Peroxisome proliferator-activated receptor gamma | / | 0.443 | |
| 2zyn | BCD | Periplasmic binding protein | / | 0.443 | |
| 3ggg | NAD | Prephenate dehydrogenase | / | 0.443 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.443 | |
| 3v8w | 0G2 | Tyrosine-protein kinase ITK/TSK | 2.7.10.2 | 0.443 | |
| 4ge4 | 0KE | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.443 | |
| 4nmb | FAD | Bifunctional protein PutA | / | 0.443 | |
| 5br4 | NAD | Lactaldehyde reductase | 1.1.1.77 | 0.443 | |
| 1eup | ASD | 6-deoxyerythronolide B hydroxylase | / | 0.442 | |
| 1n83 | CLR | Nuclear receptor ROR-alpha | / | 0.442 | |
| 2hw2 | RFP | Rifampin ADP-ribosyl transferase | / | 0.442 | |
| 2ilt | NN1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.442 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2nru | T12 | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.442 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 3h6k | 33T | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.442 | |
| 3ruk | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.442 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.442 | |
| 4ez5 | 0RS | Cyclin-dependent kinase 6 | 2.7.11.22 | 0.442 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.442 | |
| 4qe6 | JN3 | Bile acid receptor | / | 0.442 | |
| 4u2l | SFD | Cholesterol oxidase | 1.1.3.6 | 0.442 | |
| 4wa9 | AXI | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.442 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 3t8x | T8X | T-cell surface glycoprotein CD1b | / | 0.441 | |
| 4kvx | ACO | N-terminal acetyltransferase A complex catalytic subunit ard1 | 2.3.1.88 | 0.441 | |
| 1gal | FAD | Glucose oxidase | 1.1.3.4 | 0.440 | |
| 1jio | DEB | 6-deoxyerythronolide B hydroxylase | / | 0.440 | |
| 1osv | CHC | Bile acid receptor | / | 0.440 | |
| 1qkn | RAL | Estrogen receptor beta | / | 0.440 | |
| 1xu9 | CPS | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.440 | |
| 3is9 | AC7 | Gag-Pol polyprotein | 2.7.7.49 | 0.440 | |
| 3r6s | CMP | CRP-like cAMP-activated global transcriptional regulator | / | 0.440 | |
| 3w2e | NAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.440 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 4jvf | 17X | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.440 | |
| 4nh8 | 2LC | Heat shock protein HSP 90-alpha | / | 0.440 | |
| 4nxv | GDP | Mitochondrial dynamics protein MID51 | / | 0.440 | |
| 5kgp | ACO | Predicted acetyltransferase | / | 0.440 |