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 |
|---|---|---|---|
| 2ham | C33 | Vitamin D3 receptor |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2ham | C33 | Vitamin D3 receptor | / | 1.000 | |
| 2hb8 | MVD | Vitamin D3 receptor | / | 0.858 | |
| 1db1 | VDX | Vitamin D3 receptor | / | 0.801 | |
| 2has | C3O | Vitamin D3 receptor | / | 0.794 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.771 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.764 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.759 | |
| 1s19 | MC9 | Vitamin D3 receptor | / | 0.733 | |
| 3w0y | DS4 | Vitamin D3 receptor | / | 0.727 | |
| 2hb7 | O1C | Vitamin D3 receptor | / | 0.702 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.694 | |
| 2zlc | VDX | Vitamin D3 receptor | / | 0.686 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.682 | |
| 2zl9 | VDA | Vitamin D3 receptor | / | 0.677 | |
| 3vt6 | 5YI | Vitamin D3 receptor | / | 0.675 | |
| 3vt4 | 5YI | Vitamin D3 receptor | / | 0.672 | |
| 3vrv | YSD | Vitamin D3 receptor | / | 0.670 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.669 | |
| 1rkg | VD1 | Vitamin D3 receptor | / | 0.668 | |
| 1s0z | EB1 | Vitamin D3 receptor | / | 0.667 | |
| 3vt3 | VDX | Vitamin D3 receptor | / | 0.665 | |
| 1rk3 | VDX | Vitamin D3 receptor | / | 0.664 | |
| 2zla | VDB | Vitamin D3 receptor | / | 0.663 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.661 | |
| 3vru | YS3 | Vitamin D3 receptor | / | 0.661 | |
| 2har | OCC | Vitamin D3 receptor | / | 0.659 | |
| 2hc4 | VDX | Vitamin D3 receptor A | / | 0.658 | |
| 3w0j | T08 | Vitamin D3 receptor | / | 0.658 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.655 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.655 | |
| 2o4j | VD4 | Vitamin D3 receptor | / | 0.653 | |
| 4fhi | 0S4 | Vitamin D3 receptor A | / | 0.653 | |
| 4g20 | 484 | Vitamin D3 receptor A | / | 0.651 | |
| 4ruo | BIV | Vitamin D3 receptor A | / | 0.651 | |
| 4rup | H97 | Vitamin D3 receptor A | / | 0.651 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.650 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.650 | |
| 2hbh | XE4 | Vitamin D3 receptor A | / | 0.645 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.645 | |
| 4fhh | 0U3 | Vitamin D3 receptor A | / | 0.644 | |
| 4g1d | 0VK | Vitamin D3 receptor A | / | 0.644 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.643 | |
| 4itf | TFY | Vitamin D3 receptor | / | 0.643 | |
| 2o4r | VD5 | Vitamin D3 receptor | / | 0.642 | |
| 3m7r | VDX | Vitamin D3 receptor | / | 0.642 | |
| 1rjk | VDZ | Vitamin D3 receptor | / | 0.640 | |
| 3dr1 | C5D | Vitamin D3 receptor A | / | 0.639 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.636 | |
| 4g1y | 0VO | Vitamin D3 receptor A | / | 0.636 | |
| 3w0i | O11 | Vitamin D3 receptor | / | 0.633 | |
| 4g21 | 0VP | Vitamin D3 receptor A | / | 0.631 | |
| 4g2h | 0VQ | Vitamin D3 receptor A | / | 0.631 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.629 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.629 | |
| 3vrt | YS2 | Vitamin D3 receptor | / | 0.628 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.628 | |
| 4ruj | VDX | Vitamin D3 receptor A | / | 0.628 | |
| 3w5r | LOA | Vitamin D3 receptor | / | 0.627 | |
| 3vtb | TKA | Vitamin D3 receptor | / | 0.624 | |
| 4q0a | 4OA | Vitamin D3 receptor A | / | 0.624 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.620 | |
| 3w0g | W07 | Vitamin D3 receptor | / | 0.619 | |
| 3w5t | LHP | Vitamin D3 receptor | / | 0.610 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.606 | |
| 3vtc | TK3 | Vitamin D3 receptor | / | 0.606 | |
| 3w0c | 6DS | Vitamin D3 receptor | / | 0.603 | |
| 3w0h | W12 | Vitamin D3 receptor | / | 0.603 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.598 | |
| 1ie9 | VDX | Vitamin D3 receptor | / | 0.584 | |
| 3w5q | 3KL | Vitamin D3 receptor | / | 0.578 | |
| 4g2i | 0VQ | Vitamin D3 receptor | / | 0.510 | |
| 3czr | 3CZ | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.498 | |
| 4hfr | 14M | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.481 | |
| 3fco | IIG | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.470 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.470 | |
| 3bej | MUF | Bile acid receptor | / | 0.469 | |
| 2wuf | KEM | 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase | 3.7.1.17 | 0.464 | |
| 4nkv | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.461 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.458 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.457 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.457 | |
| 3g4i | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.457 | |
| 4jvb | 1M0 | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.457 | |
| 2qo4 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.456 | |
| 3d5f | L41 | Peroxisome proliferator-activated receptor delta | / | 0.456 | |
| 1nq7 | ARL | Nuclear receptor ROR-beta | / | 0.455 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.455 | |
| 2ykj | YKJ | Heat shock protein HSP 90-alpha | / | 0.455 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.455 | |
| 3wd7 | COA | Acridone synthase | / | 0.455 | |
| 2hw2 | RFP | Rifampin ADP-ribosyl transferase | / | 0.453 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.453 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.452 | |
| 1p8d | CO1 | Oxysterols receptor LXR-beta | / | 0.451 | |
| 2go4 | TUX | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.451 | |
| 3w32 | W32 | Epidermal growth factor receptor | 2.7.10.1 | 0.451 | |
| 1ppj | SMA | Cytochrome b | / | 0.450 | |
| 3byz | H11 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.450 | |
| 3mnr | SD1 | Heat shock protein HSP 90-alpha | / | 0.450 | |
| 3zep | 1NX | Tyrosine-protein kinase JAK3 | 2.7.10.2 | 0.450 | |
| 1jip | KTN | 6-deoxyerythronolide B hydroxylase | / | 0.449 | |
| 1uyd | PU8 | Heat shock protein HSP 90-alpha | / | 0.449 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.449 | |
| 3ruk | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.449 | |
| 2vn0 | TDZ | Cytochrome P450 2C8 | / | 0.448 | |
| 2ykc | YKC | Heat shock protein HSP 90-alpha | / | 0.448 | |
| 3beg | ANP | SRSF protein kinase 1 | 2.7.11.1 | 0.448 | |
| 3lkh | LT6 | Genome polyprotein | 2.7.7.48 | 0.448 | |
| 3up0 | D7S | aceDAF-12 | / | 0.448 | |
| 4l9q | 9TP | Serum albumin | / | 0.448 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 1uyf | PU1 | Heat shock protein HSP 90-alpha | / | 0.447 | |
| 4dhy | S41 | Glucokinase | 2.7.1.2 | 0.447 | |
| 3u8h | BHP | Phospholipase A2, membrane associated | / | 0.446 | |
| 4awo | 99B | Heat shock protein HSP 90-alpha | / | 0.446 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.446 | |
| 4jvf | 17X | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.446 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.446 | |
| 5itz | LOC | Tubulin beta-2B chain | / | 0.446 | |
| 1lri | CLR | Beta-elicitin cryptogein | / | 0.445 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.445 | |
| 2pr2 | DG1 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 2qo6 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.445 | |
| 4nky | 3QZ | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.445 | |
| 2nnh | REA | Cytochrome P450 2C8 | / | 0.444 | |
| 3w33 | W19 | Epidermal growth factor receptor | 2.7.10.1 | 0.444 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.443 | |
| 2nry | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.443 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 3d3e | D3E | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.441 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.441 | |
| 3vev | 0H4 | Glucokinase | 2.7.1.2 | 0.441 | |
| 4l9k | EHF | Serum albumin | / | 0.441 | |
| 4nie | NBH | Nuclear receptor ROR-gamma | / | 0.441 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1fp2 | HMO | Isoflavone-7-O-methyltransferase 8 | 2.1.1.150 | 0.440 | |
| 1tll | NAP | Nitric oxide synthase, brain | 1.14.13.39 | 0.440 | |
| 2om9 | AJA | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.440 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.440 | |
| 3gyt | DL4 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.440 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.440 |