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 |
|---|---|---|---|
| 1e3v | DXC | Steroid Delta-isomerase | 5.3.3.1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1e3v | DXC | Steroid Delta-isomerase | 5.3.3.1 | 1.000 | |
| 3fzw | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.616 | |
| 1oh0 | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.591 | |
| 1e3r | AND | Steroid Delta-isomerase | 5.3.3.1 | 0.588 | |
| 3ows | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.540 | |
| 1w6y | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.538 | |
| 3ipt | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.538 | |
| 1ogx | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.515 | |
| 1cqs | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.505 | |
| 3owy | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.505 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.487 | |
| 1gs3 | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.484 | |
| 1kl2 | FON | Serine hydroxymethyltransferase | / | 0.482 | |
| 4dsc | A8S | Abscisic acid receptor PYL3 | / | 0.478 | |
| 2hc4 | VDX | Vitamin D3 receptor A | / | 0.477 | |
| 4qa0 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.475 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.474 | |
| 4lb2 | DM5 | Serum albumin | / | 0.474 | |
| 4ea1 | 3RX | Dehydrosqualene synthase | / | 0.473 | |
| 3vgn | FNN | Steroid Delta-isomerase | 5.3.3.1 | 0.471 | |
| 5d1b | TSN | Histone deacetylase 8 | 3.5.1.98 | 0.471 | |
| 4m6l | 21V | Dihydrofolate reductase | 1.5.1.3 | 0.470 | |
| 2fzh | DH1 | Dihydrofolate reductase | 1.5.1.3 | 0.469 | |
| 3byz | H11 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.467 | |
| 1oho | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.466 | |
| 3oq1 | 3OQ | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.466 | |
| 3vru | YS3 | Vitamin D3 receptor | / | 0.465 | |
| 3h6k | 33T | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.464 | |
| 4qa1 | B3N | Histone deacetylase 8 | 3.5.1.98 | 0.464 | |
| 1xu9 | CPS | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.463 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.463 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.463 | |
| 4rup | H97 | Vitamin D3 receptor A | / | 0.463 | |
| 2fpc | SCG | Strictosidine synthase | 4.3.3.2 | 0.462 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.462 | |
| 3vtb | TKA | Vitamin D3 receptor | / | 0.461 | |
| 4qa2 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.461 | |
| 1rjk | VDZ | Vitamin D3 receptor | / | 0.460 | |
| 2o4r | VD5 | Vitamin D3 receptor | / | 0.460 | |
| 3ezp | B3N | Histone deacetylase 8 | 3.5.1.98 | 0.460 | |
| 3owu | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.460 | |
| 3tm5 | SFG | Uncharacterized protein | / | 0.459 | |
| 3vt6 | 5YI | Vitamin D3 receptor | / | 0.459 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.459 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.458 | |
| 2hb8 | MVD | Vitamin D3 receptor | / | 0.458 | |
| 3m8c | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.458 | |
| 3vt4 | 5YI | Vitamin D3 receptor | / | 0.458 | |
| 3fco | IIG | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.457 | |
| 4ez8 | DHF | Thymidylate synthase | 2.1.1.45 | 0.457 | |
| 4g20 | 484 | Vitamin D3 receptor A | / | 0.457 | |
| 1h35 | R01 | Squalene--hopene cyclase | 4.2.1.129 | 0.456 | |
| 1o6q | R17 | Squalene--hopene cyclase | 4.2.1.129 | 0.455 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.455 | |
| 2o4j | VD4 | Vitamin D3 receptor | / | 0.455 | |
| 3gmd | 2M3 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.455 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.455 | |
| 4qem | HC4 | Phospholipase A2 VRV-PL-VIIIa | / | 0.455 | |
| 5d7p | OCZ | NAD-dependent protein deacetylase sirtuin-2 | 3.5.1 | 0.455 | |
| 1eji | THF | Serine hydroxymethyltransferase, cytosolic | / | 0.454 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.454 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.454 | |
| 1ie9 | VDX | Vitamin D3 receptor | / | 0.453 | |
| 1re9 | DSO | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 1rk3 | VDX | Vitamin D3 receptor | / | 0.452 | |
| 2ilt | NN1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.452 | |
| 2w4q | CBW | Prostaglandin reductase 2 | 1.3.1.48 | 0.452 | |
| 2zlc | VDX | Vitamin D3 receptor | / | 0.451 | |
| 3da2 | 4MD | Carbonic anhydrase 13 | 4.2.1.1 | 0.451 | |
| 3nhx | ASD | Steroid Delta-isomerase | 5.3.3.1 | 0.451 | |
| 3uba | HC4 | Lactoperoxidase | 1.11.1.7 | 0.451 | |
| 4cx3 | HW8 | Nitric oxide synthase, brain | 1.14.13.39 | 0.451 | |
| 4jx1 | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.451 | |
| 3qak | UKA | Adenosine receptor A2a | / | 0.451 | |
| 1rkg | VD1 | Vitamin D3 receptor | / | 0.450 | |
| 3aos | JH2 | Hemolymph juvenile hormone binding protein | / | 0.450 | |
| 3p6o | ETG | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 3vtc | TK3 | Vitamin D3 receptor | / | 0.450 | |
| 3w0h | W12 | Vitamin D3 receptor | / | 0.450 | |
| 1ly4 | COQ | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 1s19 | MC9 | Vitamin D3 receptor | / | 0.449 | |
| 2ydo | ADN | Adenosine receptor A2a | / | 0.449 | |
| 3hxb | BD5 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.449 | |
| 3w0j | T08 | Vitamin D3 receptor | / | 0.449 | |
| 1fml | RTL | Retinol dehydratase | / | 0.448 | |
| 1p8d | CO1 | Oxysterols receptor LXR-beta | / | 0.448 | |
| 4hw3 | 19G | Induced myeloid leukemia cell differentiation protein Mcl-1 | / | 0.448 | |
| 1m9k | 7NI | Nitric oxide synthase, endothelial | 1.14.13.39 | 0.447 | |
| 3acy | 702 | Dehydrosqualene synthase | / | 0.447 | |
| 3bxx | QUE | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.447 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.447 | |
| 3l8s | BFF | Mitogen-activated protein kinase 14 | / | 0.447 | |
| 1dfo | FFO | Serine hydroxymethyltransferase | 2.1.2.1 | 0.446 | |
| 1fdu | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.446 | |
| 1w22 | NHB | Histone deacetylase 8 | 3.5.1.98 | 0.446 | |
| 2flh | ZEA | Cytokinin-specific binding protein | / | 0.446 | |
| 2prh | 238 | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.446 | |
| 3nrr | D16 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.446 | |
| 3w1w | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.446 | |
| 3w5e | NVW | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.446 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.446 | |
| 1tbb | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.445 | |
| 3nj0 | PYV | Abscisic acid receptor PYL2 | / | 0.445 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.445 | |
| 4fhi | 0S4 | Vitamin D3 receptor A | / | 0.445 | |
| 4keb | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.445 | |
| 1n83 | CLR | Nuclear receptor ROR-alpha | / | 0.444 | |
| 1yqj | 6NP | Mitogen-activated protein kinase 14 | / | 0.444 | |
| 2b36 | 5PP | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 2cd8 | PXI | Cytochrome P450 monooxygenase PikC | / | 0.444 | |
| 3ov4 | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.444 | |
| 4jx1 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 1eio | GCH | Gastrotropin | / | 0.443 | |
| 1eqb | FFO | Serine hydroxymethyltransferase | 2.1.2.1 | 0.443 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.443 | |
| 2has | C3O | Vitamin D3 receptor | / | 0.443 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.443 | |
| 3t8x | T8X | T-cell surface glycoprotein CD1b | / | 0.443 | |
| 3up3 | XCA | aceDAF-12 | / | 0.443 | |
| 3vrt | YS2 | Vitamin D3 receptor | / | 0.443 | |
| 4z34 | ON7 | Lysophosphatidic acid receptor 1 | / | 0.443 | |
| 1dkf | BMS | Retinoic acid receptor alpha | / | 0.442 | |
| 1zeo | C01 | Peroxisome proliferator-activated receptor gamma | / | 0.442 | |
| 3d3e | D3E | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.442 | |
| 3w0g | W07 | Vitamin D3 receptor | / | 0.442 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.442 | |
| 4b1f | KRH | Glutamate racemase | / | 0.442 | |
| 4ib4 | ERM | 5-hydroxytryptamine receptor 2B | / | 0.442 | |
| 4mt9 | 2D6 | Tankyrase-1 | 2.4.2.30 | 0.442 | |
| 1v7a | FRC | Adenosine deaminase | 3.5.4.4 | 0.441 | |
| 3dr1 | C5D | Vitamin D3 receptor A | / | 0.441 | |
| 3k47 | D09 | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.441 | |
| 4g1d | 0VK | Vitamin D3 receptor A | / | 0.441 | |
| 4la0 | 198 | Serum albumin | / | 0.441 | |
| 1uml | FR4 | Adenosine deaminase | 3.5.4.4 | 0.440 | |
| 2wsa | 646 | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 | |
| 2zb8 | IMN | Prostaglandin reductase 2 | 1.3.1.48 | 0.440 | |
| 3lfe | Z84 | Mitogen-activated protein kinase 14 | / | 0.440 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.440 | |
| 3ruk | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.440 | |
| 3ule | C69 | Actin-related protein 3 | / | 0.440 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.440 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.440 | |
| 5dc5 | B3N | Histone deacetylase 8 | 3.5.1.98 | 0.440 |