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 |
|---|---|---|---|
| 1n4h | REA | Nuclear receptor ROR-beta |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1n4h | REA | Nuclear receptor ROR-beta | / | 1.000 | |
| 1nq7 | ARL | Nuclear receptor ROR-beta | / | 0.611 | |
| 3kyt | HC2 | Nuclear receptor ROR-gamma | / | 0.573 | |
| 4nie | NBH | Nuclear receptor ROR-gamma | / | 0.556 | |
| 1s0x | C3S | Nuclear receptor ROR-alpha | / | 0.549 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.537 | |
| 1n83 | CLR | Nuclear receptor ROR-alpha | / | 0.526 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.521 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.502 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.500 | |
| 4bii | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.494 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.488 | |
| 2w9s | TOP | Dihydrofolate reductase type 1 from Tn4003 | 1.5.1.3 | 0.482 | |
| 1re9 | DSO | Camphor 5-monooxygenase | 1.14.15.1 | 0.481 | |
| 3p6n | DSO | Camphor 5-monooxygenase | 1.14.15.1 | 0.480 | |
| 3p6p | A6B | Camphor 5-monooxygenase | 1.14.15.1 | 0.480 | |
| 2nq8 | ZID | Enoyl-ACP reductase | / | 0.479 | |
| 2w4q | CBW | Prostaglandin reductase 2 | 1.3.1.48 | 0.479 | |
| 4jvb | 1M0 | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.479 | |
| 1p44 | GEQ | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.474 | |
| 3fco | IIG | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.474 | |
| 4h95 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.474 | |
| 1iyz | NDP | Probable quinone oxidoreductase | / | 0.472 | |
| 2c7x | NRB | Cytochrome P450 monooxygenase PikC | / | 0.472 | |
| 3i59 | N6R | CRP-like cAMP-activated global transcriptional regulator | / | 0.472 | |
| 2nsd | 4PI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.470 | |
| 3kpk | FAD | Sulfide-quinone reductase | / | 0.470 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.469 | |
| 2o65 | MYF | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.469 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.469 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.468 | |
| 4elb | 34R | Dihydrofolate reductase | / | 0.468 | |
| 4ele | 31I | Dihydrofolate reductase | / | 0.468 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.468 | |
| 4jx1 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.468 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.467 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.466 | |
| 3ar4 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.466 | |
| 3p99 | LNP | Lanosterol 14-alpha-demethylase | / | 0.466 | |
| 4jvf | 17X | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.466 | |
| 1p8d | CO1 | Oxysterols receptor LXR-beta | / | 0.465 | |
| 4g34 | 924 | Eukaryotic translation initiation factor 2-alpha kinase 3 | 2.7.11.1 | 0.465 | |
| 5k2b | ZMA | Adenosine receptor A2a | / | 0.465 | |
| 1s19 | MC9 | Vitamin D3 receptor | / | 0.464 | |
| 3bfa | 9OD | Odorant binding protein ASP1 | / | 0.464 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.464 | |
| 4n70 | 2HX | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.464 | |
| 1bvr | THT | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.463 | |
| 1jio | DEB | 6-deoxyerythronolide B hydroxylase | / | 0.463 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.463 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.463 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.463 | |
| 4wdb | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.462 | |
| 1vrw | NAI | Enoyl-ACP reductase | / | 0.461 | |
| 4l9q | 9TP | Serum albumin | / | 0.461 | |
| 1yhs | STU | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.460 | |
| 2aib | ERG | Beta-elicitin cinnamomin | / | 0.460 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.460 | |
| 2dqs | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.459 | |
| 2v5x | V5X | Histone deacetylase 8 | 3.5.1.98 | 0.459 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.459 | |
| 3qf9 | NM8 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.459 | |
| 3vt4 | 5YI | Vitamin D3 receptor | / | 0.459 | |
| 1hvy | D16 | Thymidylate synthase | 2.1.1.45 | 0.458 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.458 | |
| 4elf | 35I | Dihydrofolate reductase | / | 0.458 | |
| 4j6b | PLO | Cytochrome P450 monooxygenase | / | 0.458 | |
| 2b36 | 5PP | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.457 | |
| 3dl9 | V2H | Vitamin D 25-hydroxylase | / | 0.457 | |
| 3zk5 | Z18 | Cytochrome P450 monooxygenase PikC | / | 0.457 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 4o1m | NAD | Enoyl-acyl carrier reductase | / | 0.457 | |
| 3bgx | MEF | Thymidylate synthase | / | 0.456 | |
| 3hub | 469 | Mitogen-activated protein kinase 14 | / | 0.456 | |
| 4f7i | NAD | 3-isopropylmalate dehydrogenase | 1.1.1.85 | 0.456 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.456 | |
| 1ghe | ACO | Acetyltransferase | 2.3.1 | 0.455 | |
| 2ilt | NN1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.455 | |
| 3irm | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.455 | |
| 1ia3 | TQ5 | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 1ppj | ANY | Cytochrome b | / | 0.454 | |
| 2wsa | 646 | Glycylpeptide N-tetradecanoyltransferase | / | 0.454 | |
| 2y98 | MIV | Mycinamicin IV hydroxylase/epoxidase | / | 0.454 | |
| 3h6k | 33T | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.454 | |
| 3mee | T27 | Gag-Pol polyprotein | 2.7.7.49 | 0.454 | |
| 3r9d | X6B | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.454 | |
| 3zux | TCH | Transporter | / | 0.454 | |
| 4cax | 646 | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.454 | |
| 4o70 | 1QK | Bromodomain-containing protein 4 | / | 0.454 | |
| 4wuo | NAD | 3-isopropylmalate dehydrogenase | 1.1.1.85 | 0.454 | |
| 1db1 | VDX | Vitamin D3 receptor | / | 0.453 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.453 | |
| 3ua5 | 06X | Cytochrome P450 2B6 | 1.14.13 | 0.453 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.453 | |
| 4pd6 | URI | Nucleoside permease | / | 0.453 | |
| 1osv | CHC | Bile acid receptor | / | 0.452 | |
| 1xu9 | CPS | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.452 | |
| 2hb7 | O1C | Vitamin D3 receptor | / | 0.452 | |
| 2j9l | ATP | H(+)/Cl(-) exchange transporter 5 | / | 0.452 | |
| 2nnh | REA | Cytochrome P450 2C8 | / | 0.452 | |
| 2zlc | VDX | Vitamin D3 receptor | / | 0.452 | |
| 3dxj | NE6 | DNA-directed RNA polymerase subunit beta | / | 0.452 | |
| 3dxj | NE6 | DNA-directed RNA polymerase subunit beta' | / | 0.452 | |
| 3qlw | N22 | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 1cqp | 803 | Integrin alpha-L | / | 0.451 | |
| 2fto | CB3 | Thymidylate synthase | / | 0.451 | |
| 2o4r | VD5 | Vitamin D3 receptor | / | 0.451 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.451 | |
| 3tdl | 11D | Serum albumin | / | 0.451 | |
| 4bgi | I4I | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.451 | |
| 1fdu | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.450 | |
| 1rf7 | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1sqv | UHD | Cytochrome b | / | 0.450 | |
| 1tw4 | CHD | Fatty acid-binding protein, liver | / | 0.450 | |
| 2hb8 | MVD | Vitamin D3 receptor | / | 0.450 | |
| 3c0g | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.450 | |
| 4bb5 | HD2 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.450 | |
| 5iu8 | 6DZ | Adenosine receptor A2a | / | 0.450 | |
| 1tdr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 2e98 | B29 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.449 | |
| 3ol5 | SAW | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 3p6m | DSO | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 4dm6 | TTB | Retinoic acid receptor beta | / | 0.449 | |
| 4ubs | DIF | Pentalenic acid synthase | 1.14.15.11 | 0.449 | |
| 1kt3 | RTL | Retinol-binding protein 4 | / | 0.448 | |
| 2har | OCC | Vitamin D3 receptor | / | 0.448 | |
| 3lu8 | IQX | Serum albumin | / | 0.448 | |
| 3sz0 | FAD | Sulfide-quinone reductase | / | 0.448 | |
| 4nkv | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.448 | |
| 4pkl | 1GH | Uncharacterized protein | / | 0.448 | |
| 1tys | DHF | Thymidylate synthase | / | 0.447 | |
| 3dey | DHT | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.447 | |
| 3fl9 | TOP | Dihydrofolate reductase | / | 0.447 | |
| 3klm | DHT | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.447 | |
| 3t14 | FAD | Sulfide-quinone reductase | / | 0.447 | |
| 4a7c | E46 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.447 | |
| 4elb | 34S | Dihydrofolate reductase | / | 0.447 | |
| 4g31 | 0WH | Eukaryotic translation initiation factor 2-alpha kinase 3 | 2.7.11.1 | 0.447 | |
| 4hw3 | 19G | Induced myeloid leukemia cell differentiation protein Mcl-1 | / | 0.447 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.447 | |
| 4kwi | 1TJ | Reductase homolog | / | 0.447 | |
| 4xxv | NAD | 3-isopropylmalate dehydrogenase | / | 0.447 | |
| 2hc4 | VDX | Vitamin D3 receptor A | / | 0.446 | |
| 2hnz | PC0 | Gag-Pol polyprotein | 2.7.7.49 | 0.446 | |
| 2qa2 | FAD | Polyketide oxygenase CabE | / | 0.446 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.446 | |
| 3p6o | ETG | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.446 | |
| 3vwd | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.446 | |
| 4o7u | THF | Thymidylate synthase | / | 0.446 | |
| 5d7p | OCZ | NAD-dependent protein deacetylase sirtuin-2 | 3.5.1 | 0.446 | |
| 2azz | TCH | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.445 | |
| 3hp5 | 52P | Mitogen-activated protein kinase 14 | / | 0.445 | |
| 3vt6 | 5YI | Vitamin D3 receptor | / | 0.445 | |
| 3zc3 | NAP | Ferredoxin--NADP reductase | 1.18.1.2 | 0.445 | |
| 4lxh | C1E | Alpha/beta hydrolase fold | / | 0.445 | |
| 1ot7 | CHC | Bile acid receptor | / | 0.444 | |
| 3ar7 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.444 | |
| 3byz | H11 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.444 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.444 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.444 | |
| 4bkq | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.444 | |
| 4enh | FVX | Cholesterol 24-hydroxylase | / | 0.444 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.444 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.443 | |
| 3oom | 507 | Activin receptor type-1 | 2.7.11.30 | 0.443 | |
| 3qlh | T27 | Gag-Pol polyprotein | 2.7.7.49 | 0.443 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.443 | |
| 4jbt | ASD | Cytochrome P450 monooxygenase | / | 0.443 | |
| 5k2a | ZMA | Adenosine receptor A2a | / | 0.443 | |
| 1fml | RTL | Retinol dehydratase | / | 0.442 | |
| 1i7i | AZ2 | Peroxisome proliferator-activated receptor gamma | / | 0.442 | |
| 1ia4 | TQ6 | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 2e9c | B75 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.442 | |
| 2y03 | Y01 | Beta-1 adrenergic receptor | / | 0.442 | |
| 3cnj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.442 | |
| 3d3e | D3E | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.442 | |
| 3d7k | D7K | Benzaldehyde lyase | / | 0.442 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.442 | |
| 3h1j | SMA | Cytochrome b | / | 0.442 | |
| 3t2z | FAD | Sulfide-quinone reductase | / | 0.442 | |
| 4b1f | KRH | Glutamate racemase | / | 0.442 | |
| 4elg | 52J | Dihydrofolate reductase | / | 0.442 | |
| 4h97 | 53S | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 4ips | 1G4 | Mycocyclosin synthase | 1.14.21.9 | 0.442 | |
| 1fm9 | 570 | Peroxisome proliferator-activated receptor gamma | / | 0.441 | |
| 1ie9 | VDX | Vitamin D3 receptor | / | 0.441 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.441 | |
| 1q20 | PLO | Sulfotransferase family cytosolic 2B member 1 | 2.8.2.2 | 0.441 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1rk3 | VDX | Vitamin D3 receptor | / | 0.441 | |
| 1s6q | TPB | Gag-Pol polyprotein | 2.7.7.49 | 0.441 | |
| 1zhw | HC2 | Oxysterol-binding protein homolog 4 | / | 0.441 | |
| 2bx8 | AZQ | Serum albumin | / | 0.441 | |
| 3bxx | QUE | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.441 | |
| 3f5p | 741 | Insulin-like growth factor 1 receptor | 2.7.10.1 | 0.441 | |
| 3fl8 | RAR | Dihydrofolate reductase | / | 0.441 | |
| 3jpv | 1DR | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.441 | |
| 3t2k | FAD | Sulfide-quinone reductase | / | 0.441 | |
| 4at3 | LTI | BDNF/NT-3 growth factors receptor | 2.7.10.1 | 0.441 | |
| 4e5y | NDP | GDP-L-fucose synthase | 1.1.1.271 | 0.441 | |
| 4gev | CB3 | Thymidylate synthase | / | 0.441 | |
| 4lmu | QUE | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.441 | |
| 4r20 | AER | Cytochrome P450 family 17 polypeptide 2 | / | 0.441 | |
| 1ezv | SMA | Cytochrome b | / | 0.440 | |
| 1qxl | FR8 | Adenosine deaminase | 3.5.4.4 | 0.440 | |
| 1s60 | COA | Aminoglycoside N(6')-acetyltransferase type 1 | / | 0.440 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.440 | |
| 2ibz | SMA | Cytochrome b | / | 0.440 | |
| 3ar5 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.440 | |
| 3ar6 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.440 | |
| 3sgt | P09 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | / | 0.440 | |
| 3sgx | 0FW | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.440 | |
| 3w0c | 6DS | Vitamin D3 receptor | / | 0.440 | |
| 4fhi | 0S4 | Vitamin D3 receptor A | / | 0.440 | |
| 4irn | FAD | AnaB | / | 0.440 | |
| 4muw | 2F4 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 | |
| 5br4 | NAD | Lactaldehyde reductase | 1.1.1.77 | 0.440 | |
| 5dc5 | B3N | Histone deacetylase 8 | 3.5.1.98 | 0.440 |