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 |
|---|---|---|---|
| 2wgg | TLM | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2wgg | TLM | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 1.000 | |
| 4c72 | TLG | 3-oxoacyl-ACP synthase | / | 0.660 | |
| 4c73 | TLH | 3-oxoacyl-ACP synthase | / | 0.657 | |
| 4c6z | TLE | 3-oxoacyl-ACP synthase | / | 0.630 | |
| 3g11 | P9C | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.578 | |
| 2aq7 | TL5 | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.573 | |
| 2aqb | TL6 | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.567 | |
| 2gfx | PMN | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.549 | |
| 3g0y | P9A | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.547 | |
| 4c6u | TLG | 3-oxoacyl-ACP synthase | / | 0.547 | |
| 4c71 | 7RD | 3-oxoacyl-ACP synthase | / | 0.540 | |
| 3ho9 | N3A | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.516 | |
| 4f32 | N32 | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | / | 0.509 | |
| 3i8p | 840 | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.502 | |
| 4jv3 | N32 | Beta-ketoacyl synthase | / | 0.498 | |
| 2vb8 | TLM | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.494 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.493 | |
| 1lke | DOG | Bilin-binding protein | / | 0.486 | |
| 3hnz | PMN | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.480 | |
| 1mrq | STR | Aldo-keto reductase family 1 member C1 | / | 0.473 | |
| 4bj9 | UHB | Tankyrase-2 | 2.4.2.30 | 0.472 | |
| 1r2j | FAD | FkbI | / | 0.471 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.469 | |
| 1fml | RTL | Retinol dehydratase | / | 0.468 | |
| 4at0 | FAD | Possible succinate dehydrogenase | / | 0.468 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.466 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.465 | |
| 2hl2 | SSA | Threonine--tRNA ligase | 6.1.1.3 | 0.464 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.463 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.463 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.462 | |
| 2ab8 | MTP | Adenosine kinase | 2.7.1.20 | 0.461 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.461 | |
| 2r2n | KYN | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.460 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.460 | |
| 1ddt | APU | Diphtheria toxin | / | 0.459 | |
| 3fhx | PXL | Pyridoxal kinase | 2.7.1.35 | 0.459 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.458 | |
| 2a9z | 26A | Adenosine kinase | 2.7.1.20 | 0.457 | |
| 2rdn | 1PL | 1-deoxypentalenic acid 11-beta-hydroxylase | 1.14.11.35 | 0.457 | |
| 2v3w | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.456 | |
| 3ho2 | N32 | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.456 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.455 | |
| 2cib | CM6 | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.455 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.454 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.454 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.454 | |
| 3pm1 | ET | HTH-type transcriptional regulator QacR | / | 0.454 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.454 | |
| 4zj8 | SUV | Orexin receptor type 1 | / | 0.454 | |
| 3sn6 | P0G | Beta-2 adrenergic receptor | / | 0.454 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.453 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.453 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.453 | |
| 4qa0 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.453 | |
| 4std | BFS | Scytalone dehydratase | 4.2.1.94 | 0.453 | |
| 1akc | PPE | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.452 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.452 | |
| 4s0v | SUV | Orexin receptor type 2 | / | 0.452 | |
| 3ch6 | 311 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.451 | |
| 3i28 | 34N | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.451 | |
| 3uwl | FOZ | Thymidylate synthase | / | 0.451 | |
| 1akb | PPD | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.450 | |
| 1jtq | LY3 | Thymidylate synthase | / | 0.450 | |
| 1tow | CRZ | Fatty acid-binding protein, adipocyte | / | 0.450 | |
| 2iod | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.450 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.450 | |
| 4n1g | CEI | Obelin | / | 0.450 | |
| 1jtu | LYB | Thymidylate synthase | / | 0.449 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.449 | |
| 2j9g | ADP | Biotin carboxylase | 6.3.4.14 | 0.449 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.449 | |
| 3oia | A31 | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 3zku | HCV | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 4ge9 | 0L0 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.449 | |
| 4okx | 198 | Androgen receptor | / | 0.449 | |
| 1kt6 | RTL | Retinol-binding protein 4 | / | 0.448 | |
| 1uyc | PU7 | Heat shock protein HSP 90-alpha | / | 0.448 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.448 | |
| 3c1t | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.448 | |
| 5dc5 | B3N | Histone deacetylase 8 | 3.5.1.98 | 0.448 | |
| 1crb | RTL | Retinol-binding protein 1 | / | 0.447 | |
| 1dtp | APU | Diphtheria toxin | / | 0.447 | |
| 1fvp | FMA | Non-fluorescent flavoprotein | / | 0.447 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.447 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.447 | |
| 2qg2 | A91 | Heat shock protein HSP 90-alpha | / | 0.447 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.447 | |
| 2vnj | FAD | NADPH:ferredoxin reductase | / | 0.447 | |
| 4a6e | ASE | Acetylserotonin O-methyltransferase | 2.1.1.4 | 0.447 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.446 | |
| 2bpo | NAP | NADPH--cytochrome P450 reductase | / | 0.446 | |
| 2on6 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.446 | |
| 3aos | JH2 | Hemolymph juvenile hormone binding protein | / | 0.446 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.446 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.446 | |
| 3hv3 | R49 | Mitogen-activated protein kinase 14 | / | 0.446 | |
| 3ksl | SZH | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.446 | |
| 4jda | A9S | Abscisic acid receptor PYL3 | / | 0.446 | |
| 4mv8 | ACP | Biotin carboxylase | 6.3.4.14 | 0.446 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.445 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.445 | |
| 2zju | IM4 | Acetylcholine-binding protein | / | 0.445 | |
| 3byz | H11 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.445 | |
| 3jqp | A2P | Ferredoxin--NADP reductase, apicoplast | / | 0.445 | |
| 4h97 | 53S | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 4nh8 | 2LC | Heat shock protein HSP 90-alpha | / | 0.445 | |
| 1e7a | PFL | Serum albumin | / | 0.444 | |
| 1n95 | HFP | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.444 | |
| 1n95 | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.444 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.444 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 3k9u | ACO | Spermidine N(1)-acetyltransferase | / | 0.444 | |
| 4dbc | 3QP | Aspartate aminotransferase | 2.6.1.1 | 0.444 | |
| 4rrm | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.444 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.444 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1ja0 | FMN | NADPH--cytochrome P450 reductase | / | 0.443 | |
| 1rfg | GMP | Purine nucleoside phosphorylase | 2.4.2.1 | 0.443 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.442 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 1kce | CB3 | Thymidylate synthase | / | 0.442 | |
| 1o8c | NDP | Probable acrylyl-CoA reductase AcuI | 1.3.1.84 | 0.442 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 1uyh | PU0 | Heat shock protein HSP 90-alpha | / | 0.442 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.442 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.442 | |
| 4bfy | ZVY | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.442 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1zeo | C01 | Peroxisome proliferator-activated receptor gamma | / | 0.441 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2v58 | LZJ | Biotin carboxylase | 6.3.4.14 | 0.441 | |
| 2wgj | VGH | Hepatocyte growth factor receptor | 2.7.10.1 | 0.441 | |
| 2xls | NAP | Putative flavin-containing monooxygenase | / | 0.441 | |
| 3ntz | 3TZ | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3zvm | ADP | Bifunctional polynucleotide phosphatase/kinase | 2.7.1.78 | 0.441 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.441 | |
| 4rrd | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.441 | |
| 4tkg | 09L | Tankyrase-2 | 2.4.2.30 | 0.441 | |
| 1cq7 | PY5 | Aspartate aminotransferase | 2.6.1.1 | 0.440 | |
| 1f20 | FAD | Nitric oxide synthase, brain | 1.14.13.39 | 0.440 | |
| 1uyd | PU8 | Heat shock protein HSP 90-alpha | / | 0.440 | |
| 1wxy | FRK | Adenosine deaminase | 3.5.4.4 | 0.440 | |
| 1yhj | R6C | Pyridoxal kinase | 2.7.1.35 | 0.440 | |
| 2a9y | 26A | Adenosine kinase | 2.7.1.20 | 0.440 | |
| 2z7h | GG3 | Geranylgeranyl pyrophosphate synthase | / | 0.440 | |
| 3eu5 | GBO | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.440 | |
| 3wav | DWV | Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 | 3.1.4.39 | 0.440 | |
| 4b63 | NAP | L-ornithine N(5)-monooxygenase | / | 0.440 | |
| 4ht2 | V50 | Carbonic anhydrase 12 | 4.2.1.1 | 0.440 | |
| 4if5 | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.440 | |
| 5k2d | ZMA | Adenosine receptor A2a | / | 0.440 |