sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Cavities 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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 4cec | 2SS | Integrase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4cec | 2SS | Integrase | / | 1.000 | |
| 3zt1 | OM1 | Integrase | / | 0.671 | |
| 4ceq | QCH | Integrase | / | 0.636 | |
| 4cf8 | V7H | Integrase | / | 0.611 | |
| 4cgd | 8P3 | Integrase | / | 0.605 | |
| 4cef | D0T | Integrase | / | 0.601 | |
| 4cju | JNS | Integrase | / | 0.594 | |
| 4ceo | G0T | Integrase | / | 0.588 | |
| 4ces | NFW | Integrase | / | 0.583 | |
| 4cgi | NZL | Integrase | / | 0.578 | |
| 4cjf | RVN | Integrase | / | 0.577 | |
| 4cfa | WOP | Integrase | / | 0.575 | |
| 4cer | VL4 | Integrase | / | 0.572 | |
| 4ck2 | NVU | Integrase | / | 0.569 | |
| 3zsr | O3N | Integrase | / | 0.564 | |
| 4cez | O3N | Integrase | / | 0.564 | |
| 4cf0 | O5U | Integrase | / | 0.564 | |
| 4cea | ZSW | Integrase | / | 0.562 | |
| 4ced | 9NS | Integrase | / | 0.556 | |
| 4cj3 | E4F | Integrase | / | 0.555 | |
| 4cfc | 7NV | Integrase | / | 0.551 | |
| 4cjr | FYM | Integrase | / | 0.550 | |
| 4cf2 | 3GM | Integrase | / | 0.549 | |
| 4cfd | S8Y | Integrase | / | 0.549 | |
| 3zsv | ZSV | Integrase | / | 0.544 | |
| 4ceb | ZSV | Integrase | / | 0.544 | |
| 4cgj | NZL | Integrase | / | 0.543 | |
| 3zt3 | ZT4 | Integrase | / | 0.542 | |
| 4cee | B0T | Integrase | / | 0.542 | |
| 4cif | JDX | Integrase | / | 0.541 | |
| 3zsw | ZSW | Integrase | / | 0.540 | |
| 4cgg | K5Q | Integrase | / | 0.540 | |
| 4cjq | VXO | Integrase | / | 0.539 | |
| 4cgh | LOZ | Integrase | / | 0.536 | |
| 4cie | Y7N | Integrase | / | 0.534 | |
| 4cje | Q31 | Integrase | / | 0.534 | |
| 4cig | X0P | Integrase | / | 0.532 | |
| 4cf1 | IY7 | Integrase | / | 0.531 | |
| 3zt0 | ZT0 | Integrase | / | 0.530 | |
| 4ck1 | OM1 | Integrase | / | 0.528 | |
| 4cjk | H39 | Integrase | / | 0.527 | |
| 4ce9 | O3N | Integrase | / | 0.526 | |
| 4chq | CWU | Integrase | / | 0.526 | |
| 3zsy | OM3 | Integrase | / | 0.524 | |
| 4cfb | OM3 | Integrase | / | 0.524 | |
| 4cjp | 4D2 | Integrase | / | 0.523 | |
| 3zsq | O4N | Integrase | / | 0.521 | |
| 4chy | C5Q | Integrase | / | 0.519 | |
| 3zsx | N44 | Integrase | / | 0.515 | |
| 4ck3 | K1T | Integrase | / | 0.511 | |
| 4cj5 | 4VW | Integrase | / | 0.506 | |
| 3zt2 | ZT2 | Integrase | / | 0.496 | |
| 3zsz | OM2 | Integrase | / | 0.488 | |
| 4cj4 | S3G | Integrase | / | 0.485 | |
| 4cjs | L0Y | Integrase | / | 0.484 | |
| 2nry | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.473 | |
| 3zcm | PX3 | Integrase | / | 0.470 | |
| 2aa0 | MTP | Adenosine kinase | 2.7.1.20 | 0.466 | |
| 1di8 | DTQ | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.463 | |
| 5iub | CLR | Adenosine receptor A2a | / | 0.463 | |
| 2q9f | C3S | Cholesterol 24-hydroxylase | / | 0.462 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.462 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.459 | |
| 5k2c | ZMA | Adenosine receptor A2a | / | 0.459 | |
| 1rx8 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.458 | |
| 3wv9 | FEG | Hmd co-occurring protein HcgE | / | 0.458 | |
| 1bdb | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | / | 0.457 | |
| 5iua | 6DX | Adenosine receptor A2a | / | 0.457 | |
| 4e8y | IHA | D-beta-D-heptose 7-phosphate kinase | / | 0.456 | |
| 5k2d | ZMA | Adenosine receptor A2a | / | 0.456 | |
| 1wwk | NAD | 307aa long hypothetical phosphoglycerate dehydrogenase | / | 0.455 | |
| 4kug | NAD | 3-hydroxybutyryl-CoA dehydrogenase | / | 0.455 | |
| 2qoc | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.453 | |
| 2r7b | 253 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.453 | |
| 2rg6 | 287 | Mitogen-activated protein kinase 14 | / | 0.453 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.451 | |
| 2w0j | ZAT | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.451 | |
| 3mkn | DNB | Pyrimidine-specific ribonucleoside hydrolase RihB | / | 0.451 | |
| 3sp6 | IL2 | Peroxisome proliferator-activated receptor alpha | / | 0.451 | |
| 5iu8 | 6DZ | Adenosine receptor A2a | / | 0.451 | |
| 1jpa | ANP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.450 | |
| 2ylz | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.450 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.450 | |
| 3u9e | COA | Lmo1369 protein | / | 0.450 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.450 | |
| 4tvb | NAD | Homospermidine synthase | 2.5.1.44 | 0.450 | |
| 5k2a | ZMA | Adenosine receptor A2a | / | 0.450 | |
| 2ekl | NAD | D-3-phosphoglycerate dehydrogenase | / | 0.449 | |
| 4k28 | NAD | Shikimate dehydrogenase family protein | / | 0.449 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.448 | |
| 2vwq | NAP | Glucose 1-dehydrogenase | / | 0.448 | |
| 3ch6 | 311 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.448 | |
| 3nuu | JOZ | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.448 | |
| 3rbv | NAP | Sugar 3-ketoreductase | / | 0.448 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.448 | |
| 4eiy | ZMA | Adenosine receptor A2a | / | 0.448 | |
| 2ggs | NDP | dTDP-4-dehydrorhamnose reductase | / | 0.447 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.447 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.447 | |
| 2yer | TQ1 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.447 | |
| 3q71 | AR6 | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.447 | |
| 4gt3 | ATP | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.447 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.446 | |
| 2bri | ANP | Uridylate kinase | 2.7.4.22 | 0.446 | |
| 3bv2 | P38 | Mitogen-activated protein kinase 14 | / | 0.446 | |
| 3dt1 | P40 | Mitogen-activated protein kinase 14 | / | 0.446 | |
| 3p82 | FMN | Pentaerythritol tetranitrate reductase | / | 0.446 | |
| 4dt9 | GMP | APH(2'')-Id | / | 0.446 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.446 | |
| 5k2b | ZMA | Adenosine receptor A2a | / | 0.446 | |
| 1kc1 | NDP | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.445 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.445 | |
| 1szg | FNS | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.445 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.445 | |
| 4wdb | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.445 | |
| 5dp2 | NAP | CurF | / | 0.445 | |
| 5iu4 | ZMA | Adenosine receptor A2a | / | 0.445 | |
| 5uvi | ZMA | Adenosine receptor A2a | / | 0.445 | |
| 3eml | ZMA | Adenosine receptor A2a | / | 0.445 | |
| 1x2h | LPA | Lipoate-protein ligase A | 6.3.1.20 | 0.444 | |
| 1zxm | ANP | DNA topoisomerase 2-alpha | 5.99.1.3 | 0.444 | |
| 2dfv | NAD | L-threonine 3-dehydrogenase | / | 0.444 | |
| 2ix5 | FAD | Acyl-coenzyme A oxidase 4, peroxisomal | 1.3.3.6 | 0.444 | |
| 3ics | COA | Coenzyme A disulfide reductase | / | 0.444 | |
| 3r35 | 4CO | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.444 | |
| 4ft5 | H2K | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.444 | |
| 4wqm | FAD | Toluene-4-monooxygenase electron transfer component | 1.18.1.3 | 0.444 | |
| 1llu | NAD | Alcohol dehydrogenase | / | 0.443 | |
| 2xvu | 9DN | Serum albumin | / | 0.443 | |
| 2xyu | Q9G | Ephrin type-A receptor 4 | 2.7.10.1 | 0.443 | |
| 3cs8 | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.443 | |
| 3edj | BCD | Cyclomaltodextrinase | / | 0.443 | |
| 3fly | FLY | Mitogen-activated protein kinase 14 | / | 0.443 | |
| 3mpt | 1GK | Mitogen-activated protein kinase 14 | / | 0.443 | |
| 1zrz | BI1 | Protein kinase C iota type | 2.7.11.13 | 0.442 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.442 | |
| 2i65 | NAD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.442 | |
| 3hdm | MMG | Serine/threonine-protein kinase Sgk1 | 2.7.11.1 | 0.442 | |
| 3zuy | TCH | Transporter | / | 0.442 | |
| 4an4 | DUD | Putative glycosyl transferase | / | 0.442 | |
| 4bdc | ODH | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.442 | |
| 4jlo | ADP | Adenylate kinase | / | 0.442 | |
| 4mdh | NAD | Malate dehydrogenase, cytoplasmic | 1.1.1.37 | 0.442 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1jtv | TES | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.441 | |
| 1nzf | UPG | DNA beta-glucosyltransferase | / | 0.441 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.441 | |
| 3au8 | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic | 1.1.1.267 | 0.441 | |
| 3mzh | CMP | CRP-like cAMP-activated global transcriptional regulator | / | 0.441 | |
| 3v8w | 0G2 | Tyrosine-protein kinase ITK/TSK | 2.7.10.2 | 0.441 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.441 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.440 | |
| 2npx | NAD | NADH peroxidase | 1.11.1.1 | 0.440 | |
| 2p9c | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.440 | |
| 2yyu | C5P | Orotidine 5'-phosphate decarboxylase | / | 0.440 | |
| 2znq | 401 | Peroxisome proliferator-activated receptor delta | / | 0.440 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.440 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.440 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.440 | |
| 3vjo | ANP | Epidermal growth factor receptor | 2.7.10.1 | 0.440 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.440 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.440 |