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 |
|---|---|---|---|
| 2xb8 | XNW | 3-dehydroquinate dehydratase | 4.2.1.10 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2xb8 | XNW | 3-dehydroquinate dehydratase | 4.2.1.10 | 1.000 | |
| 2y71 | CB6 | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.599 | |
| 2cjf | RP4 | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.579 | |
| 3n76 | CA2 | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.569 | |
| 2xda | JPS | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.566 | |
| 2bt4 | CA2 | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.549 | |
| 2wks | CB6 | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.538 | |
| 4b6s | 2HN | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.526 | |
| 1c3x | 8IG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.525 | |
| 4b6r | 3DQ | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.522 | |
| 2xb9 | XNW | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.521 | |
| 4g8j | THM | Uridine phosphorylase | / | 0.499 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.498 | |
| 2our | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.493 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.493 | |
| 3v0m | 5GW | Histo-blood group ABO system transferase | / | 0.487 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.483 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.483 | |
| 4l0o | PLP | Cystathionine gamma-synthase | 2.5.1.48 | 0.482 | |
| 1x2h | LPA | Lipoate-protein ligase A | 6.3.1.20 | 0.480 | |
| 4j53 | 1J4 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.480 | |
| 4p9d | TMP | Deoxycytidylate deaminase | / | 0.478 | |
| 1u1d | 181 | Uridine phosphorylase | 2.4.2.3 | 0.476 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.475 | |
| 4dlc | UMP | Deoxyuridine triphosphatase, putative | / | 0.475 | |
| 2clf | F6F | Tryptophan synthase alpha chain | / | 0.474 | |
| 2fjd | SFD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.473 | |
| 1u1f | 183 | Uridine phosphorylase | 2.4.2.3 | 0.471 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.469 | |
| 2z9d | FMN | FMN-dependent NADH-azoreductase | / | 0.469 | |
| 4lzw | THM | Uridine phosphorylase | / | 0.469 | |
| 1pwy | AC2 | Purine nucleoside phosphorylase | 2.4.2.1 | 0.468 | |
| 1w19 | T1P | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.468 | |
| 1y2b | DEE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.468 | |
| 2x06 | NAD | L-sulfolactate dehydrogenase | / | 0.468 | |
| 3sso | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.468 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.467 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.467 | |
| 3bjc | WAN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.467 | |
| 1kw6 | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.466 | |
| 1w19 | T5P | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.466 | |
| 2ejz | SAH | Diphthine synthase | / | 0.466 | |
| 3b9l | AZZ | Serum albumin | / | 0.466 | |
| 2a9y | 26A | Adenosine kinase | 2.7.1.20 | 0.465 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.465 | |
| 2wzg | UPG | Uncharacterized protein | / | 0.465 | |
| 4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.465 | |
| 4kc1 | WS1 | Histo-blood group ABO system transferase | / | 0.465 | |
| 2h3w | HC5 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.464 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.462 | |
| 2zyt | PPS | Sulfotransferase 1 family member D1 | / | 0.462 | |
| 3o56 | ZG1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.461 | |
| 4u0s | ADP | Adenosine monophosphate-protein transferase FICD | 2.7.7.n1 | 0.461 | |
| 5a88 | ADP | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.460 | |
| 3sni | 546 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.459 | |
| 4bb2 | STR | Corticosteroid-binding globulin | / | 0.459 | |
| 3e8x | NAP | BH1520 protein | / | 0.458 | |
| 3n87 | N87 | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.458 | |
| 4ajf | F03 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.458 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.458 | |
| 4tyq | AP5 | Adenylate kinase | / | 0.458 | |
| 1gky | 5GP | Guanylate kinase | 2.7.4.8 | 0.457 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.457 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.457 | |
| 4do3 | 0LA | Fatty-acid amide hydrolase 1 | 3.5.1.99 | 0.457 | |
| 5c1g | GDU | Histo-blood group ABO system transferase | / | 0.457 | |
| 2fja | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.456 | |
| 3biz | 61E | Wee1-like protein kinase | 2.7.10.2 | 0.456 | |
| 4b67 | FAD | L-ornithine N(5)-monooxygenase | / | 0.456 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.456 | |
| 4ryv | ZEA | Protein LlR18A | / | 0.456 | |
| 1gg5 | E09 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.455 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.455 | |
| 2o1x | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.455 | |
| 3fkt | SII | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 3to3 | ATP | Petrobactin biosynthesis protein AsbB | / | 0.455 | |
| 4l5b | 1UX | Deoxycytidine kinase | 2.7.1.74 | 0.455 | |
| 5cpb | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.455 | |
| 1jnr | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.454 | |
| 2bxq | IMN | Serum albumin | / | 0.454 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.454 | |
| 2zrx | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.454 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 3sn7 | 540 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.453 | |
| 3v0n | 4GW | Histo-blood group ABO system transferase | / | 0.453 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.453 | |
| 2ouy | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.452 | |
| 3ixp | 834 | Ecdysone receptor | / | 0.452 | |
| 4fhf | 0TT | Spore photoproduct lyase | / | 0.452 | |
| 1fdt | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.451 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 2fb3 | 5AD | GTP 3',8-cyclase | 4.1.99.18 | 0.451 | |
| 2fr0 | NDP | 6-deoxyerythronolide-B synthase EryA1, modules 1 and 2 | / | 0.451 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.451 | |
| 3euf | BAU | Uridine phosphorylase 1 | / | 0.451 | |
| 3sl2 | ATP | Sensor histidine kinase WalK | / | 0.451 | |
| 3uax | NOS | Purine nucleoside phosphorylase DeoD-type | / | 0.451 | |
| 4h9t | HL4 | Phosphotriesterase | / | 0.451 | |
| 4jau | ADP | Sensor histidine kinase | / | 0.451 | |
| 4umy | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.451 | |
| 1txt | CAA | HMG-CoA synthase | / | 0.450 | |
| 2p9c | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.450 | |
| 3qj0 | QI3 | Botulinum neurotoxin type A | 3.4.24.69 | 0.450 | |
| 5il2 | SAH | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.450 | |
| 1odj | GMP | Purine nucleoside phosphorylase | / | 0.449 | |
| 1rsg | FAD | Polyamine oxidase FMS1 | / | 0.449 | |
| 2bxm | IMN | Serum albumin | / | 0.449 | |
| 2o6h | INI | 6,7-dimethyl-8-ribityllumazine synthase 1 | 2.5.1.78 | 0.449 | |
| 2yvw | EPU | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.449 | |
| 3p0f | BAU | Uridine phosphorylase 2 | 2.4.2.3 | 0.449 | |
| 3uaw | ADN | Purine nucleoside phosphorylase DeoD-type | / | 0.449 | |
| 4cuk | NAI | D-lactate dehydrogenase | / | 0.449 | |
| 1h60 | STR | Pentaerythritol tetranitrate reductase | / | 0.448 | |
| 1mxf | MTX | Putative pteridine reductase 2 | / | 0.448 | |
| 1wur | 8DG | GTP cyclohydrolase 1 | / | 0.448 | |
| 3hxe | BD8 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.448 | |
| 4g2y | NI5 | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.448 | |
| 4v0s | 2HN | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.448 | |
| 1h61 | PDN | Pentaerythritol tetranitrate reductase | / | 0.447 | |
| 1i59 | ANP | Chemotaxis protein CheA | 2.7.13.3 | 0.447 | |
| 1jnz | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.447 | |
| 1qbq | HFP | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.447 | |
| 1qbq | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.447 | |
| 1vft | DCS | Alanine racemase | / | 0.447 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.447 | |
| 2ojg | 19A | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.447 | |
| 3b05 | IPE | Isopentenyl-diphosphate delta-isomerase | / | 0.447 | |
| 3ssm | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.447 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.447 | |
| 4fhd | 0TT | Spore photoproduct lyase | / | 0.447 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 4itx | IN5 | Cystathionine beta-lyase MetC | 4.4.1.8 | 0.447 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.447 | |
| 1bvr | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.446 | |
| 1ftl | DNQ | Glutamate receptor 2 | / | 0.446 | |
| 1h66 | RH1 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.446 | |
| 1x28 | PGU | Aspartate aminotransferase | 2.6.1.1 | 0.446 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.446 | |
| 2e0n | SAH | Precorrin-2 C20-methyltransferase | / | 0.446 | |
| 2hve | ADP | Nucleoside diphosphate kinase A | 2.7.4.6 | 0.446 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.446 | |
| 4g2w | NI0 | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.446 | |
| 5std | UNN | Scytalone dehydratase | 4.2.1.94 | 0.446 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.445 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.445 | |
| 2zry | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.445 | |
| 3gc4 | AAQ | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.445 | |
| 3kr6 | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.445 | |
| 4hbm | 0Y7 | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 | 0.445 | |
| 4rh1 | 0TT | Spore photoproduct lyase | / | 0.445 | |
| 1ejb | INJ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.444 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 1uho | VDN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.444 | |
| 2c1a | I5S | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.444 | |
| 2ylr | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.444 | |
| 3cr0 | 809 | Wee1-like protein kinase | 2.7.10.2 | 0.444 | |
| 3iex | GMP | Purine nucleoside phosphorylase | / | 0.444 | |
| 3juo | AJD | Phenazine biosynthesis protein A/B | / | 0.444 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3qh2 | 3NM | Thiazole tautomerase | / | 0.444 | |
| 3w2f | NAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.444 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 4a2a | ATP | Cell division protein FtsA | / | 0.444 | |
| 4bfy | ZVY | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 4du6 | GTP | GTP cyclohydrolase 1 | / | 0.444 | |
| 4jva | 1OR | cAMP-dependent protein kinase type II-beta regulatory subunit | / | 0.444 | |
| 4rsy | B3N | Leukotriene A-4 hydrolase | 3.3.2.6 | 0.444 | |
| 1pr6 | XYA | Purine nucleoside phosphorylase DeoD-type | / | 0.443 | |
| 1thn | ADP | Anti-sigma F factor | / | 0.443 | |
| 2qo4 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.443 | |
| 3arq | DM5 | Chitinase A | / | 0.443 | |
| 3c1o | NAP | Eugenol synthase | / | 0.443 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3of3 | DIH | Purine nucleoside phosphorylase DeoD-type 1 | / | 0.443 | |
| 3t74 | UBY | Thermolysin | 3.4.24.27 | 0.443 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 4br0 | AU1 | Ectonucleoside triphosphate diphosphohydrolase 2 | / | 0.443 | |
| 1t0i | FMN | NAD(P)H-dependent FMN reductase LOT6 | / | 0.442 | |
| 1ylu | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.442 | |
| 2xvw | 9NR | Serum albumin | / | 0.442 | |
| 2zi5 | 3L1 | Deoxycytidine kinase | 2.7.1.74 | 0.442 | |
| 3b05 | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.442 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3fzn | D7K | Benzoylformate decarboxylase | 4.1.1.7 | 0.442 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.442 | |
| 4ffr | ATP | Uncharacterized protein | / | 0.442 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.442 | |
| 4wdb | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.442 | |
| 1fx9 | MJI | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.441 | |
| 1piw | NAP | NADP-dependent alcohol dehydrogenase 6 | 1.1.1.2 | 0.441 | |
| 1pr0 | NOS | Purine nucleoside phosphorylase DeoD-type | / | 0.441 | |
| 1vg8 | GNP | Ras-related protein Rab-7a | / | 0.441 | |
| 2po3 | T4K | 4-dehydrase | / | 0.441 | |
| 2wjo | QUD | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 2zru | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.441 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 4fcb | 0T7 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.441 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.441 | |
| 4tln | LNO | Thermolysin | 3.4.24.27 | 0.441 | |
| 1lb9 | DNQ | Glutamate receptor 2 | / | 0.440 | |
| 1tll | FAD | Nitric oxide synthase, brain | 1.14.13.39 | 0.440 | |
| 1trg | CB3 | Thymidylate synthase | / | 0.440 | |
| 1vfs | DCS | Alanine racemase | / | 0.440 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.440 | |
| 2gev | COK | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.440 | |
| 3ae4 | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.440 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3pgh | FLP | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.440 | |
| 4pl9 | ADP | Ethylene receptor 1 | / | 0.440 | |
| 4rph | GDU | UDP-galactopyranose mutase | 5.4.99.9 | 0.440 |