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 |
|---|---|---|---|
| 4hld | 16T | Thymidylate kinase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4hld | 16T | Thymidylate kinase | / | 1.000 | |
| 4gsy | 0Y5 | Thymidylate kinase | / | 0.729 | |
| 4hej | 14D | Thymidylate kinase | / | 0.588 | |
| 3l05 | SN0 | N-acetylornithine carbamoyltransferase | 2.1.3.9 | 0.506 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.500 | |
| 1u1g | BBB | Uridine phosphorylase | 2.4.2.3 | 0.495 | |
| 3qpg | 3QP | Aspartate aminotransferase | 2.6.1.1 | 0.495 | |
| 1dr4 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.482 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.479 | |
| 2ejz | SAH | Diphthine synthase | / | 0.478 | |
| 3p0f | BAU | Uridine phosphorylase 2 | 2.4.2.3 | 0.477 | |
| 4b11 | 7I1 | Glycylpeptide N-tetradecanoyltransferase | / | 0.473 | |
| 2hk9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.472 | |
| 1ivr | CBA | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.471 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.471 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.471 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.470 | |
| 1cq6 | PY4 | Aspartate aminotransferase | 2.6.1.1 | 0.468 | |
| 1toi | HCI | Aspartate aminotransferase | 2.6.1.1 | 0.468 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.468 | |
| 4c3y | ANB | 3-ketosteroid dehydrogenase | / | 0.468 | |
| 1dgh | NDP | Catalase | 1.11.1.6 | 0.467 | |
| 1el4 | CTZ | Obelin | / | 0.466 | |
| 1pnq | NDP | NAD(P) transhydrogenase subunit beta | 1.6.1.2 | 0.466 | |
| 4dch | 4DC | Glucokinase | 2.7.1.2 | 0.466 | |
| 1map | KET | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.463 | |
| 3zhq | TPP | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.462 | |
| 5std | UNN | Scytalone dehydratase | 4.2.1.94 | 0.462 | |
| 1cq7 | PY5 | Aspartate aminotransferase | 2.6.1.1 | 0.461 | |
| 1cq8 | PY6 | Aspartate aminotransferase | 2.6.1.1 | 0.461 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 3bsy | ACO | UDP-N-acetylbacillosamine N-acetyltransferase | 2.3.1.203 | 0.461 | |
| 4isg | 1FY | Glucokinase | 2.7.1.2 | 0.461 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 2f98 | NGV | Aklanonic acid methyl ester cyclase AcmA | 5.5.1.23 | 0.460 | |
| 3s41 | S41 | Glucokinase | 2.7.1.2 | 0.460 | |
| 1ahg | TYR_PLP | Aspartate aminotransferase | 2.6.1.1 | 0.459 | |
| 1yci | NDF | Hypoxia-inducible factor 1-alpha inhibitor | 1.14.11.30 | 0.459 | |
| 2bf7 | HBI | Pteridine reductase 1 | 1.5.1.33 | 0.458 | |
| 2gby | BRN | HTH-type transcriptional regulator QacR | / | 0.458 | |
| 3rtn | RTN | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.457 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.457 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.457 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 2bfa | CB3 | Pteridine reductase 1 | 1.5.1.33 | 0.456 | |
| 4h7c | 10H | Aldo-keto reductase family 1 member C3 | / | 0.456 | |
| 1drf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 1gt5 | BZQ | Odorant-binding protein | / | 0.455 | |
| 1je1 | GMP | Purine nucleoside phosphorylase | / | 0.455 | |
| 2fb8 | 215 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.455 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.454 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.454 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.454 | |
| 2o6h | INI | 6,7-dimethyl-8-ribityllumazine synthase 1 | 2.5.1.78 | 0.454 | |
| 1x2e | ATX | Proline iminopeptidase | 3.4.11.5 | 0.453 | |
| 1yrs | ADP | Kinesin-like protein KIF11 | / | 0.453 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 5cc9 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 1dgg | NDP | Catalase | 1.11.1.6 | 0.452 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.452 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.452 | |
| 1x2b | STX | Proline iminopeptidase | 3.4.11.5 | 0.452 | |
| 3n0h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 4bfy | ZVY | Pantothenate kinase | 2.7.1.33 | 0.452 | |
| 4i10 | 1BS | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 1jf2 | CZH | Obelin | / | 0.451 | |
| 1s7g | NAD | NAD-dependent protein deacylase 2 | / | 0.451 | |
| 2our | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.451 | |
| 3ufl | 508 | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 2abj | CBC | Branched-chain-amino-acid aminotransferase, cytosolic | 2.6.1.42 | 0.450 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.450 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.450 | |
| 4dbc | 3QP | Aspartate aminotransferase | 2.6.1.1 | 0.450 | |
| 4hmn | 16J | Aldo-keto reductase family 1 member C3 | / | 0.450 | |
| 1nqu | RDL | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.449 | |
| 1uae | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.449 | |
| 3s3v | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 3tky | N7I | (Iso)eugenol O-methyltransferase | 2.1.1.146 | 0.449 | |
| 4rh1 | 0TT | Spore photoproduct lyase | / | 0.449 | |
| 1toj | HCI | Aspartate aminotransferase | 2.6.1.1 | 0.448 | |
| 1xor | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.448 | |
| 3b9l | AZZ | Serum albumin | / | 0.448 | |
| 4ajd | F04 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.448 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 1g7u | PEP | 2-dehydro-3-deoxyphosphooctonate aldolase | 2.5.1.55 | 0.447 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 3l6j | Z90 | Alr2278 protein | / | 0.447 | |
| 3d4b | DZD | NAD-dependent protein deacetylase | / | 0.446 | |
| 3lla | ACP | Myosin heavy chain kinase A | 2.7.11.7 | 0.446 | |
| 3lm1 | LEC | Agglutinin alpha chain | / | 0.446 | |
| 3std | MQ0 | Scytalone dehydratase | 4.2.1.94 | 0.446 | |
| 1maq | PGU | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.445 | |
| 1pq6 | 965 | Oxysterols receptor LXR-beta | / | 0.445 | |
| 1yw8 | A75 | Methionine aminopeptidase 2 | / | 0.445 | |
| 1yhj | R6C | Pyridoxal kinase | 2.7.1.35 | 0.444 | |
| 1z4i | UMP | 5'(3')-deoxyribonucleotidase, mitochondrial | 3.1.3 | 0.444 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 2tpl | HPP | Tyrosine phenol-lyase | 4.1.99.2 | 0.444 | |
| 2tsr | UMP | Thymidylate synthase | 2.1.1.45 | 0.444 | |
| 3arq | DM5 | Chitinase A | / | 0.444 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.444 | |
| 2rku | R78 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.443 | |
| 2x1e | X1E | Acyl-coenzyme A:6-aminopenicillanic-acid-acyltransferase 40 kDa form | 2.3.1.164 | 0.443 | |
| 3er9 | 3AT | Poly(A) polymerase catalytic subunit | 2.7.7.19 | 0.443 | |
| 3r8g | IZP | Aldo-keto reductase family 1 member C3 | / | 0.443 | |
| 4keb | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 4lzw | THM | Uridine phosphorylase | / | 0.443 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.442 | |
| 2psj | CEI | Renilla-luciferin 2-monooxygenase | 1.13.12.5 | 0.442 | |
| 3c1o | NAP | Eugenol synthase | / | 0.442 | |
| 3ikt | NAD | Redox-sensing transcriptional repressor Rex | / | 0.442 | |
| 4k6i | 9RA | Retinoic acid receptor RXR-alpha | / | 0.442 | |
| 4zqc | F6F | Tryptophan synthase alpha chain | / | 0.442 | |
| 5ero | 210 | Fusicoccadiene synthase | 2.5.1.29 | 0.442 | |
| 1akb | PPD | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.441 | |
| 1dlr | MXA | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1yqz | COA | Coenzyme A disulfide reductase | / | 0.441 | |
| 2f99 | AKV | Aklanonic acid methyl ester cyclase AcmA | 5.5.1.23 | 0.441 | |
| 2vat | COA | Acetyl-CoA--deacetylcephalosporin C acetyltransferase | 2.3.1.175 | 0.441 | |
| 2w3m | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 2zs8 | ADP | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 3i0a | DBH | Neutrophil gelatinase-associated lipocalin | / | 0.441 | |
| 3nhl | YTR | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.441 | |
| 3s7a | 684 | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 4zas | TYD | CalS13 | / | 0.441 | |
| 1dgf | NDP | Catalase | 1.11.1.6 | 0.440 | |
| 1fml | RTL | Retinol dehydratase | / | 0.440 | |
| 1pr4 | MTP | Purine nucleoside phosphorylase DeoD-type | / | 0.440 | |
| 2q2z | ADP | Kinesin-like protein KIF11 | / | 0.440 | |
| 3h4v | NAP | Pteridine reductase 1 | 1.5.1.33 | 0.440 | |
| 3n0y | APC | Adenylate cyclase 2 | / | 0.440 | |
| 3pft | FMN | Flavin reductase | / | 0.440 | |
| 4dan | 2FA | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.440 | |
| 4fcd | 0T6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 | |
| 4g8j | THM | Uridine phosphorylase | / | 0.440 | |
| 4u16 | 3C0 | Muscarinic acetylcholine receptor M3 | / | 0.440 |