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 |
|---|---|---|---|
| 4xt8 | TMQ | Possible bifunctional enzyme riboflavin biosynthesis protein RibD: diaminohydroxyphosphoribosylaminopyrimidine deaminase (Riboflavin-specific deaminase) + 5-amino-6-(5-phosphoribosylamino)uracil reduc |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4xt8 | TMQ | Possible bifunctional enzyme riboflavin biosynthesis protein RibD: diaminohydroxyphosphoribosylaminopyrimidine deaminase (Riboflavin-specific deaminase) + 5-amino-6-(5-phosphoribosylamino)uracil reduc | / | 1.000 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.492 | |
| 4dz5 | NAP | Aldo-keto reductase family 1 member C3 | / | 0.479 | |
| 1e66 | HUX | Acetylcholinesterase | 3.1.1.7 | 0.476 | |
| 2xje | U5P | Cytosolic purine 5'-nucleotidase | 3.1.3.5 | 0.476 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.474 | |
| 1rxj | BNI | Streptavidin | / | 0.472 | |
| 3ppk | FNI | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.472 | |
| 1ry0 | PG2 | Aldo-keto reductase family 1 member C3 | / | 0.468 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.467 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.467 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.466 | |
| 3dzj | NMN | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.466 | |
| 4fm8 | 0UQ | Beta-secretase 1 | 3.4.23.46 | 0.466 | |
| 3rtn | RTN | Beta-secretase 1 | 3.4.23.46 | 0.465 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.463 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.463 | |
| 3pft | FMN | Flavin reductase | / | 0.463 | |
| 3ufl | 508 | Beta-secretase 1 | 3.4.23.46 | 0.463 | |
| 1zq5 | E04 | Aldo-keto reductase family 1 member C3 | / | 0.462 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 2ejz | SAH | Diphthine synthase | / | 0.461 | |
| 2ipi | AKY | Aclacinomycin-N/aclacinomycin-A oxidase | / | 0.461 | |
| 3jq6 | DX1 | Pteridine reductase, putative | / | 0.461 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.461 | |
| 1ftl | DNQ | Glutamate receptor 2 | / | 0.460 | |
| 1yry | MSG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.460 | |
| 3prf | FP3 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.460 | |
| 4fhd | 0TT | Spore photoproduct lyase | / | 0.460 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.459 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.459 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.459 | |
| 1qxo | FMN | Chorismate synthase | / | 0.458 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.458 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.457 | |
| 3br3 | ET | HTH-type transcriptional regulator QacR | / | 0.457 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.457 | |
| 5cxv | 0HK | Muscarinic acetylcholine receptor M1 | / | 0.457 | |
| 2poq | ISD | Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase | 1.3.1.20 | 0.456 | |
| 3ihg | VAK | Aklavinone 12-hydroxylase RdmE | / | 0.456 | |
| 3jqc | JU2 | Pteridine reductase, putative | / | 0.456 | |
| 1gtr | ATP | Glutamine--tRNA ligase | 6.1.1.18 | 0.455 | |
| 3gn7 | 3GN | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.455 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 3hl4 | CDC | Choline-phosphate cytidylyltransferase A | / | 0.454 | |
| 3uax | NOS | Purine nucleoside phosphorylase DeoD-type | / | 0.454 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 4r81 | FMN | Predicted NADH dehydrogenase | / | 0.453 | |
| 4yao | 2AM | NADPH--cytochrome P450 reductase | / | 0.453 | |
| 2cle | F6F | Tryptophan synthase alpha chain | / | 0.452 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 2wjo | QUD | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 4aoa | IK2 | Beta-phenylalanine transaminase | 2.6.1 | 0.452 | |
| 4hfp | 15U | Prothrombin | 3.4.21.5 | 0.452 | |
| 4ms1 | 381 | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.452 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.451 | |
| 1zgc | A2E | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 3ai0 | PNW | Beta-glucosidase | / | 0.451 | |
| 3dhk | 23U | Prothrombin | 3.4.21.5 | 0.451 | |
| 4j53 | 1J4 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.451 | |
| 1ejb | INJ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.450 | |
| 1uae | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.450 | |
| 3ihz | FK5 | Peptidylprolyl isomerase | / | 0.450 | |
| 4j1k | 1HG | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 4zzj | CNA | NAD-dependent protein deacetylase sirtuin-1 | 3.5.1 | 0.450 | |
| 1kyy | INI | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.449 | |
| 3fkt | SII | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 3tqx | PLP | 2-amino-3-ketobutyrate coenzyme A ligase | / | 0.449 | |
| 4h3g | 10Q | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 4i10 | 1BS | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 1nj5 | P5A | Proline--tRNA ligase | / | 0.447 | |
| 1nqu | RDL | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.447 | |
| 2a2d | ANP | N-acetylgalactosamine kinase | 2.7.1.157 | 0.447 | |
| 2o6h | INI | 6,7-dimethyl-8-ribityllumazine synthase 1 | 2.5.1.78 | 0.447 | |
| 2z4s | ADP | Chromosomal replication initiator protein DnaA | / | 0.447 | |
| 3aiv | HBO | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase, chloroplastic | 3.2.1.182 | 0.447 | |
| 3gnc | QQQ | Glutaryl-CoA dehydrogenase | / | 0.447 | |
| 4h6p | FMN | Chromate reductase | / | 0.447 | |
| 4yfy | 0FX | VioF | / | 0.447 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.446 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.446 | |
| 2izk | GLL | Streptavidin | / | 0.446 | |
| 3pm1 | ET | HTH-type transcriptional regulator QacR | / | 0.446 | |
| 3uzx | AOX | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.446 | |
| 4b6u | M7G | Eukaryotic translation initiation factor 4E type 3 | / | 0.446 | |
| 4bfd | 8T3 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.445 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.445 | |
| 2f99 | AKV | Aklanonic acid methyl ester cyclase AcmA | 5.5.1.23 | 0.445 | |
| 3nyt | ULP | UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase | 2.6.1.98 | 0.445 | |
| 3rvi | RVI | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3ry2 | BTN | Streptavidin | / | 0.445 | |
| 3tpr | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4mv1 | ADP | Biotin carboxylase | 6.3.4.14 | 0.445 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.445 | |
| 5ah5 | LSS | Leucine--tRNA ligase | / | 0.445 | |
| 1ozq | PRF | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.444 | |
| 1w19 | T4P | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.444 | |
| 2rtn | IMI | Streptavidin | / | 0.444 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 1c7o | PPG | Hemolysin | / | 0.443 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.443 | |
| 1pnq | NDP | NAD(P) transhydrogenase subunit beta | 1.6.1.2 | 0.443 | |
| 1zkl | IBM | High affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A | 3.1.4.53 | 0.443 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.443 | |
| 3zov | WZV | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4fri | DWA | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4lcw | 1VY | Major histocompatibility complex class I-related gene protein | / | 0.443 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.442 | |
| 3blo | QEI | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.442 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 1ype | UIP | Prothrombin | 3.4.21.5 | 0.441 | |
| 2cmf | F11 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2vz0 | D64 | Pteridine reductase | / | 0.441 | |
| 2x06 | NAD | L-sulfolactate dehydrogenase | / | 0.441 | |
| 2zc9 | 22U | Prothrombin | 3.4.21.5 | 0.441 | |
| 3af1 | GDP | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 3kn0 | 3TO | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3zc3 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.441 | |
| 4bzb | DGT | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.441 | |
| 5cc9 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.440 | |
| 1lb9 | DNQ | Glutamate receptor 2 | / | 0.440 | |
| 1v08 | NTZ | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1, chloroplastic | 3.2.1.182 | 0.440 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.440 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.440 | |
| 3ntq | NAD | Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase | 1.1.1.18 | 0.440 | |
| 3uzz | ASD | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.440 | |
| 4dne | DTB | Streptavidin | / | 0.440 |