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 |
|---|---|---|---|
| 2y4s | BCD | Limit dextrinase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2y4s | BCD | Limit dextrinase | / | 1.000 | |
| 1amo | FMN | NADPH--cytochrome P450 reductase | / | 0.488 | |
| 2bn4 | FMN | NADPH--cytochrome P450 reductase | / | 0.487 | |
| 4tvj | 09L | Poly [ADP-ribose] polymerase 2 | 2.4.2.30 | 0.486 | |
| 4dxl | C5P | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.481 | |
| 2j7c | IDE | Beta-glucosidase A | 3.2.1.21 | 0.480 | |
| 3l3l | L3L | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.472 | |
| 2b82 | ADN | Class B acid phosphatase | 3.1.3.2 | 0.469 | |
| 2c1z | KMP | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.464 | |
| 3fap | ARD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.463 | |
| 3fap | ARD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.463 | |
| 1ja0 | FMN | NADPH--cytochrome P450 reductase | / | 0.462 | |
| 2c9z | QUE | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.462 | |
| 3u57 | DH8 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.461 | |
| 4ajg | F07 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.461 | |
| 1xoq | ROF | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.460 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.460 | |
| 1n0s | FLU | Bilin-binding protein | / | 0.459 | |
| 4gv8 | DUP | DUTPase | / | 0.459 | |
| 2bf4 | FMN | NADPH--cytochrome P450 reductase | / | 0.458 | |
| 2vf3 | GVS | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.458 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.457 | |
| 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 | |
| 2gg3 | U13 | Methionine aminopeptidase | / | 0.455 | |
| 1xor | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.454 | |
| 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 | 0.453 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.453 | |
| 4emd | C5P | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.453 | |
| 2v5u | FMN | Flavodoxin | / | 0.451 | |
| 3rth | RTH | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 4d6q | PD2 | Lysine-specific demethylase 4D | 1.14.11 | 0.451 | |
| 2r86 | ATP | 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase | / | 0.450 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.449 | |
| 4nv0 | MG7 | 7-methylguanosine phosphate-specific 5'-nucleotidase | / | 0.449 | |
| 1z5u | CMP | Class B acid phosphatase | / | 0.447 | |
| 4b11 | 7I1 | Glycylpeptide N-tetradecanoyltransferase | / | 0.447 | |
| 1uk1 | FRQ | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.446 | |
| 3d3p | 20A | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.446 | |
| 3sqx | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.446 | |
| 3u5y | SCG | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.446 | |
| 4ajf | F03 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.446 | |
| 4l7g | 1W0 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 1dig | L37 | C-1-tetrahydrofolate synthase, cytoplasmic | 1.5.1.5 | 0.445 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 2vrj | NCW | Beta-glucosidase A | 3.2.1.21 | 0.444 | |
| 4c1i | EH9 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.444 | |
| 2c97 | JCL | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.443 | |
| 2xej | OKD | Glutamate carboxypeptidase 2 | 3.4.17.21 | 0.443 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.443 | |
| 4qfz | TTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.443 | |
| 2ipi | AKY | Aclacinomycin-N/aclacinomycin-A oxidase | / | 0.442 | |
| 2psj | CEI | Renilla-luciferin 2-monooxygenase | 1.13.12.5 | 0.442 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 2y03 | 5FW | Beta-1 adrenergic receptor | / | 0.442 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.442 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 3udq | 09E | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.442 | |
| 2rcw | AAI | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.441 | |
| 2rd6 | 78P | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.441 | |
| 2v34 | CTN | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.441 | |
| 1jqd | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.440 | |
| 2f38 | 15M | Aldo-keto reductase family 1 member C3 | / | 0.440 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 |