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 |
|---|---|---|---|
| 3dz7 | O8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3dz7 | O8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 1.000 | |
| 3h0w | N8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.789 | |
| 3dz2 | A8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.674 | |
| 3h0v | M2T | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.651 | |
| 3dz4 | C8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.646 | |
| 3dz6 | M8E | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.638 | |
| 1i7c | MGB | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.574 | |
| 1i7m | CG | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.560 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.497 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.494 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.494 | |
| 2ejz | SAH | Diphthine synthase | / | 0.489 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.485 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.485 | |
| 3qgf | 46F | Genome polyprotein | 2.7.7.48 | 0.483 | |
| 3to3 | ATP | Petrobactin biosynthesis protein AsbB | / | 0.481 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.479 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.478 | |
| 2wsa | 646 | Glycylpeptide N-tetradecanoyltransferase | / | 0.478 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.478 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.477 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.477 | |
| 2j83 | BAT | Ulilysin | 3.4.24 | 0.474 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.473 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.473 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.472 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.471 | |
| 2fut | H1S | Heparin and heparin-sulfate lyase | / | 0.470 | |
| 4c2z | 646 | Glycylpeptide N-tetradecanoyltransferase 1 | / | 0.470 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.466 | |
| 3hdy | GDU | UDP-galactopyranose mutase | / | 0.465 | |
| 4gv0 | 8ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.465 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.465 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.464 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.464 | |
| 2h44 | 7CA | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.463 | |
| 2xq0 | BES | Leukotriene A-4 hydrolase homolog | 3.3.2.6 | 0.463 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.463 | |
| 3uon | QNB | Muscarinic acetylcholine receptor M2 | / | 0.463 | |
| 1s7g | NAD | NAD-dependent protein deacylase 2 | / | 0.462 | |
| 4b66 | NAP | L-ornithine N(5)-monooxygenase | / | 0.461 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.460 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.460 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.459 | |
| 3ufl | 508 | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 4kfq | KFQ | Glutamate receptor ionotropic, NMDA 1 | / | 0.459 | |
| 2jl1 | NAP | Triphenylmethane reductase | / | 0.457 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.457 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.457 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 4j7g | TRH | PCZA361.3 | / | 0.456 | |
| 4xrg | NAD | Homospermidine synthase | 2.5.1.44 | 0.456 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.455 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 2bf4 | FMN | NADPH--cytochrome P450 reductase | / | 0.455 | |
| 2xlp | NAP | Putative flavin-containing monooxygenase | / | 0.455 | |
| 3hii | PNT | Amiloride-sensitive amine oxidase [copper-containing] | / | 0.455 | |
| 4mrm | 2BY | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.455 | |
| 2c1z | KMP | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.453 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.453 | |
| 3jus | BCD | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.452 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 4xq9 | NAD | Homospermidine synthase | 2.5.1.44 | 0.452 | |
| 1ry0 | PG2 | Aldo-keto reductase family 1 member C3 | / | 0.451 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.451 | |
| 3c49 | KU8 | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.451 | |
| 4j1e | 1HM | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 1kyy | INI | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.450 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 2yne | YNE | Glycylpeptide N-tetradecanoyltransferase | / | 0.450 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.450 | |
| 4b6u | M7G | Eukaryotic translation initiation factor 4E type 3 | / | 0.450 | |
| 2e9a | B28 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.449 | |
| 3rvi | RVI | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 4b63 | NAP | L-ornithine N(5)-monooxygenase | / | 0.449 | |
| 4b78 | KGG | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 4jyz | ATP | Glutamine--tRNA ligase | 6.1.1.18 | 0.449 | |
| 4wbd | ADP | Putative cysteine ligase BshC | / | 0.449 | |
| 5f54 | TMP | Single-stranded-DNA-specific exonuclease | / | 0.449 | |
| 1k4m | NAD | Nicotinate-nucleotide adenylyltransferase | 2.7.7.18 | 0.448 | |
| 1tco | FK5 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.448 | |
| 1tco | FK5 | Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform | 3.1.3.16 | 0.448 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.448 | |
| 3gnc | QQQ | Glutaryl-CoA dehydrogenase | / | 0.448 | |
| 3klb | FMN | Uncharacterized protein | / | 0.448 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.448 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.448 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.448 | |
| 4j7h | TRH | PCZA361.3 | / | 0.448 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 1nqv | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.447 | |
| 1zgc | A2E | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 3s5w | FAD | L-ornithine N(5)-monooxygenase | / | 0.447 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.447 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.447 | |
| 5c1g | GDU | Histo-blood group ABO system transferase | / | 0.447 | |
| 5d6l | CAU | Beta-2 adrenergic receptor | / | 0.447 | |
| 1lwi | NAP | 3-alpha-hydroxysteroid dehydrogenase | 1.1.1.50 | 0.446 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.446 | |
| 2pb1 | NFG | Glucan 1,3-beta-glucosidase | / | 0.446 | |
| 2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.446 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 4j53 | 1J4 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.446 | |
| 1amo | FMN | NADPH--cytochrome P450 reductase | / | 0.445 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.445 | |
| 3br3 | ET | HTH-type transcriptional regulator QacR | / | 0.445 | |
| 3fsj | D7K | Benzoylformate decarboxylase | 4.1.1.7 | 0.445 | |
| 4b65 | NDP | L-ornithine N(5)-monooxygenase | / | 0.445 | |
| 1fap | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.444 | |
| 1fap | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.444 | |
| 2clf | F6F | Tryptophan synthase alpha chain | / | 0.444 | |
| 2g1a | 5HG | Class B acid phosphatase | 3.1.3.2 | 0.444 | |
| 2x06 | NAD | L-sulfolactate dehydrogenase | / | 0.444 | |
| 2xiq | 5AD | Methylmalonyl-CoA mutase, mitochondrial | / | 0.444 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.444 | |
| 4hb9 | FAD | Uncharacterized protein | / | 0.444 | |
| 4tnz | TTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.444 | |
| 4tvj | 09L | Poly [ADP-ribose] polymerase 2 | 2.4.2.30 | 0.444 | |
| 1h60 | STR | Pentaerythritol tetranitrate reductase | / | 0.443 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1xf0 | ASD | Aldo-keto reductase family 1 member C3 | / | 0.443 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.443 | |
| 2v57 | PRL | TetR family transcriptional regulator | / | 0.443 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3owa | FAD | Acyl-CoA dehydrogenase | / | 0.443 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1aqu | EST | Estrogen sulfotransferase, testis isoform | 2.8.2.4 | 0.442 | |
| 1lc3 | NAD | Biliverdin reductase A | 1.3.1.24 | 0.442 | |
| 1txt | CAA | HMG-CoA synthase | / | 0.442 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.442 | |
| 2bn4 | FMN | NADPH--cytochrome P450 reductase | / | 0.442 | |
| 2nmt | MIM | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.442 | |
| 2pj4 | 414 | Carboxypeptidase B | / | 0.442 | |
| 2zs9 | ADP | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 3af1 | GDP | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 4b68 | FAD | L-ornithine N(5)-monooxygenase | / | 0.442 | |
| 4b77 | 54M | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4gv2 | 5ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.442 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.442 | |
| 1c7o | PPG | Hemolysin | / | 0.441 | |
| 1dig | L37 | C-1-tetrahydrofolate synthase, cytoplasmic | 1.5.1.5 | 0.441 | |
| 1jum | BER | HTH-type transcriptional regulator QacR | / | 0.441 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 2z1q | FAD | Acyl-CoA dehydrogenase | / | 0.441 | |
| 1e79 | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.440 | |
| 1e79 | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.440 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2e8u | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.440 | |
| 2wzy | SQX | Soluble acetylcholine receptor | / | 0.440 | |
| 4z87 | GDP | Inosine-5'-monophosphate dehydrogenase | / | 0.440 |