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 |
|---|---|---|---|
| 1vfs | DCS | Alanine racemase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1vfs | DCS | Alanine racemase | / | 1.000 | |
| 1vft | DCS | Alanine racemase | / | 0.600 | |
| 3e6e | DCS | Alanine racemase | / | 0.572 | |
| 4xbj | IN5 | Alanine racemase, biosynthetic | / | 0.557 | |
| 4lut | DCS | Alanine racemase | / | 0.524 | |
| 2eix | FAD | NADH-cytochrome b5 reductase | / | 0.508 | |
| 4j7h | TRH | PCZA361.3 | / | 0.494 | |
| 2xyt | TC9 | Soluble acetylcholine receptor | / | 0.492 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.491 | |
| 1lke | DOG | Bilin-binding protein | / | 0.488 | |
| 2i65 | NAD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.488 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.488 | |
| 3sfh | 1DI | Histone deacetylase 8 | 3.5.1.98 | 0.487 | |
| 1w6j | R71 | Lanosterol synthase | 5.4.99.7 | 0.486 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.486 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.485 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.482 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.482 | |
| 1e66 | HUX | Acetylcholinesterase | 3.1.1.7 | 0.480 | |
| 2q96 | A18 | Methionine aminopeptidase | / | 0.480 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.480 | |
| 2ckm | AA7 | Acetylcholinesterase | 3.1.1.7 | 0.479 | |
| 2vq7 | NAP | Putative flavin-containing monooxygenase | / | 0.479 | |
| 3buv | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.479 | |
| 1k4m | NAD | Nicotinate-nucleotide adenylyltransferase | 2.7.7.18 | 0.477 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.477 | |
| 1h60 | STR | Pentaerythritol tetranitrate reductase | / | 0.476 | |
| 1icq | OPD | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.475 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.475 | |
| 2xq0 | BES | Leukotriene A-4 hydrolase homolog | 3.3.2.6 | 0.475 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.474 | |
| 1kyv | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.474 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.474 | |
| 3vjk | M51 | Dipeptidyl peptidase 4 | / | 0.474 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.473 | |
| 1acj | THA | Acetylcholinesterase | 3.1.1.7 | 0.470 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.470 | |
| 4b68 | NAP | L-ornithine N(5)-monooxygenase | / | 0.469 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.468 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.468 | |
| 2vf3 | GVS | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.467 | |
| 3iu7 | FCD | Methionine aminopeptidase 2 | / | 0.467 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.467 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.466 | |
| 1rkw | PNT | HTH-type transcriptional regulator QacR | / | 0.466 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.466 | |
| 2pb1 | NFG | Glucan 1,3-beta-glucosidase | / | 0.466 | |
| 5kwv | ANP | Pantothenate synthetase | / | 0.466 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.465 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.465 | |
| 4x7z | ZM3 | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.465 | |
| 2dxd | ANP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.464 | |
| 4wdg | A2P | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.464 | |
| 1c7o | PPG | Hemolysin | / | 0.463 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.463 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.463 | |
| 4gv0 | 8ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.463 | |
| 3af1 | GDP | Pantothenate kinase | 2.7.1.33 | 0.462 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.462 | |
| 1lvu | 9PP | Purine nucleoside phosphorylase | 2.4.2.1 | 0.461 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.461 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.461 | |
| 4b1e | 6T6 | Beta-secretase 1 | 3.4.23.46 | 0.461 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 1rpw | DID | HTH-type transcriptional regulator QacR | / | 0.460 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.460 | |
| 2p99 | YE6 | Methionine aminopeptidase | / | 0.460 | |
| 4b63 | NAP | L-ornithine N(5)-monooxygenase | / | 0.460 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.459 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.459 | |
| 3bgs | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.458 | |
| 4c49 | HCY | Corticosteroid-binding globulin | / | 0.457 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.457 | |
| 1a9c | GTP | GTP cyclohydrolase 1 | 3.5.4.16 | 0.456 | |
| 1e2n | RCA | Thymidine kinase | / | 0.456 | |
| 1h66 | RH1 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.456 | |
| 1lnm | DTX | Bilin-binding protein | / | 0.456 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.455 | |
| 2g5w | 8PG | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.455 | |
| 3l7g | M44 | Xaa-Pro dipeptidase | 3.4.13.9 | 0.455 | |
| 4b66 | NAP | L-ornithine N(5)-monooxygenase | / | 0.455 | |
| 1u1d | 181 | Uridine phosphorylase | 2.4.2.3 | 0.454 | |
| 2h3w | HC5 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.454 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 3hdy | GDU | UDP-galactopyranose mutase | / | 0.454 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.454 | |
| 4mo2 | FAD | UDP-galactopyranose mutase | / | 0.454 | |
| 1cnf | FAD | Nitrate reductase [NADH] | 1.7.1.1 | 0.453 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.453 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.453 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.453 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.452 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.452 | |
| 2x94 | X94 | Angiotensin-converting enzyme | 3.4.15.1 | 0.452 | |
| 2xug | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.452 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.452 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.451 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.451 | |
| 3f8s | PF2 | Dipeptidyl peptidase 4 | / | 0.451 | |
| 3frk | TQP | QdtB | / | 0.451 | |
| 3s5w | FAD | L-ornithine N(5)-monooxygenase | / | 0.451 | |
| 5c1g | GDU | Histo-blood group ABO system transferase | / | 0.451 | |
| 1qpf | 858 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.450 | |
| 1w76 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.450 | |
| 2ixk | TDO | dTDP-4-dehydrorhamnose 3,5-epimerase | 5.1.3.13 | 0.450 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.450 | |
| 3sff | 0DI | Histone deacetylase 8 | 3.5.1.98 | 0.450 | |
| 4b65 | NDP | L-ornithine N(5)-monooxygenase | / | 0.450 | |
| 4cax | 646 | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.450 | |
| 1rft | PXM | Pyridoxal kinase | 2.7.1.35 | 0.449 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 2a0x | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.449 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.449 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.449 | |
| 2pj4 | 414 | Carboxypeptidase B | / | 0.449 | |
| 3u57 | DH8 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.449 | |
| 4rph | GDU | UDP-galactopyranose mutase | 5.4.99.9 | 0.449 | |
| 1h61 | PDN | Pentaerythritol tetranitrate reductase | / | 0.448 | |
| 1ib0 | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.448 | |
| 1ygj | RMC | Pyridoxal kinase | 2.7.1.35 | 0.448 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 3mj4 | URM | UDP-galactopyranose mutase | / | 0.448 | |
| 4cf6 | CBD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 4e2y | JHZ | Methyltransferase | / | 0.448 | |
| 4nv1 | 0FX | Formyl transferase | / | 0.448 | |
| 5c1d | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.448 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.447 | |
| 1xh7 | R96 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.447 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.447 | |
| 2gyu | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 2q7o | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.447 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.447 | |
| 3qgf | 46F | Genome polyprotein | 2.7.7.48 | 0.447 | |
| 5cfl | C2E | Stimulator of interferon genes protein | / | 0.447 | |
| 1ahn | FMN | Flavodoxin 1 | / | 0.446 | |
| 2g21 | L1B | Renin | 3.4.23.15 | 0.446 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.446 | |
| 2x06 | NAD | L-sulfolactate dehydrogenase | / | 0.446 | |
| 2ylr | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.446 | |
| 3sqz | COA | Putative hydroxymethylglutaryl-CoA synthase | / | 0.446 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.446 | |
| 4yp6 | NAP | Nicotinamide-nucleotide adenylyltransferase | 2.7.7.1 | 0.446 | |
| 4mqt | 2CU | Muscarinic acetylcholine receptor M2 | / | 0.446 | |
| 2e8u | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.445 | |
| 2ok7 | A2P | Ferredoxin--NADP reductase, apicoplast | / | 0.445 | |
| 2rd2 | QSI | Glutamine--tRNA ligase | 6.1.1.18 | 0.445 | |
| 2z1q | FAD | Acyl-CoA dehydrogenase | / | 0.445 | |
| 3uzz | ASD | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.445 | |
| 3zcn | ATP | Adenosine monophosphate-protein transferase SoFic | 2.7.7.n1 | 0.445 | |
| 3zhs | TD6 | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.445 | |
| 4xsv | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.445 | |
| 1fx9 | MJI | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.444 | |
| 1ld8 | U49 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.444 | |
| 2wsa | 646 | Glycylpeptide N-tetradecanoyltransferase | / | 0.444 | |
| 2wzy | SQX | Soluble acetylcholine receptor | / | 0.444 | |
| 2zrx | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.444 | |
| 3cgt | BCD | Cyclomaltodextrin glucanotransferase | 2.4.1.19 | 0.444 | |
| 3jus | BCD | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.444 | |
| 4du6 | GTP | GTP cyclohydrolase 1 | / | 0.444 | |
| 4j7g | TRH | PCZA361.3 | / | 0.444 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.444 | |
| 4x7v | MIV | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.444 | |
| 1akc | PPE | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.443 | |
| 1gvr | TNL | Pentaerythritol tetranitrate reductase | / | 0.443 | |
| 1tu8 | GTX | Glutathione S-transferase 2 | 2.5.1.18 | 0.443 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.443 | |
| 2q94 | A04 | Methionine aminopeptidase | / | 0.443 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.443 | |
| 3dz2 | A8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.443 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.443 | |
| 4a6r | TA8 | Probable aminotransferase | / | 0.443 | |
| 4jsr | 1NQ | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | 3.5.1 | 0.443 | |
| 4jt8 | 1NR | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | 3.5.1 | 0.443 | |
| 4nv1 | 4TG | Formyl transferase | / | 0.443 | |
| 1rr6 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.442 | |
| 1sq5 | ADP | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 1z6t | ADP | Apoptotic protease-activating factor 1 | / | 0.442 | |
| 3br3 | ET | HTH-type transcriptional regulator QacR | / | 0.442 | |
| 3ck7 | ACX | Starch-binding protein SusD | / | 0.442 | |
| 3k8q | 22A | Purine nucleoside phosphorylase | 2.4.2.1 | 0.442 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.442 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.442 | |
| 3ojw | FMN | NADPH--cytochrome P450 reductase | / | 0.442 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.442 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.442 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.442 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.442 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.442 | |
| 1mxf | MTX | Putative pteridine reductase 2 | / | 0.441 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.441 | |
| 1sa4 | JAN | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.441 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 3dz6 | M8E | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.441 | |
| 3ihg | VAK | Aklavinone 12-hydroxylase RdmE | / | 0.441 | |
| 3iu9 | T07 | Methionine aminopeptidase 2 | / | 0.441 | |
| 3m2u | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.441 | |
| 3ojx | FMN | NADPH--cytochrome P450 reductase | / | 0.441 | |
| 3qeo | LLT | Deoxycytidine kinase | 2.7.1.74 | 0.441 | |
| 4b64 | NAP | L-ornithine N(5)-monooxygenase | / | 0.441 | |
| 4c71 | 7RD | 3-oxoacyl-ACP synthase | / | 0.441 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.441 | |
| 4eb7 | PLP | Cysteine desulfurase IscS 2 | / | 0.441 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.441 | |
| 4k88 | HFG | Bifunctional glutamate/proline--tRNA ligase | 6.1.1.15 | 0.441 | |
| 4n3r | 2GU | Tankyrase-1 | 2.4.2.30 | 0.441 | |
| 4qg1 | DTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.441 | |
| 4tnz | TTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.441 | |
| 5dp2 | NAP | CurF | / | 0.441 | |
| 1gg5 | E09 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2bf4 | FMN | NADPH--cytochrome P450 reductase | / | 0.440 | |
| 2gg3 | U13 | Methionine aminopeptidase | / | 0.440 | |
| 3g0g | RUM | Dipeptidyl peptidase 4 | / | 0.440 | |
| 3mau | EXT | Putative sphingosine-1-phosphate lyase | / | 0.440 | |
| 3nzp | PLP | Arginine decarboxylase | / | 0.440 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 4f0r | MTA | 5-methylthioadenosine/S-adenosylhomocysteine deaminase | / | 0.440 |