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 |
|---|---|---|---|
| 1aka | PLP | Aspartate aminotransferase, mitochondrial | 2.6.1.1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1aka | PLP | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 1.000 | |
| 1oxo | IK2 | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.592 | |
| 4w5k | PLP | Aspartate aminotransferase, mitochondrial | / | 0.573 | |
| 1ahg | TYR_PLP | Aspartate aminotransferase | 2.6.1.1 | 0.560 | |
| 4rkd | KET | Aminotransferase | / | 0.556 | |
| 1x28 | PGU | Aspartate aminotransferase | 2.6.1.1 | 0.523 | |
| 4wlj | IK2 | Kynurenine--oxoglutarate transaminase 1 | 2.6.1.7 | 0.518 | |
| 1akc | PPE | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.512 | |
| 3dr7 | GPD | GDP-perosamine synthase | / | 0.508 | |
| 3ei8 | PL5 | LL-diaminopimelate aminotransferase, chloroplastic | / | 0.504 | |
| 4emy | PLP | Aminotransferase class I and II | / | 0.503 | |
| 4fl0 | PLP | Aminotransferase ALD1, chloroplastic | 2.6.1 | 0.500 | |
| 1akb | PPD | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.496 | |
| 4dbc | 3QP | Aspartate aminotransferase | 2.6.1.1 | 0.495 | |
| 1cq6 | PY4 | Aspartate aminotransferase | 2.6.1.1 | 0.493 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.491 | |
| 1tco | FK5 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.486 | |
| 1tco | FK5 | Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform | 3.1.3.16 | 0.486 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.482 | |
| 3eu5 | GBO | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.482 | |
| 3dr4 | G4M | GDP-perosamine synthase | / | 0.477 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.476 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.475 | |
| 2ay3 | MPP | Aromatic-amino-acid aminotransferase | 2.6.1.57 | 0.472 | |
| 2ejz | SAH | Diphthine synthase | / | 0.472 | |
| 2fut | H1S | Heparin and heparin-sulfate lyase | / | 0.472 | |
| 3e6e | DCS | Alanine racemase | / | 0.472 | |
| 1arg | PPD | Aspartate aminotransferase | 2.6.1.1 | 0.471 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.471 | |
| 4geb | 0LD | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.471 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.470 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.470 | |
| 2ay9 | 5PV | Aromatic-amino-acid aminotransferase | 2.6.1.57 | 0.468 | |
| 3e32 | ED2 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.468 | |
| 1rft | PXM | Pyridoxal kinase | 2.7.1.35 | 0.466 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.466 | |
| 4df2 | FMN | NADPH dehydrogenase | / | 0.466 | |
| 4je5 | PLP | Aromatic/aminoadipate aminotransferase 1 | 2.6.1.39 | 0.466 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.465 | |
| 1n4p | CYS_VAL_ILE_LEU_GER | Geranylgeranyl transferase type-1 subunit beta | 2.5.1.59 | 0.465 | |
| 1n95 | HFP | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.465 | |
| 1n95 | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.465 | |
| 1pz0 | NAP | Protein IolS | 1.1.1 | 0.465 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.465 | |
| 2xq0 | BES | Leukotriene A-4 hydrolase homolog | 3.3.2.6 | 0.465 | |
| 3cgt | BCD | Cyclomaltodextrin glucanotransferase | 2.4.1.19 | 0.465 | |
| 4c13 | UML | UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase | / | 0.465 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.464 | |
| 4dpt | AGS | Mevalonate diphosphate decarboxylase | / | 0.464 | |
| 2g5w | 8PG | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.463 | |
| 2xiq | 5AD | Methylmalonyl-CoA mutase, mitochondrial | / | 0.463 | |
| 4eb5 | PLP | Cysteine desulfurase IscS 2 | / | 0.462 | |
| 1maq | PGU | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.461 | |
| 2ay5 | IOP | Aromatic-amino-acid aminotransferase | 2.6.1.57 | 0.461 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.461 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 4eb7 | PLP | Cysteine desulfurase IscS 2 | / | 0.461 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.460 | |
| 2fxu | BID | Actin, alpha skeletal muscle | / | 0.460 | |
| 2q7o | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.460 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.460 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.460 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.459 | |
| 2gev | COK | Pantothenate kinase | 2.7.1.33 | 0.459 | |
| 3q44 | D50 | M1 family aminopeptidase | 3.4.11 | 0.459 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.459 | |
| 1dig | L37 | C-1-tetrahydrofolate synthase, cytoplasmic | 1.5.1.5 | 0.458 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.458 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.458 | |
| 2q85 | 973 | UDP-N-acetylenolpyruvoylglucosamine reductase | 1.3.1.98 | 0.458 | |
| 4to4 | DCP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.458 | |
| 1h60 | STR | Pentaerythritol tetranitrate reductase | / | 0.457 | |
| 1nl4 | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.457 | |
| 3b4f | TUO | Carbonic anhydrase 2 | 4.2.1.1 | 0.457 | |
| 3eft | 3BS | Carbonic anhydrase 2 | 4.2.1.1 | 0.457 | |
| 1icp | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.456 | |
| 2a9y | 26A | Adenosine kinase | 2.7.1.20 | 0.456 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 2hs6 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.456 | |
| 2oc9 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.456 | |
| 2xi4 | AFT | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.456 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.456 | |
| 4iah | 1DX | Alr2278 protein | / | 0.456 | |
| 2gmu | PDG | Putative pyridoxamine 5-phosphate-dependent dehydrase | / | 0.455 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.455 | |
| 1ejb | INJ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.454 | |
| 1pl1 | ABY | Glutathione S-transferase A1 | 2.5.1.18 | 0.454 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.454 | |
| 3b1d | PLS | BetaC-S lyase | / | 0.454 | |
| 1dfo | PLG | Serine hydroxymethyltransferase | 2.1.2.1 | 0.453 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.453 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.452 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.452 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.452 | |
| 6std | MS2 | Scytalone dehydratase | 4.2.1.94 | 0.452 | |
| 1asc | NPL | Aspartate aminotransferase | 2.6.1.1 | 0.451 | |
| 2vqb | FAD | Putative flavin-containing monooxygenase | / | 0.451 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.451 | |
| 3zht | TD9 | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.451 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.451 | |
| 4g09 | 0VD | Histidinol dehydrogenase | / | 0.451 | |
| 2tpl | HPP | Tyrosine phenol-lyase | 4.1.99.2 | 0.450 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 3tza | TZG | Glutamate receptor 2 | / | 0.450 | |
| 3uzz | ASD | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.450 | |
| 1icq | OPD | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.449 | |
| 1o1s | 1NH | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.449 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.449 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.449 | |
| 2pgt | GPR | Glutathione S-transferase P | 2.5.1.18 | 0.449 | |
| 2wd2 | MS5 | Carbonic anhydrase 2 | 4.2.1.1 | 0.449 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.449 | |
| 3fvu | IAC | Kynurenine--oxoglutarate transaminase 1 | 2.6.1.7 | 0.449 | |
| 3irh | DTP | HD domain protein | / | 0.449 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.449 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.449 | |
| 7std | CRP | Scytalone dehydratase | 4.2.1.94 | 0.449 | |
| 3kig | DA4 | Carbonic anhydrase 2 | 4.2.1.1 | 0.448 | |
| 4rvf | TYD | D-mycarose 3-C-methyltransferase | / | 0.448 | |
| 1a9c | GTP | GTP cyclohydrolase 1 | 3.5.4.16 | 0.447 | |
| 1g52 | F2B | Carbonic anhydrase 2 | 4.2.1.1 | 0.447 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.447 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.447 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.447 | |
| 3s8x | E59 | Carbonic anhydrase 2 | 4.2.1.1 | 0.447 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.447 | |
| 1qbq | HFP | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.446 | |
| 1qbq | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.446 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.446 | |
| 2a5h | SAM | L-lysine 2,3-aminomutase | 5.4.3.2 | 0.446 | |
| 2eu3 | FF3 | Carbonic anhydrase 2 | 4.2.1.1 | 0.446 | |
| 2gyw | OBI | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 2pnc | CLU | Primary amine oxidase, liver isozyme | / | 0.446 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 3djj | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.446 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.446 | |
| 3lxe | TOR | Carbonic anhydrase 1 | 4.2.1.1 | 0.446 | |
| 3znc | BZ1 | Carbonic anhydrase 4 | 4.2.1.1 | 0.446 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.446 | |
| 1cq7 | PY5 | Aspartate aminotransferase | 2.6.1.1 | 0.445 | |
| 1ni1 | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.445 | |
| 1q5m | NDP | Prostaglandin-E(2) 9-reductase | 1.1.1.189 | 0.445 | |
| 2r2l | PB9 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.445 | |
| 3igp | DT7 | Carbonic anhydrase 2 | 4.2.1.1 | 0.445 | |
| 4cf6 | CBD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 4de2 | DN3 | Beta-lactamase | / | 0.445 | |
| 1arh | PPD | Aspartate aminotransferase | 2.6.1.1 | 0.444 | |
| 1t4c | COA | Formyl-CoA:oxalate CoA-transferase | / | 0.444 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.444 | |
| 3dcs | MZM | Carbonic anhydrase 2 | 4.2.1.1 | 0.444 | |
| 3gf4 | UPG | UDP-galactopyranose mutase | 5.4.99.9 | 0.444 | |
| 3mmf | D9H | Carbonic anhydrase 2 | 4.2.1.1 | 0.444 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.444 | |
| 4yp6 | NAP | Nicotinamide-nucleotide adenylyltransferase | 2.7.7.1 | 0.444 | |
| 1gve | NAP | Aflatoxin B1 aldehyde reductase member 3 | 1 | 0.443 | |
| 1kyv | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.443 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.443 | |
| 2vf3 | GVS | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.443 | |
| 3uay | ADN | Purine nucleoside phosphorylase DeoD-type | / | 0.443 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.443 | |
| 1c7o | PPG | Hemolysin | / | 0.442 | |
| 1e66 | HUX | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 1i5c | ADP | Chemotaxis protein CheA | 2.7.13.3 | 0.442 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.442 | |
| 1s4o | GDP | Glycolipid 2-alpha-mannosyltransferase | / | 0.442 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.442 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.442 | |
| 2gyu | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 2vn1 | FK5 | Peptidylprolyl isomerase | / | 0.442 | |
| 2wzy | SQX | Soluble acetylcholine receptor | / | 0.442 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3eks | CY9 | Actin-5C | / | 0.442 | |
| 3p80 | P80 | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 4a3u | FMN | NADH:flavin oxidoreductase/NADH oxidase | / | 0.442 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.442 | |
| 5ao1 | DG3 | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.442 | |
| 1dmy | AZM | Carbonic anhydrase 5A, mitochondrial | 4.2.1.1 | 0.441 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.441 | |
| 1qpl | 587 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.441 | |
| 1wua | AP8 | Actin, alpha skeletal muscle | / | 0.441 | |
| 1yw8 | A75 | Methionine aminopeptidase 2 | / | 0.441 | |
| 2rdn | 1PL | 1-deoxypentalenic acid 11-beta-hydroxylase | 1.14.11.35 | 0.441 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3rtn | RTN | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3t85 | SG7 | Carbonic anhydrase 2 | 4.2.1.1 | 0.441 | |
| 4de1 | 0J6 | Beta-lactamase | / | 0.441 | |
| 1jf0 | CZH | Obelin | / | 0.440 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.440 | |
| 1okn | STB | Carbonic anhydrase 2 | 4.2.1.1 | 0.440 | |
| 2b58 | COA | Diamine acetyltransferase 1 | / | 0.440 | |
| 2ex1 | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.440 | |
| 3i8p | 840 | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.440 | |
| 3isj | A8D | Pantothenate synthetase | 6.3.2.1 | 0.440 | |
| 3ukf | GDU | UDP-galactopyranose mutase | / | 0.440 | |
| 4j7h | TRH | PCZA361.3 | / | 0.440 | |
| 4mr9 | 2BX | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.440 | |
| 4ms1 | 381 | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.440 | |
| 5ah5 | LSS | Leucine--tRNA ligase | / | 0.440 |