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 |
|---|---|---|---|
| 3ei8 | PL5 | LL-diaminopimelate aminotransferase, chloroplastic |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3ei8 | PL5 | LL-diaminopimelate aminotransferase, chloroplastic | / | 1.000 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.515 | |
| 4fl0 | PLP | Aminotransferase ALD1, chloroplastic | 2.6.1 | 0.503 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.498 | |
| 1w19 | T5P | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.494 | |
| 4geb | 0LD | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.490 | |
| 1oxo | IK2 | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.487 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.485 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.484 | |
| 4wlj | IK2 | Kynurenine--oxoglutarate transaminase 1 | 2.6.1.7 | 0.484 | |
| 1aka | PLP | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.479 | |
| 1akb | PPD | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.477 | |
| 3fvu | IAC | Kynurenine--oxoglutarate transaminase 1 | 2.6.1.7 | 0.476 | |
| 2pj4 | 414 | Carboxypeptidase B | / | 0.475 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.474 | |
| 1w19 | T1P | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.473 | |
| 1x28 | PGU | Aspartate aminotransferase | 2.6.1.1 | 0.472 | |
| 4a87 | NAR | Major pollen allergen Bet v 1-A | / | 0.470 | |
| 3bbp | GTP | Ras-related protein Rab-6A | / | 0.469 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.468 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.467 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.466 | |
| 4ge4 | 0KE | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.466 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.465 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.465 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.463 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.463 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.462 | |
| 3ojw | FMN | NADPH--cytochrome P450 reductase | / | 0.462 | |
| 1c7o | PPG | Hemolysin | / | 0.461 | |
| 1wkh | PPE | [LysW]-aminoadipate semialdehyde transaminase | / | 0.461 | |
| 4bva | T3 | Ketimine reductase mu-crystallin | 1.5.1.25 | 0.461 | |
| 2anb | 5GP | Guanylate kinase | 2.7.4.8 | 0.460 | |
| 2lfo | GCH | Fatty acid-binding protein, liver | / | 0.460 | |
| 2xq0 | BES | Leukotriene A-4 hydrolase homolog | 3.3.2.6 | 0.460 | |
| 3u5y | SCG | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.460 | |
| 2dxd | ANP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.459 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.459 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.459 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.458 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.458 | |
| 4zgs | NAD | Putative D-lactate dehydrogenase | / | 0.458 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.457 | |
| 1yhn | GTP | Ras-related protein Rab-7a | / | 0.457 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.457 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.457 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.457 | |
| 4w5k | PLP | Aspartate aminotransferase, mitochondrial | / | 0.457 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 2h3w | HC5 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.456 | |
| 3ndj | JHZ | Methyltransferase | / | 0.456 | |
| 1ypg | UIR | Prothrombin | 3.4.21.5 | 0.455 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 4mr7 | 2BV | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.455 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.454 | |
| 4e2z | JHZ | Methyltransferase | / | 0.454 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.453 | |
| 1h60 | STR | Pentaerythritol tetranitrate reductase | / | 0.453 | |
| 1icq | OPD | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.453 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.453 | |
| 2a5h | SAM | L-lysine 2,3-aminomutase | 5.4.3.2 | 0.453 | |
| 2vn1 | FK5 | Peptidylprolyl isomerase | / | 0.453 | |
| 3g1r | FIT | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.453 | |
| 3img | BZ3 | Pantothenate synthetase | 6.3.2.1 | 0.453 | |
| 3lqs | PSZ | D-alanine aminotransferase | 2.6.1.21 | 0.453 | |
| 1s4o | GDP | Glycolipid 2-alpha-mannosyltransferase | / | 0.452 | |
| 3b1d | PLS | BetaC-S lyase | / | 0.452 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 4x7v | MIV | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.452 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.451 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.451 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.451 | |
| 3k8q | 22A | Purine nucleoside phosphorylase | 2.4.2.1 | 0.451 | |
| 3opm | LUI | Dipeptidyl peptidase 4 | / | 0.451 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.451 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 4gv7 | MEW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.451 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 2c1z | KMP | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.450 | |
| 3ele | PLP | Aminotransferase | / | 0.450 | |
| 3q8u | ADP | Nucleoside diphosphate kinase | / | 0.450 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.449 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.449 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 3ha5 | SFG | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.449 | |
| 3ihg | VAK | Aklavinone 12-hydroxylase RdmE | / | 0.449 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.449 | |
| 4eb5 | PLP | Cysteine desulfurase IscS 2 | / | 0.449 | |
| 4x7u | ZM3 | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.449 | |
| 7std | CRP | Scytalone dehydratase | 4.2.1.94 | 0.449 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.448 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.448 | |
| 3dr7 | GPD | GDP-perosamine synthase | / | 0.448 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.448 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.448 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.448 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 2xyt | TC9 | Soluble acetylcholine receptor | / | 0.447 | |
| 3lzw | NAP | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.447 | |
| 3uov | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.447 | |
| 3v2u | ATP | Protein GAL3 | / | 0.447 | |
| 4n1g | CEI | Obelin | / | 0.447 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.446 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.446 | |
| 3tfu | PL8 | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | 2.6.1.62 | 0.446 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4dbc | 3QP | Aspartate aminotransferase | 2.6.1.1 | 0.446 | |
| 4ge9 | 0L0 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.446 | |
| 1by5 | GLY_GLY_GLY_AHO_AHO_AHO_FE | Ferrichrome-iron receptor | / | 0.445 | |
| 1c3x | 8IG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.445 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.445 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 2jl1 | NAP | Triphenylmethane reductase | / | 0.445 | |
| 3dr4 | G4M | GDP-perosamine synthase | / | 0.445 | |
| 4b65 | FAD | L-ornithine N(5)-monooxygenase | / | 0.445 | |
| 4hr2 | ADP | Nucleoside diphosphate kinase | / | 0.445 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.444 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 2g21 | L1B | Renin | 3.4.23.15 | 0.444 | |
| 2gil | GTP | Ras-related protein Rab-6A | / | 0.444 | |
| 3e5h | GNP | Ras-related protein Rab-28 | / | 0.444 | |
| 3eq6 | BCO | Acyl-coenzyme A synthetase ACSM2A, mitochondrial | 6.2.1.2 | 0.444 | |
| 4de0 | 0JB | Beta-lactamase | / | 0.444 | |
| 4k8s | 1QT | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 1akc | PPE | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.443 | |
| 1kbi | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.443 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 3qto | 10P | Prothrombin | 3.4.21.5 | 0.443 | |
| 3tne | RIT | Candidapepsin-1 | 3.4.23.24 | 0.443 | |
| 4i6g | FAD | Cryptochrome-2 | / | 0.443 | |
| 4ms1 | 381 | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.443 | |
| 1e66 | HUX | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 2a0x | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.442 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.442 | |
| 4cf6 | CBD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.442 | |
| 4nie | NBH | Nuclear receptor ROR-gamma | / | 0.442 | |
| 4x7z | ZM3 | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.442 | |
| 5d6l | CAU | Beta-2 adrenergic receptor | / | 0.442 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.441 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.441 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.441 | |
| 3b7d | CNI | Glutamate receptor 2 | / | 0.441 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 3t85 | SG7 | Carbonic anhydrase 2 | 4.2.1.1 | 0.441 | |
| 3uzz | ASD | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.441 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.441 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.440 | |
| 2b58 | COA | Diamine acetyltransferase 1 | / | 0.440 | |
| 2bbw | GP5 | Adenylate kinase 4, mitochondrial | / | 0.440 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.440 | |
| 2hxz | H7J | Cathepsin S | 3.4.22.27 | 0.440 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3zbz | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.440 | |
| 4drm | 0MC | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.440 | |
| 4mr9 | 2BX | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.440 |